[gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/

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* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-02-13 17:27 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2011-02-13 17:27 UTC (permalink / raw
  To: gentoo-commits

commit:     ba4229c06aa54439b5efe0010b6b8a3ddfc55bfd
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 13 17:10:57 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sun Feb 13 17:10:57 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ba4229c0

[sci-chemistry/gromacs] qa fixes

(Portage version: 2.1.9.25/git/Linux i686, signed Manifest commit with key C2000586)

---
 ...acs-4.5.9999.ebuild => gromacs-4.5.3-r1.ebuild} |   18 ++++++++++-----
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild      |   18 ++++++++++-----
 sci-chemistry/gromacs/metadata.xml                 |   22 ++++++++++---------
 3 files changed, 36 insertions(+), 22 deletions(-)

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.3-r1.ebuild
similarity index 96%
copy from sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
copy to sci-chemistry/gromacs/gromacs-4.5.3-r1.ebuild
index 8d6dea9..88290b8 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.3-r1.ebuild
@@ -8,17 +8,23 @@ LIBTOOLIZE="true"
 TEST_PV="4.0.4"
 MANUAL_PV="4.5.3"
 
-EGIT_REPO_URI="git://git.gromacs.org/gromacs"
-EGIT_BRANCH="release-4-5-patches"
+inherit autotools-utils bash-completion multilib toolchain-funcs
 
-inherit autotools-utils bash-completion git multilib toolchain-funcs
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 		doc? (
 		http://www.gromacs.org/@api/deki/files/133/=manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
 
+if [ "${PV%9999}" != "${PV}" ]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
+	EGIT_BRANCH="release-4-5-patches"
+	inherit git
+else
+	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
+fi
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index 8d6dea9..88290b8 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -8,17 +8,23 @@ LIBTOOLIZE="true"
 TEST_PV="4.0.4"
 MANUAL_PV="4.5.3"
 
-EGIT_REPO_URI="git://git.gromacs.org/gromacs"
-EGIT_BRANCH="release-4-5-patches"
+inherit autotools-utils bash-completion multilib toolchain-funcs
 
-inherit autotools-utils bash-completion git multilib toolchain-funcs
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 		doc? (
 		http://www.gromacs.org/@api/deki/files/133/=manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
 
+if [ "${PV%9999}" != "${PV}" ]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
+	EGIT_BRANCH="release-4-5-patches"
+	inherit git
+else
+	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
+fi
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index be7c210..7c3c78c 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -1,14 +1,16 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-chemistry</herd>
-<use>
-  <flag name='dmalloc'>Enable use of Debug Malloc</flag>
-  <flag name='double-precision'>More precise calculations at the expense of speed</flag>
-  <flag name='ffamber'>Enable ffamber ports for gromacs</flag>
-  <flag name='fkernels'>Enable building of Fortran Kernels for platforms
-	  that dont have assembly loops</flag>
-  <flag name='single-precision'>Single precision version of gromacs (default)</flag>
-  <flag name='zsh-completion'>Enable zsh completion support</flag>
-</use>
+	<herd>sci-chemistry</herd>
+	<maintainer>
+		<email>ottxor@gentoo.org</email>
+		<name>Christoph Junghans</name>
+	</maintainer>
+	<use>
+		<flag name='dmalloc'>Enable use of Debug Malloc</flag>
+		<flag name='double-precision'>More precise calculations at the expense of speed</flag>
+		<flag name='ffamber'>Enable ffamber ports for gromacs</flag>
+		<flag name='fkernels'>Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
+		<flag name='single-precision'>Single precision version of gromacs (default)</flag>
+	</use>
 </pkgmetadata>



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-02-14 21:00 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2011-02-14 21:00 UTC (permalink / raw
  To: gentoo-commits

commit:     5564dd22f510b2ea28010a63cc0eee6a2814c59a
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 14 21:10:56 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Mon Feb 14 21:11:22 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5564dd22

[sci-chemistry/gromacs] fixes bug #339837

(Portage version: 2.1.9.25/git/Linux i686, signed Manifest commit with key C2000586)

---
 sci-chemistry/gromacs/ChangeLog                    |    6 ++++++
 ...acs-4.5.3-r1.ebuild => gromacs-4.5.3-r2.ebuild} |   17 ++++++++++++++---
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild      |   17 ++++++++++++++---
 sci-chemistry/gromacs/gromacs-9999.ebuild          |   20 ++++++++++----------
 4 files changed, 44 insertions(+), 16 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 4415e5b..0aef6dd 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*gromacs-4.5.3-r2 (14 Feb 2011)
+
+  14 Feb 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.3-r1.ebuild,
+  +gromacs-4.5.3-r2.ebuild, gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+  bring back sse/sse2 useflag (bug #339837)
+
   20 Jan 2011; Christoph Junghans <kleiner_otti@gmx.de> gromacs-9999.ebuild:
   add back live manual
 

diff --git a/sci-chemistry/gromacs/gromacs-4.5.3-r1.ebuild b/sci-chemistry/gromacs/gromacs-4.5.3-r2.ebuild
similarity index 93%
rename from sci-chemistry/gromacs/gromacs-4.5.3-r1.ebuild
rename to sci-chemistry/gromacs/gromacs-4.5.3-r2.ebuild
index 88290b8..ac987b2 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.3-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.3-r2.ebuild
@@ -8,7 +8,7 @@ LIBTOOLIZE="true"
 TEST_PV="4.0.4"
 MANUAL_PV="4.5.3"
 
-inherit autotools-utils bash-completion multilib toolchain-funcs
+inherit autotools-utils bash-completion flag-o-matic multilib toolchain-funcs
 
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 		doc? (
@@ -29,7 +29,7 @@ LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
 IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
-mpi +single-precision static-libs test +threads +xml zsh-completion"
+mpi +single-precision sse sse2 static-libs test +threads +xml zsh-completion"
 
 DEPEND="app-shells/tcsh
 	X? ( x11-libs/libX11
@@ -122,12 +122,19 @@ src_configure() {
 	# if we need external blas or lapack
 	use blas && export LIBS+=" -lblas"
 	use lapack && export LIBS+=" -llapack"
+	local sseflag="x86-64-sse"
+	use x86 && sseflag="ia32-sse"
+
+	#a bug in gromacs autotools
+	use sse && append-flags -msse
+	use sse2 && append-flags -msse2
 
 	for x in ${GMX_DIRS}; do
-		local suffix=""
+		local suffix="" sse="sse"
 		#if we build single and double - double is suffixed
 		use double-precision && use single-precision && \
 			[ "${x}" = "double" ] && suffix="_d"
+		[ "${x}" = "double" ] && sse="sse2"
 		myeconfargs=(
 			--bindir="${EPREFIX}"/usr/bin
 			--docdir="${EPREFIX}"/usr/share/doc/"${PF}"
@@ -146,7 +153,11 @@ src_configure() {
 			--disable-bluegene
 			--disable-la-files
 			--disable-power6
+			--disable-ia32-sse
+			--disable-x86-64-sse
+			$(use_enable $sse $sseflag)
 		)
+		#disable ia32-sse and x86-64-sse and enable what we really need in last line
 
 		einfo "Configuring for ${x} precision"
 		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index 88290b8..ac987b2 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -8,7 +8,7 @@ LIBTOOLIZE="true"
 TEST_PV="4.0.4"
 MANUAL_PV="4.5.3"
 
-inherit autotools-utils bash-completion multilib toolchain-funcs
+inherit autotools-utils bash-completion flag-o-matic multilib toolchain-funcs
 
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 		doc? (
@@ -29,7 +29,7 @@ LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
 IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
-mpi +single-precision static-libs test +threads +xml zsh-completion"
+mpi +single-precision sse sse2 static-libs test +threads +xml zsh-completion"
 
 DEPEND="app-shells/tcsh
 	X? ( x11-libs/libX11
@@ -122,12 +122,19 @@ src_configure() {
 	# if we need external blas or lapack
 	use blas && export LIBS+=" -lblas"
 	use lapack && export LIBS+=" -llapack"
+	local sseflag="x86-64-sse"
+	use x86 && sseflag="ia32-sse"
+
+	#a bug in gromacs autotools
+	use sse && append-flags -msse
+	use sse2 && append-flags -msse2
 
 	for x in ${GMX_DIRS}; do
-		local suffix=""
+		local suffix="" sse="sse"
 		#if we build single and double - double is suffixed
 		use double-precision && use single-precision && \
 			[ "${x}" = "double" ] && suffix="_d"
+		[ "${x}" = "double" ] && sse="sse2"
 		myeconfargs=(
 			--bindir="${EPREFIX}"/usr/bin
 			--docdir="${EPREFIX}"/usr/share/doc/"${PF}"
@@ -146,7 +153,11 @@ src_configure() {
 			--disable-bluegene
 			--disable-la-files
 			--disable-power6
+			--disable-ia32-sse
+			--disable-x86-64-sse
+			$(use_enable $sse $sseflag)
 		)
+		#disable ia32-sse and x86-64-sse and enable what we really need in last line
 
 		einfo "Configuring for ${x} precision"
 		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 327978a..b6f5119 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -20,7 +20,7 @@ LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
 IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
-mpi +single-precision sse test +threads xml zsh-completion"
+mpi +single-precision sse sse2 test +threads xml zsh-completion"
 
 DEPEND="X? ( x11-libs/libX11
 			x11-libs/libSM
@@ -114,11 +114,10 @@ src_configure() {
 	fi
 
 	#go from slowest to faster acceleration
-	local acce="none"
-	use altivec && acce="altivec"
-	use ia64 && acce="ia64"
-	use fkernels && acce="fortran"
-	use sse && acce="sse"
+	local acce_pre="none"
+	use fkernels && acce_pre="fortran"
+	use altivec && acce_pre="altivec"
+	use ia64 && acce_pre="ia64"
 
 	mycmakeargs_pre+=(
 		$(cmake-utils_use X GMX_X11)
@@ -127,24 +126,25 @@ src_configure() {
 		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
 		$(cmake-utils_use threads GMX_THREADS)
 		$(cmake-utils_use xml GMX_XML)
-		-DGMX_ACCELERATION="$acce"
 		-DGMX_DEFAULT_SUFFIX=off
 	)
 
 	for x in ${GMX_DIRS}; do
 		einfo "Configuring for ${x} precision"
-		local suffix=""
+		local suffix="" acce="$acce_pre"
 		#if we build single and double - double is suffixed
 		use double-precision && use single-precision && \
 			[ "${x}" = "double" ] && suffix="_d"
+		[ "${x}" = "float" ] && use sse && acce="sse"
+		[ "${x}" = "double" ] && use sse2 && acce="sse"
 		local p
 		[ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF -DGMX_ACCELERATION="$acce"
 			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON -DGMX_ACCELERATION="$acce"
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
 	done



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-02-17 22:29 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2011-02-17 22:29 UTC (permalink / raw
  To: gentoo-commits

commit:     7815198b945c7d987169e578522be5412eb365c6
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Feb 17 22:39:17 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Thu Feb 17 22:39:44 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7815198b

[sci-chemistry/gromacs] version bump

(Portage version: 2.1.9.25/git/Linux i686, signed Manifest commit with key C2000586)

---
 sci-chemistry/gromacs/ChangeLog                    |    6 ++++++
 ...acs-4.5.3-r2.ebuild => gromacs-4.5.3-r3.ebuild} |   11 +++++++++--
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 0aef6dd..ddbf77b 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*gromacs-4.5.3-r3 (17 Feb 2011)
+
+  17 Feb 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.3-r2.ebuild,
+  +gromacs-4.5.3-r3.ebuild:
+  version bump
+
 *gromacs-4.5.3-r2 (14 Feb 2011)
 
   14 Feb 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.3-r1.ebuild,

diff --git a/sci-chemistry/gromacs/gromacs-4.5.3-r2.ebuild b/sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild
similarity index 96%
rename from sci-chemistry/gromacs/gromacs-4.5.3-r2.ebuild
rename to sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild
index ac987b2..b45ac1b 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.3-r2.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild
@@ -19,7 +19,9 @@ if [ "${PV%9999}" != "${PV}" ]; then
 	EGIT_BRANCH="release-4-5-patches"
 	inherit git
 else
-	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
+	PATCHES=( ${WORKDIR}/${P}_upstream20110217.patch.bz2 )
+	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
+	mirror://gentoo/${P}_upstream20110217.patch.bz2"
 fi
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
@@ -59,7 +61,12 @@ src_prepare() {
 		elog "machines only, you can safely disable mpi"
 	fi
 
-	eautoreconf
+	autotools-utils_src_prepare || die
+
+	sed -e '/AC_INIT/s/4\.5\.3-dev/4.5.3-2011-02-17/' -i configure.ac \
+		|| die "Failed to change version in configure.ac"
+
+	eautoreconf || die
 
 	GMX_DIRS=""
 	use single-precision && GMX_DIRS+=" float"



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-02-19 14:50 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2011-02-19 14:50 UTC (permalink / raw
  To: gentoo-commits

commit:     a1ede7522ea24fe66830f0ab16e10452275fbe1c
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 19 15:00:14 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sat Feb 19 15:00:14 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a1ede752

[sci-chemistry/gromacs] 4.5.3-r3 InCVS

(Portage version: 2.1.9.25/git/Linux i686, signed Manifest commit with key C2000586)

---
 sci-chemistry/gromacs/ChangeLog               |    3 +
 sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild |  259 -------------------------
 2 files changed, 3 insertions(+), 259 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index ddbf77b..4642b67 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  19 Feb 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.3-r3.ebuild:
+  InCVS
+
 *gromacs-4.5.3-r3 (17 Feb 2011)
 
   17 Feb 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.3-r2.ebuild,

diff --git a/sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild b/sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild
deleted file mode 100644
index b45ac1b..0000000
--- a/sci-chemistry/gromacs/gromacs-4.5.3-r3.ebuild
+++ /dev/null
@@ -1,259 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="3"
-
-LIBTOOLIZE="true"
-TEST_PV="4.0.4"
-MANUAL_PV="4.5.3"
-
-inherit autotools-utils bash-completion flag-o-matic multilib toolchain-funcs
-
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? (
-		http://www.gromacs.org/@api/deki/files/133/=manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
-
-if [ "${PV%9999}" != "${PV}" ]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
-	EGIT_BRANCH="release-4-5-patches"
-	inherit git
-else
-	PATCHES=( ${WORKDIR}/${P}_upstream20110217.patch.bz2 )
-	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
-	mirror://gentoo/${P}_upstream20110217.patch.bz2"
-fi
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
-mpi +single-precision sse sse2 static-libs test +threads +xml zsh-completion"
-
-DEPEND="app-shells/tcsh
-	X? ( x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE )
-	dmalloc? ( dev-libs/dmalloc )
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2 )"
-
-RDEPEND="${DEPEND}"
-
-RESTRICT="test"
-
-#gromacs has gnu exec stacks for speedup
-QA_EXECSTACK="usr/lib/libgmx.so.*
-	usr/lib/libgmx_d.so.*"
-
-src_prepare() {
-	if use mpi && use threads; then
-		elog "mdrun uses only threads OR mpi, and gromacs favours the"
-		elog "use of mpi over threads, so a mpi-version of mdrun will"
-		elog "be compiled. If you want to run mdrun on shared memory"
-		elog "machines only, you can safely disable mpi"
-	fi
-
-	autotools-utils_src_prepare || die
-
-	sed -e '/AC_INIT/s/4\.5\.3-dev/4.5.3-2011-02-17/' -i configure.ac \
-		|| die "Failed to change version in configure.ac"
-
-	eautoreconf || die
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-	#if neither single-precision nor double-precision is enabled
-	#build at least default (single)
-	[ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
-
-	for x in ${GMX_DIRS}; do
-		mkdir -p "${WORKDIR}/${P}_${x}" || die
-		use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
-	done
-}
-
-src_configure() {
-	#from gromacs configure
-	if ! use fftw; then
-		ewarn "WARNING: The built-in FFTPACK routines are slow."
-		ewarn "Are you sure you don\'t want to use FFTW?"
-		ewarn "It is free and much faster..."
-	fi
-
-	if [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
-
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	#fortran will gone in gromacs 5.0 anyway
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		use threads && eerror "You cannot compile fortran kernel with threads"
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-	fi
-
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
-
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
-	fi
-
-	# if we need external blas or lapack
-	use blas && export LIBS+=" -lblas"
-	use lapack && export LIBS+=" -llapack"
-	local sseflag="x86-64-sse"
-	use x86 && sseflag="ia32-sse"
-
-	#a bug in gromacs autotools
-	use sse && append-flags -msse
-	use sse2 && append-flags -msse2
-
-	for x in ${GMX_DIRS}; do
-		local suffix="" sse="sse"
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[ "${x}" = "double" ] && suffix="_d"
-		[ "${x}" = "double" ] && sse="sse2"
-		myeconfargs=(
-			--bindir="${EPREFIX}"/usr/bin
-			--docdir="${EPREFIX}"/usr/share/doc/"${PF}"
-			--enable-"${x}"
-			$(use_with dmalloc)
-			$(use_with fftw fft fftw3)
-			$(use_with gsl)
-			$(use_with X x)
-			$(use_with xml)
-			$(use_enable threads)
-			$(use_enable altivec ppc-altivec)
-			$(use_enable ia64 ia64-asm)
-			$(use_with lapack external-lapack)
-			$(use_with blas external-blas)
-			$(use_enable fkernels fortran)
-			--disable-bluegene
-			--disable-la-files
-			--disable-power6
-			--disable-ia32-sse
-			--disable-x86-64-sse
-			$(use_enable $sse $sseflag)
-		)
-		#disable ia32-sse and x86-64-sse and enable what we really need in last line
-
-		einfo "Configuring for ${x} precision"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			autotools-utils_src_configure --disable-mpi	--program-suffix="${suffix}" \
-			CC="$(tc-getCC)" F77="$(tc-getFC)"
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			autotools-utils_src_configure --enable-mpi --program-suffix="_mpi${suffix}" \
-			CC="$(tc-getCC)" F77="$(tc-getFC)"
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			autotools-utils_src_compile
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			autotools-utils_src_compile mdrun
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		local oldpath="${PATH}"
-		export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
-		cd "${WORKDIR}/${P}_${x}"
-		emake -j1 tests || die "${x} Precision test failed"
-		export PATH="${oldpath}"
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			autotools-utils_src_install
-		use mpi || continue
-		#autotools-utils_src_install does not support args
-		#using autotools-utils_src_compile instead
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			autotools-utils_src_compile install-mdrun DESTDIR="${D}"
-
-		#stolen from autotools-utils_src_install see comment above
-		local args
-		has static-libs ${IUSE//+} && ! use	static-libs || args='none'
-		remove_libtool_files ${args}
-	done
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
-
-	doenvd "${T}/80gromacs"
-	rm -f "${ED}"/usr/bin/GMXRC*
-
-	dobashcompletion "${ED}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${ED}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -f "${ED}"/usr/bin/completion.*
-
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL* README*
-	if use doc; then
-		newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
-		dohtml -r "${ED}usr/share/gromacs/html/"
-	fi
-	rm -rf "${ED}usr/share/gromacs/html/"
-}
-
-pkg_postinst() {
-	env-update && source /etc/profile
-	elog
-	elog "Please read and cite:"
-	elog "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	elog "http://dx.doi.org/10.1021/ct700301q"
-	elog
-	bash-completion_pkg_postinst
-	elog
-	elog $(g_luck)
-	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
-	elog
-	elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
-	elog
-}



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-03-01 15:31 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2011-03-01 15:31 UTC (permalink / raw
  To: gentoo-commits

commit:     14c06611ed982ae4aaf87b11edc18af2b1171c20
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Tue Mar  1 15:31:39 2011 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Tue Mar  1 15:31:39 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=14c06611

Add epatch_user back for gromacs live ebuilds

(Portage version: 2.2.0_alpha25/git/Linux x86_64, signed Manifest commit with key F82F92E6)

---
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |    5 ++++-
 sci-chemistry/gromacs/gromacs-9999.ebuild     |    5 ++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index ac987b2..111bb37 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -8,7 +8,7 @@ LIBTOOLIZE="true"
 TEST_PV="4.0.4"
 MANUAL_PV="4.5.3"
 
-inherit autotools-utils bash-completion flag-o-matic multilib toolchain-funcs
+inherit autotools-utils bash-completion eutils flag-o-matic multilib toolchain-funcs
 
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 		doc? (
@@ -52,6 +52,9 @@ QA_EXECSTACK="usr/lib/libgmx.so.*
 	usr/lib/libgmx_d.so.*"
 
 src_prepare() {
+	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
+	epatch_user
+
 	if use mpi && use threads; then
 		elog "mdrun uses only threads OR mpi, and gromacs favours the"
 		elog "use of mpi over threads, so a mpi-version of mdrun will"

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index b6f5119..15dbf24 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -10,7 +10,7 @@ TEST_PV="4.0.4"
 EGIT_REPO_URI="git://git.gromacs.org/gromacs"
 EGIT_BRANCH="master"
 
-inherit bash-completion cmake-utils git multilib toolchain-funcs
+inherit bash-completion cmake-utils eutils git multilib toolchain-funcs
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -44,6 +44,9 @@ QA_EXECSTACK="usr/lib/libgmx.so.*
 	usr/lib/libgmx_d.so.*"
 
 src_prepare() {
+	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
+	epatch_user
+
 	if use mpi && use threads; then
 		elog "mdrun uses only threads OR mpi, and gromacs favours the"
 		elog "use of mpi over threads, so a mpi-version of mdrun will"



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-03-07 12:01 Justin Lecher
  0 siblings, 0 replies; 102+ messages in thread
From: Justin Lecher @ 2011-03-07 12:01 UTC (permalink / raw
  To: gentoo-commits

commit:     c4143f06aa3f3f547e46f65ea1e4b1e742d8d459
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Mar  7 11:13:45 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Mar  7 11:13:45 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c4143f06

Correct Slots for gtk 3 introduction to tree

(Portage version: 2.2.0_alpha26/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.0.9999.ebuild |   16 +++++++++-------
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |   14 ++++++++------
 sci-chemistry/gromacs/gromacs-9999.ebuild     |   17 +++++++++--------
 4 files changed, 30 insertions(+), 21 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 4642b67..61e3852 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  07 Mar 2011; Justin Lecher <jlec@gentoo.org> gromacs-4.0.9999.ebuild,
+  gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+  Correct Slots for gtk 3 introduction to tree
+
   19 Feb 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.3-r3.ebuild:
   InCVS
 

diff --git a/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild
index 502c84c..a2f52b6 100644
--- a/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -24,19 +24,21 @@ KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
 IUSE="X blas dmalloc doc -double-precision ffamber +fftw fkernels +gsl lapack
 mpi +single-precision static static-libs test +xml zsh-completion"
 
-DEPEND="app-shells/tcsh
-	X? ( x11-libs/libX11
+DEPEND="
+	X? (
+		x11-libs/libX11
 		x11-libs/libSM
-		x11-libs/libICE )
+		x11-libs/libICE
+		)
 	dmalloc? ( dev-libs/dmalloc )
 	blas? ( virtual/blas )
 	fftw? ( sci-libs/fftw:3.0 )
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
 	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2 )"
-
-RDEPEND="${DEPEND}"
+	xml? ( dev-libs/libxml2:2 )"
+RDEPEND="${DEPEND}
+	app-shells/tcsh"
 
 RESTRICT="test"
 

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index 111bb37..0a071db 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -31,19 +31,21 @@ KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
 IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
 mpi +single-precision sse sse2 static-libs test +threads +xml zsh-completion"
 
-DEPEND="app-shells/tcsh
-	X? ( x11-libs/libX11
+DEPEND="
+	X? (
+		x11-libs/libX11
 		x11-libs/libSM
-		x11-libs/libICE )
+		x11-libs/libICE
+		)
 	dmalloc? ( dev-libs/dmalloc )
 	blas? ( virtual/blas )
 	fftw? ( sci-libs/fftw:3.0 )
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
 	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2 )"
-
-RDEPEND="${DEPEND}"
+	xml? ( dev-libs/libxml2:2 )"
+RDEPEND="${DEPEND}
+	app-shells/tcsh"
 
 RESTRICT="test"
 

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 15dbf24..031310b 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -22,19 +22,20 @@ KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
 IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
 mpi +single-precision sse sse2 test +threads xml zsh-completion"
 
-DEPEND="X? ( x11-libs/libX11
-			x11-libs/libSM
-			x11-libs/libICE )
+DEPEND="
+	X? (
+		x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE
+		)
 	blas? ( virtual/blas )
 	fftw? ( sci-libs/fftw:3.0 )
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
 	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2 )"
-
-RDEPEND="app-shells/tcsh
-	${DEPEND}"
-
+	xml? ( dev-libs/libxml2:2 )"
+RDEPEND="${DEPEND}
+	app-shells/tcsh"
 PDEPEND="doc? ( app-doc/gromacs-manual )"
 
 RESTRICT="test"



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-03-08 20:59 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2011-03-08 20:59 UTC (permalink / raw
  To: gentoo-commits

commit:     576823408f684b1cbedc5dc1b6f4886d5a0eb841
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Mar  8 21:10:37 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Tue Mar  8 21:10:37 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=57682340

[sci-chemistry/gromacs] added fixes from 4.5.3-r4

(Portage version: 2.1.9.25/git/Linux i686, signed Manifest commit with key C2000586)

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |   22 ++++++++++++----------
 sci-chemistry/gromacs/gromacs-9999.ebuild     |    1 +
 3 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 61e3852..206d8b4 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  08 Mar 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-9999.ebuild:
+  added fixes from 4.5.3-r4
+
   07 Mar 2011; Justin Lecher <jlec@gentoo.org> gromacs-4.0.9999.ebuild,
   gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
   Correct Slots for gtk 3 introduction to tree

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index 0a071db..8d3c8f8 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -8,7 +8,7 @@ LIBTOOLIZE="true"
 TEST_PV="4.0.4"
 MANUAL_PV="4.5.3"
 
-inherit autotools-utils bash-completion eutils flag-o-matic multilib toolchain-funcs
+inherit autotools-utils bash-completion flag-o-matic multilib toolchain-funcs
 
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 		doc? (
@@ -31,7 +31,7 @@ KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
 IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
 mpi +single-precision sse sse2 static-libs test +threads +xml zsh-completion"
 
-DEPEND="
+CDEPEND="
 	X? (
 		x11-libs/libX11
 		x11-libs/libSM
@@ -44,7 +44,9 @@ DEPEND="
 	lapack? ( virtual/lapack )
 	mpi? ( virtual/mpi )
 	xml? ( dev-libs/libxml2:2 )"
-RDEPEND="${DEPEND}
+DEPEND="${CDEPEND}
+	dev-util/pkgconfig"
+RDEPEND="${CDEPEND}
 	app-shells/tcsh"
 
 RESTRICT="test"
@@ -54,9 +56,6 @@ QA_EXECSTACK="usr/lib/libgmx.so.*
 	usr/lib/libgmx_d.so.*"
 
 src_prepare() {
-	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
-	epatch_user
-
 	if use mpi && use threads; then
 		elog "mdrun uses only threads OR mpi, and gromacs favours the"
 		elog "use of mpi over threads, so a mpi-version of mdrun will"
@@ -64,7 +63,9 @@ src_prepare() {
 		elog "machines only, you can safely disable mpi"
 	fi
 
-	eautoreconf
+	autotools-utils_src_prepare || die
+
+	eautoreconf || die
 
 	GMX_DIRS=""
 	use single-precision && GMX_DIRS+=" float"
@@ -125,8 +126,8 @@ src_configure() {
 	fi
 
 	# if we need external blas or lapack
-	use blas && export LIBS+=" -lblas"
-	use lapack && export LIBS+=" -llapack"
+	use blas && export LIBS+=" $(pkg-config blas cblas --libs)"
+	use lapack && export LIBS+=" $(pkg-config lapack --libs)"
 	local sseflag="x86-64-sse"
 	use x86 && sseflag="ia32-sse"
 
@@ -139,6 +140,7 @@ src_configure() {
 		#if we build single and double - double is suffixed
 		use double-precision && use single-precision && \
 			[ "${x}" = "double" ] && suffix="_d"
+		#double uses sse2, single sse
 		[ "${x}" = "double" ] && sse="sse2"
 		myeconfargs=(
 			--bindir="${EPREFIX}"/usr/bin
@@ -183,7 +185,7 @@ src_compile() {
 			autotools-utils_src_compile
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
+		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
 			autotools-utils_src_compile mdrun
 	done
 }

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 031310b..a2718f0 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -139,6 +139,7 @@ src_configure() {
 		#if we build single and double - double is suffixed
 		use double-precision && use single-precision && \
 			[ "${x}" = "double" ] && suffix="_d"
+		#double uses sse2, single sse
 		[ "${x}" = "float" ] && use sse && acce="sse"
 		[ "${x}" = "double" ] && use sse2 && acce="sse"
 		local p



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-03-17 23:18 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2011-03-17 23:18 UTC (permalink / raw
  To: gentoo-commits

commit:     cc73d86ce3fc5071d952572c28210c812a567622
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 17 22:31:07 2011 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Mar 17 23:18:34 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cc73d86c

[sci-chemistry/gromacs] Update ebuild for using pkg-config and blas

(Portage version: 2.2.0_alpha27/git/Linux x86_64, signed Manifest commit with key F82F92E6)

---
 sci-chemistry/gromacs/gromacs-4.0.9999.ebuild |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild
index a2f52b6..61f8cc2 100644
--- a/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild
@@ -112,13 +112,13 @@ src_configure() {
 
 	# if we need external blas
 	if use blas; then
-		export LIBS="${LIBS} -lblas"
+		export LIBS="${LIBS} $(pkg-config --libs blas)"
 		myconf="${myconf} $(use_with blas external-blas)"
 	fi
 
 	# if we need external lapack
 	if use lapack; then
-		export LIBS="${LIBS} -llapack"
+		export LIBS="${LIBS} $(pkg-config --libs lapack)"
 		myconf="${myconf} $(use_with lapack external-lapack)"
 	fi
 



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-04-10 12:28 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2011-04-10 12:28 UTC (permalink / raw
  To: gentoo-commits

commit:     368c9147cba1ee104621c52d0c25fa298ca93614
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 10 12:27:32 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sun Apr 10 12:27:32 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=368c9147

[sci-chemistry/gromacs] remove 4.0.* (EOM)

(Portage version: 2.1.9.42/git/Linux i686, signed Manifest commit with key C2000586)

---
 sci-chemistry/gromacs/ChangeLog               |    3 +
 sci-chemistry/gromacs/gromacs-4.0.9999.ebuild |  297 -------------------------
 sci-chemistry/gromacs/metadata.xml            |    1 -
 3 files changed, 3 insertions(+), 298 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 206d8b4..0aeec1b 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  10 Apr 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.0.9999.ebuild:
+  remove 4.0.* (EOM)
+
   08 Mar 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
   gromacs-9999.ebuild:
   added fixes from 4.5.3-r4

diff --git a/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild
deleted file mode 100644
index 61f8cc2..0000000
--- a/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild
+++ /dev/null
@@ -1,297 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="3"
-
-LIBTOOLIZE="true"
-TEST_PV="4.0.4"
-
-EGIT_REPO_URI="git://git.gromacs.org/gromacs"
-EGIT_BRANCH="release-4-0-patches"
-
-inherit autotools bash-completion eutils git multilib toolchain-funcs
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf -> gromacs-manual-4.0.pdf )
-		ffamber? ( http://ffamber.cnsm.csulb.edu/ffamber_v4.0-doc.tar.gz )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X blas dmalloc doc -double-precision ffamber +fftw fkernels +gsl lapack
-mpi +single-precision static static-libs test +xml zsh-completion"
-
-DEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	dmalloc? ( dev-libs/dmalloc )
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2:2 )"
-RDEPEND="${DEPEND}
-	app-shells/tcsh"
-
-RESTRICT="test"
-
-QA_EXECSTACK="usr/lib/libgmx.so.*
-	usr/lib/libgmx_d.so.*"
-
-use static && QA_EXECSTACK="$QA_EXECSTACK usr/bin/*"
-
-src_prepare() {
-
-	( use single-precision || use double-precision ) || \
-		die "Nothing to compile, enable single-precision and/or double-precision"
-
-	if use static; then
-		use X && die "You cannot compile a static version with X support, disable X or static"
-		use xml && die "You cannot compile a static version with xml support
-		(see bug #306479), disable xml or static"
-	fi
-
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	epatch_user
-	eautoreconf
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" single"
-	use double-precision && GMX_DIRS+=" double"
-	for x in ${GMX_DIRS}; do
-		mkdir "${S}-${x}" || die
-		use test && cp -r "${WORKDIR}"/gmxtest "${S}-${x}"
-		use mpi || continue
-		mkdir "${S}-${x}_mpi" || die
-	done
-}
-
-src_configure() {
-	local myconf
-	local myconfsingle
-	local myconfdouble
-	local suffixdouble
-
-	#leave all assembly options enabled mdrun is smart enough to deside itself
-	#there so no gentoo on bluegene!
-	myconf="${myconf} --disable-bluegene"
-
-	#from gromacs configure
-	if ! use fftw; then
-		ewarn "WARNING: The built-in FFTPACK routines are slow."
-		ewarn "Are you sure you don\'t want to use FFTW?"
-		ewarn "It is free and much faster..."
-	fi
-
-	if [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
-
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	#fortran will gone in gromacs 4.1 anyway
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-		myconf="${myconf} --enable-fortran"
-	else
-		myconf="${myconf} --disable-fortran"
-	fi
-
-	# if we need external blas
-	if use blas; then
-		export LIBS="${LIBS} $(pkg-config --libs blas)"
-		myconf="${myconf} $(use_with blas external-blas)"
-	fi
-
-	# if we need external lapack
-	if use lapack; then
-		export LIBS="${LIBS} $(pkg-config --libs lapack)"
-		myconf="${myconf} $(use_with lapack external-lapack)"
-	fi
-
-	# by default its better to have dynamicaly linked binaries
-	if use static; then
-		#gmx build static libs by default
-		myconf="${myconf} --disable-shared $(use_enable static all-static)"
-	else
-		myconf="${myconf} --disable-all-static --enable-shared $(use_enable static-libs static)"
-	fi
-
-	myconf="--datadir="${EPREFIX}"/usr/share \
-			--bindir="${EPREFIX}"/usr/bin \
-			--libdir="${EPREFIX}"/usr/$(get_libdir) \
-			--docdir="${EPREFIX}"/usr/share/doc/"${PF}" \
-			$(use_with dmalloc) \
-			$(use_with fftw fft fftw3) \
-			$(use_with gsl) \
-			$(use_with X x) \
-			$(use_with xml) \
-			${myconf}"
-
-	#if we build single and double - double is suffixed
-	if ( use double-precision && use single-precision ); then
-		suffixdouble="_d"
-	else
-		suffixdouble=""
-	fi
-
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
-
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
-	fi
-
-	myconfdouble="${myconf} --enable-double --program-suffix='${suffixdouble}'"
-	myconfsingle="${myconf} --enable-float --program-suffix=''"
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		cd "${S}-${x}"
-		local p=myconf${x}
-		ECONF_SOURCE="${S}" econf ${!p} --disable-mpi CC="$(tc-getCC)" F77="$(tc-getFC)"
-		use mpi || continue
-		cd "${S}-${x}_mpi"
-		ECONF_SOURCE="${S}" econf ${!p} --enable-mpi CC="$(tc-getCC)" F77="$(tc-getFC)"
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		cd "${S}-${x}"
-		einfo "Compiling for ${x} precision"
-		emake || die "emake for ${x} precision failed"
-		use mpi || continue
-		cd "${S}-${x}_mpi"
-		emake mdrun || die "emake mdrun for ${x} precision failed"
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		local oldpath="${PATH}"
-		export PATH="${S}-${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
-		cd "${S}-${x}"
-		emake -j1 tests || die "${x} Precision test failed"
-		export PATH="${oldpath}"
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		cd "${S}-${x}"
-		emake DESTDIR="${D}" install || die "emake install for ${x} failed"
-		use mpi || continue
-		cd "${S}-${x}_mpi"
-		emake DESTDIR="${D}" install-mdrun || die "emake install-mdrun for ${x} failed"
-	done
-	#we have pkg-config files
-	rm "${ED}"/usr/$(get_libdir)/*.la
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	doenvd "${T}/80gromacs"
-	rm -f "${ED}"/usr/bin/GMXRC*
-
-	dobashcompletion "${ED}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${ED}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -f "${ED}"/usr/bin/completion.*
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL README
-	if use doc; then
-		newdoc "${DISTDIR}/gromacs-manual-4.0.pdf" "manual-4.0.pdf"
-		dohtml -r "${ED}usr/share/gromacs/html/"
-	fi
-	rm -rf "${ED}usr/share/gromacs/html/"
-
-	if use ffamber; then
-		use doc && dodoc "${WORKDIR}/ffamber_v4.0/README/pdfs/*.pdf"
-		# prepare vdwradii.dat
-		cat >>"${ED}"/usr/share/gromacs/top/vdwradii.dat <<-EOF
-			SOL  MW    0
-			SOL  LP    0
-		EOF
-		# regenerate aminoacids.dat
-		cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
-		"${ED}"/usr/share/gromacs/top/aminoacids.dat \
-		| awk '{print $1}' | sort -u | tail -n+4 | wc -l \
-		>> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new
-		cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \
-		"${ED}"/usr/share/gromacs/top/aminoacids.dat \
-		| awk '{print $1}' | sort -u | tail -n+4 \
-		>> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new
-		mv -f "${ED}"/usr/share/gromacs/top/aminoacids.dat.new \
-		"${ED}"/usr/share/gromacs/top/aminoacids.dat
-		# copy ff files
-		for x in ffamber94 ffamber96 ffamber99 ffamber99p ffamber99sb \
-				ffamberGS ffamberGSs ffamber03 ; do
-			einfo "Adding ${x} to gromacs"
-			cp "${WORKDIR}"/ffamber_v4.0/${x}/* "${ED}"/usr/share/gromacs/top
-		done
-		# copy suplementary files
-		cp "${WORKDIR}"/ffamber_v4.0/*.gro "${ED}"/usr/share/gromacs/top
-		cp "${WORKDIR}"/ffamber_v4.0/*.itp "${ED}"/usr/share/gromacs/top
-		# actualy add records to FF.dat
-		cat >>"${ED}"/usr/share/gromacs/top/FF.dat.new <<-EOF
-			ffamber94   AMBER94 Cornell protein/nucleic forcefield
-			ffamber96   AMBER96 Kollman protein/nucleic forcefield
-			ffamberGS   AMBER-GS Garcia &  Sanbonmatsu forcefield
-			ffamberGSs  AMBER-GSs Nymeyer &  Garcia forcefield
-			ffamber99   AMBER99 Wang protein/nucleic acid forcefield
-			ffamber99p  AMBER99p protein/nucleic forcefield
-			ffamber99sb AMBER99sb Hornak protein/nucleic forcefield
-			ffamber03   AMBER03 Duan protein/nucleic forcefield
-		EOF
-		cat "${ED}"/usr/share/gromacs/top/FF.dat \
-			"${ED}"/usr/share/gromacs/top/FF.dat.new \
-			| tail -n+2 > "${ED}"/usr/share/gromacs/top/FF.dat.new2
-		cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 | wc -l > \
-			"${ED}"/usr/share/gromacs/top/FF.dat
-		cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 >> \
-			"${ED}"/usr/share/gromacs/top/FF.dat
-		rm -f "${ED}"/usr/share/gromacs/top/FF.dat.new*
-	fi
-}
-
-pkg_postinst() {
-	env-update && source /etc/profile
-	elog
-	elog "Please read and cite:"
-	elog "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	elog "http://dx.doi.org/10.1021/ct700301q"
-	elog
-	bash-completion_pkg_postinst
-	elog
-	elog $(luck)
-	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
-	elog
-}

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 7c3c78c..4aa2d99 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -9,7 +9,6 @@
 	<use>
 		<flag name='dmalloc'>Enable use of Debug Malloc</flag>
 		<flag name='double-precision'>More precise calculations at the expense of speed</flag>
-		<flag name='ffamber'>Enable ffamber ports for gromacs</flag>
 		<flag name='fkernels'>Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
 		<flag name='single-precision'>Single precision version of gromacs (default)</flag>
 	</use>



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-05-01 15:13 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2011-05-01 15:13 UTC (permalink / raw
  To: gentoo-commits

commit:     726d5118d71546b6c8a190ad39b179ca39fdeced
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun May  1 15:13:35 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sun May  1 15:13:35 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=726d5118

[sci-chemistry/gromacs] sync with tree

(Portage version: 2.1.9.42/git/Linux i686, signed Manifest commit with key C2000586)

---
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |   27 ++++++-----------
 sci-chemistry/gromacs/gromacs-9999.ebuild     |   39 +++++++++++--------------
 2 files changed, 26 insertions(+), 40 deletions(-)

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index 8d3c8f8..469f604 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -2,17 +2,16 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="3"
+EAPI="4"
 
 LIBTOOLIZE="true"
 TEST_PV="4.0.4"
-MANUAL_PV="4.5.3"
+MANUAL_PV="4.5.4"
 
 inherit autotools-utils bash-completion flag-o-matic multilib toolchain-funcs
 
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? (
-		http://www.gromacs.org/@api/deki/files/133/=manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
 
 if [ "${PV%9999}" != "${PV}" ]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
@@ -29,7 +28,8 @@ LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
 IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
-mpi +single-precision sse sse2 static-libs test +threads +xml zsh-completion"
+mpi +single-precision sse2 static-libs test +threads +xml zsh-completion"
+REQUIRED_USE="fkernels? ( !threads )"
 
 CDEPEND="
 	X? (
@@ -51,10 +51,6 @@ RDEPEND="${CDEPEND}
 
 RESTRICT="test"
 
-#gromacs has gnu exec stacks for speedup
-QA_EXECSTACK="usr/lib/libgmx.so.*
-	usr/lib/libgmx_d.so.*"
-
 src_prepare() {
 	if use mpi && use threads; then
 		elog "mdrun uses only threads OR mpi, and gromacs favours the"
@@ -96,10 +92,8 @@ src_configure() {
 
 	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
 
-	#fortran will gone in gromacs 5.0 anyway
 	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
 	if use fkernels; then
-		use threads && eerror "You cannot compile fortran kernel with threads"
 		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
 		ewarn "I hope, you know what are you doing..."
 	fi
@@ -126,22 +120,19 @@ src_configure() {
 	fi
 
 	# if we need external blas or lapack
-	use blas && export LIBS+=" $(pkg-config blas cblas --libs)"
+	use blas && export LIBS+=" $(pkg-config blas --libs)"
 	use lapack && export LIBS+=" $(pkg-config lapack --libs)"
 	local sseflag="x86-64-sse"
 	use x86 && sseflag="ia32-sse"
 
-	#a bug in gromacs autotools
-	use sse && append-flags -msse
+	#missing flag in autotools (bug #339837)
 	use sse2 && append-flags -msse2
 
 	for x in ${GMX_DIRS}; do
-		local suffix="" sse="sse"
+		local suffix=""
 		#if we build single and double - double is suffixed
 		use double-precision && use single-precision && \
 			[ "${x}" = "double" ] && suffix="_d"
-		#double uses sse2, single sse
-		[ "${x}" = "double" ] && sse="sse2"
 		myeconfargs=(
 			--bindir="${EPREFIX}"/usr/bin
 			--docdir="${EPREFIX}"/usr/share/doc/"${PF}"
@@ -162,7 +153,7 @@ src_configure() {
 			--disable-power6
 			--disable-ia32-sse
 			--disable-x86-64-sse
-			$(use_enable $sse $sseflag)
+			$(use_enable sse2 $sseflag)
 		)
 		#disable ia32-sse and x86-64-sse and enable what we really need in last line
 

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index a2718f0..817444e 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -2,9 +2,8 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="3"
+EAPI="4"
 
-LIBTOOLIZE="true"
 TEST_PV="4.0.4"
 
 EGIT_REPO_URI="git://git.gromacs.org/gromacs"
@@ -20,9 +19,10 @@ LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
 IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
-mpi +single-precision sse sse2 test +threads xml zsh-completion"
+mpi +single-precision sse2 test +threads xml zsh-completion"
+REQUIRED_USE="fkernels? ( !threads )"
 
-DEPEND="
+CDEPEND="
 	X? (
 		x11-libs/libX11
 		x11-libs/libSM
@@ -34,16 +34,14 @@ DEPEND="
 	lapack? ( virtual/lapack )
 	mpi? ( virtual/mpi )
 	xml? ( dev-libs/libxml2:2 )"
-RDEPEND="${DEPEND}
+DEPEND="${CDEPEND}
+	dev-util/pkgconfig"
+RDEPEND="${CDEPEND}
 	app-shells/tcsh"
 PDEPEND="doc? ( app-doc/gromacs-manual )"
 
 RESTRICT="test"
 
-#gromacs has gnu exec stacks for speedup
-QA_EXECSTACK="usr/lib/libgmx.so.*
-	usr/lib/libgmx_d.so.*"
-
 src_prepare() {
 	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
 	epatch_user
@@ -88,10 +86,8 @@ src_configure() {
 
 	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
 
-	#fortran will gone in gromacs 5.0 anyway
 	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
 	if use fkernels; then
-		use threads && eerror "You cannot compile fortran kernel with threads"
 		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
 		ewarn "I hope, you know what are you doing..."
 	fi
@@ -117,11 +113,12 @@ src_configure() {
 		elog "libmd with and without mpi support."
 	fi
 
-	#go from slowest to faster acceleration
-	local acce_pre="none"
-	use fkernels && acce_pre="fortran"
-	use altivec && acce_pre="altivec"
-	use ia64 && acce_pre="ia64"
+	#go from slowest to fasterest acceleration
+	local acce="none"
+	use fkernels && acce="fortran"
+	use altivec && acce="altivec"
+	use ia64 && acce="ia64"
+	use sse2 && acce="sse"
 
 	mycmakeargs_pre+=(
 		$(cmake-utils_use X GMX_X11)
@@ -131,25 +128,23 @@ src_configure() {
 		$(cmake-utils_use threads GMX_THREADS)
 		$(cmake-utils_use xml GMX_XML)
 		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_ACCELERATION="$acce"
 	)
 
 	for x in ${GMX_DIRS}; do
 		einfo "Configuring for ${x} precision"
-		local suffix="" acce="$acce_pre"
+		local suffix=""
 		#if we build single and double - double is suffixed
 		use double-precision && use single-precision && \
 			[ "${x}" = "double" ] && suffix="_d"
-		#double uses sse2, single sse
-		[ "${x}" = "float" ] && use sse && acce="sse"
-		[ "${x}" = "double" ] && use sse2 && acce="sse"
 		local p
 		[ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF -DGMX_ACCELERATION="$acce"
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
 			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON -DGMX_ACCELERATION="$acce"
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
 	done



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-06-19 20:28 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2011-06-19 20:28 UTC (permalink / raw
  To: gentoo-commits

commit:     8f34362af1c2708fe3d022c177fbbd275e2fe00a
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 19 20:27:52 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sun Jun 19 20:27:52 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8f34362a

[sci-chemistry/gromacs] switch to cmake

(Portage version: 2.1.9.42/git/Linux i686, signed Manifest commit with key C2000586)

---
 sci-chemistry/gromacs/ChangeLog               |    4 +
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |  111 +++++++++++--------------
 sci-chemistry/gromacs/metadata.xml            |    1 -
 3 files changed, 51 insertions(+), 65 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 0aeec1b..e6f868f 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  19 Jun 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  metadata.xml:
+  autotools is broken
+
   10 Apr 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.0.9999.ebuild:
   remove 4.0.* (EOM)
 

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index 469f604..f144a3f 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -4,11 +4,10 @@
 
 EAPI="4"
 
-LIBTOOLIZE="true"
 TEST_PV="4.0.4"
 MANUAL_PV="4.5.4"
 
-inherit autotools-utils bash-completion flag-o-matic multilib toolchain-funcs
+inherit bash-completion cmake-utils eutils multilib toolchain-funcs
 
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
@@ -27,8 +26,8 @@ HOMEPAGE="http://www.gromacs.org/"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
-mpi +single-precision sse2 static-libs test +threads +xml zsh-completion"
+IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
+mpi +single-precision sse2 test +threads xml zsh-completion"
 REQUIRED_USE="fkernels? ( !threads )"
 
 CDEPEND="
@@ -37,7 +36,6 @@ CDEPEND="
 		x11-libs/libSM
 		x11-libs/libICE
 		)
-	dmalloc? ( dev-libs/dmalloc )
 	blas? ( virtual/blas )
 	fftw? ( sci-libs/fftw:3.0 )
 	gsl? ( sci-libs/gsl )
@@ -52,6 +50,9 @@ RDEPEND="${CDEPEND}
 RESTRICT="test"
 
 src_prepare() {
+	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
+	epatch_user
+
 	if use mpi && use threads; then
 		elog "mdrun uses only threads OR mpi, and gromacs favours the"
 		elog "use of mpi over threads, so a mpi-version of mdrun will"
@@ -59,10 +60,6 @@ src_prepare() {
 		elog "machines only, you can safely disable mpi"
 	fi
 
-	autotools-utils_src_prepare || die
-
-	eautoreconf || die
-
 	GMX_DIRS=""
 	use single-precision && GMX_DIRS+=" float"
 	use double-precision && GMX_DIRS+=" double"
@@ -77,8 +74,12 @@ src_prepare() {
 }
 
 src_configure() {
+	local mycmakeargs_pre=( )
 	#from gromacs configure
-	if ! use fftw; then
+	if use fftw; then
+		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
+	else
+		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
 		ewarn "WARNING: The built-in FFTPACK routines are slow."
 		ewarn "Are you sure you don\'t want to use FFTW?"
 		ewarn "It is free and much faster..."
@@ -119,65 +120,52 @@ src_configure() {
 		elog "libmd with and without mpi support."
 	fi
 
-	# if we need external blas or lapack
-	use blas && export LIBS+=" $(pkg-config blas --libs)"
-	use lapack && export LIBS+=" $(pkg-config lapack --libs)"
-	local sseflag="x86-64-sse"
-	use x86 && sseflag="ia32-sse"
-
-	#missing flag in autotools (bug #339837)
-	use sse2 && append-flags -msse2
+	#go from slowest to fasterest acceleration
+	local acce="none"
+	use fkernels && acce="fortran"
+	use altivec && acce="altivec"
+	use ia64 && acce="ia64"
+	use sse2 && acce="sse"
+
+	mycmakeargs_pre+=(
+		$(cmake-utils_use X GMX_X11)
+		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
+		$(cmake-utils_use gsl GMX_GSL)
+		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
+		$(cmake-utils_use threads GMX_THREADS)
+		$(cmake-utils_use xml GMX_XML)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_ACCELERATION="$acce"
+	)
 
 	for x in ${GMX_DIRS}; do
+		einfo "Configuring for ${x} precision"
 		local suffix=""
 		#if we build single and double - double is suffixed
 		use double-precision && use single-precision && \
 			[ "${x}" = "double" ] && suffix="_d"
-		myeconfargs=(
-			--bindir="${EPREFIX}"/usr/bin
-			--docdir="${EPREFIX}"/usr/share/doc/"${PF}"
-			--enable-"${x}"
-			$(use_with dmalloc)
-			$(use_with fftw fft fftw3)
-			$(use_with gsl)
-			$(use_with X x)
-			$(use_with xml)
-			$(use_enable threads)
-			$(use_enable altivec ppc-altivec)
-			$(use_enable ia64 ia64-asm)
-			$(use_with lapack external-lapack)
-			$(use_with blas external-blas)
-			$(use_enable fkernels fortran)
-			--disable-bluegene
-			--disable-la-files
-			--disable-power6
-			--disable-ia32-sse
-			--disable-x86-64-sse
-			$(use_enable sse2 $sseflag)
-		)
-		#disable ia32-sse and x86-64-sse and enable what we really need in last line
-
-		einfo "Configuring for ${x} precision"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			autotools-utils_src_configure --disable-mpi	--program-suffix="${suffix}" \
-			CC="$(tc-getCC)" F77="$(tc-getFC)"
+		local p
+		[ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
+			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			autotools-utils_src_configure --enable-mpi --program-suffix="_mpi${suffix}" \
-			CC="$(tc-getCC)" F77="$(tc-getFC)"
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
+			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
 	done
 }
 
 src_compile() {
 	for x in ${GMX_DIRS}; do
 		einfo "Compiling for ${x} precision"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			autotools-utils_src_compile
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			autotools-utils_src_compile mdrun
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+			cmake-utils_src_compile mdrun
 	done
 }
 
@@ -193,18 +181,13 @@ src_test() {
 
 src_install() {
 	for x in ${GMX_DIRS}; do
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			autotools-utils_src_install
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \
+			cmake-utils_src_install
 		use mpi || continue
-		#autotools-utils_src_install does not support args
-		#using autotools-utils_src_compile instead
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			autotools-utils_src_compile install-mdrun DESTDIR="${D}"
-
-		#stolen from autotools-utils_src_install see comment above
-		local args
-		has static-libs ${IUSE//+} && ! use	static-libs || args='none'
-		remove_libtool_files ${args}
+		#cmake-utils_src_install does not support args
+		#using cmake-utils_src_compile instead
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+			cmake-utils_src_make install-mdrun DESTDIR="${D}"
 	done
 
 	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 4aa2d99..1126439 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -7,7 +7,6 @@
 		<name>Christoph Junghans</name>
 	</maintainer>
 	<use>
-		<flag name='dmalloc'>Enable use of Debug Malloc</flag>
 		<flag name='double-precision'>More precise calculations at the expense of speed</flag>
 		<flag name='fkernels'>Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
 		<flag name='single-precision'>Single precision version of gromacs (default)</flag>



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-06-21 11:54 Justin Lecher
  0 siblings, 0 replies; 102+ messages in thread
From: Justin Lecher @ 2011-06-21 11:54 UTC (permalink / raw
  To: gentoo-commits

commit:     8f256d2ad5f0168c0f7319d6c2a0451f0b5dca9e
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 21 11:33:24 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 21 11:33:24 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8f256d2a

Added fortran-2.eclass support

(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |    2 +-
 sci-chemistry/gromacs/gromacs-9999.ebuild     |    2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index e6f868f..791408f 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  21 Jun 2011; Justin Lecher <jlec@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-9999.ebuild:
+  Added fortran-2.eclass support
+
   19 Jun 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
   metadata.xml:
   autotools is broken

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index f144a3f..39c75c6 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -7,7 +7,7 @@ EAPI="4"
 TEST_PV="4.0.4"
 MANUAL_PV="4.5.4"
 
-inherit bash-completion cmake-utils eutils multilib toolchain-funcs
+inherit bash-completion cmake-utils eutils fortran-2 multilib toolchain-funcs
 
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 817444e..8328119 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -9,7 +9,7 @@ TEST_PV="4.0.4"
 EGIT_REPO_URI="git://git.gromacs.org/gromacs"
 EGIT_BRANCH="master"
 
-inherit bash-completion cmake-utils eutils git multilib toolchain-funcs
+inherit bash-completion cmake-utils eutils fortran-2 git multilib toolchain-funcs
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-06-21 20:26 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2011-06-21 20:26 UTC (permalink / raw
  To: gentoo-commits

commit:     a2af1a79c6016d16da3894ee82675dfb99898648
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 21 20:26:01 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Tue Jun 21 20:26:01 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a2af1a79

[sci-chemistry/gromacs] only USE=fkernels needs fortran

(Portage version: 2.1.9.42/git/Linux i686, signed Manifest commit with key C2000586)

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |    5 +++++
 sci-chemistry/gromacs/gromacs-9999.ebuild     |    5 +++++
 3 files changed, 14 insertions(+), 0 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 791408f..c1d748b 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  21 Jun 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-9999.ebuild:
+  only USE=fkernels needs fortran
+
   21 Jun 2011; Justin Lecher <jlec@gentoo.org> gromacs-4.5.9999.ebuild,
   gromacs-9999.ebuild:
   Added fortran-2.eclass support

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index 39c75c6..bcb796e 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -31,6 +31,7 @@ mpi +single-precision sse2 test +threads xml zsh-completion"
 REQUIRED_USE="fkernels? ( !threads )"
 
 CDEPEND="
+	fkernels? ( virtual/fortran )
 	X? (
 		x11-libs/libX11
 		x11-libs/libSM
@@ -49,6 +50,10 @@ RDEPEND="${CDEPEND}
 
 RESTRICT="test"
 
+pkg_setup() {
+	use fkernels && fortran-2_pkg_setup
+}
+
 src_prepare() {
 	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
 	epatch_user

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 8328119..9b79589 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -23,6 +23,7 @@ mpi +single-precision sse2 test +threads xml zsh-completion"
 REQUIRED_USE="fkernels? ( !threads )"
 
 CDEPEND="
+	fkernels? ( virtual/fortran )
 	X? (
 		x11-libs/libX11
 		x11-libs/libSM
@@ -42,6 +43,10 @@ PDEPEND="doc? ( app-doc/gromacs-manual )"
 
 RESTRICT="test"
 
+pkg_setup() {
+	use fkernels && fortran-2_pkg_setup
+}
+
 src_prepare() {
 	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
 	epatch_user



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-06-25 12:58 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2011-06-25 12:58 UTC (permalink / raw
  To: gentoo-commits

commit:     26e67074d2d03136312d49bce09d7a6e24c659a8
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 25 11:58:15 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sat Jun 25 11:58:15 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=26e67074

[sci-chemistry/gromacs] migrate to git-2

(Portage version: 2.1.9.42/git/Linux i686, signed Manifest commit with key C2000586)

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |    2 +-
 sci-chemistry/gromacs/gromacs-9999.ebuild     |    2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index c1d748b..588a10b 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  25 Jun 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-9999.ebuild:
+  migrate to git-2
+
   21 Jun 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
   gromacs-9999.ebuild:
   only USE=fkernels needs fortran

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index bcb796e..349e828 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -15,7 +15,7 @@ SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 if [ "${PV%9999}" != "${PV}" ]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
 	EGIT_BRANCH="release-4-5-patches"
-	inherit git
+	inherit git-2
 else
 	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
 fi

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 9b79589..4a98882 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -9,7 +9,7 @@ TEST_PV="4.0.4"
 EGIT_REPO_URI="git://git.gromacs.org/gromacs"
 EGIT_BRANCH="master"
 
-inherit bash-completion cmake-utils eutils fortran-2 git multilib toolchain-funcs
+inherit bash-completion cmake-utils eutils fortran-2 git-2 multilib toolchain-funcs
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-06-25 17:22 Justin Lecher
  0 siblings, 0 replies; 102+ messages in thread
From: Justin Lecher @ 2011-06-25 17:22 UTC (permalink / raw
  To: gentoo-commits

commit:     5ebb3a71719cb0078ed79cf5a15780ccbdeeac59
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 25 15:48:48 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun 25 15:48:48 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5ebb3a71

migrate from 'git' to 'git-2'

(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |    2 +-
 sci-chemistry/gromacs/gromacs-9999.ebuild     |    2 +-
 sci-chemistry/gromacs/metadata.xml            |    6 +++---
 4 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index c1d748b..b4b2bc3 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  25 Jun 2011; Justin Lecher <jlec@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-9999.ebuild, metadata.xml:
+  migrate from 'git' to 'git-2'
+
   21 Jun 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
   gromacs-9999.ebuild:
   only USE=fkernels needs fortran

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index bcb796e..349e828 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -15,7 +15,7 @@ SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 if [ "${PV%9999}" != "${PV}" ]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
 	EGIT_BRANCH="release-4-5-patches"
-	inherit git
+	inherit git-2
 else
 	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
 fi

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 9b79589..4a98882 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -9,7 +9,7 @@ TEST_PV="4.0.4"
 EGIT_REPO_URI="git://git.gromacs.org/gromacs"
 EGIT_BRANCH="master"
 
-inherit bash-completion cmake-utils eutils fortran-2 git multilib toolchain-funcs
+inherit bash-completion cmake-utils eutils fortran-2 git-2 multilib toolchain-funcs
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 1126439..3735fb7 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -7,8 +7,8 @@
 		<name>Christoph Junghans</name>
 	</maintainer>
 	<use>
-		<flag name='double-precision'>More precise calculations at the expense of speed</flag>
-		<flag name='fkernels'>Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
-		<flag name='single-precision'>Single precision version of gromacs (default)</flag>
+		<flag name="double-precision">More precise calculations at the expense of speed</flag>
+		<flag name="fkernels">Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
+		<flag name="single-precision">Single precision version of gromacs (default)</flag>
 	</use>
 </pkgmetadata>



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-07-18 18:30 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2011-07-18 18:30 UTC (permalink / raw
  To: gentoo-commits

commit:     20fa00bedff3a9f94ae96642459d0cef2d4d9459
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Jul 18 18:30:34 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Mon Jul 18 18:30:34 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=20fa00be

[sci-chemistry/gromacs] sync with tree

(Portage version: 2.1.10.3/git/Linux i686, signed Manifest commit with key C2000586)

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |    6 +++++-
 sci-chemistry/gromacs/gromacs-9999.ebuild     |    6 +++++-
 3 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index dfa2b28..07318f1 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  18 Jul 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-9999.ebuild:
+  sync with tree
+
   25 Jun 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
   gromacs-9999.ebuild:
   migrate to git-2

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index 349e828..8235a5b 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -7,6 +7,9 @@ EAPI="4"
 TEST_PV="4.0.4"
 MANUAL_PV="4.5.4"
 
+#to find external blas/lapack
+CMAKE_MIN_VERSION="2.8.5-r2"
+
 inherit bash-completion cmake-utils eutils fortran-2 multilib toolchain-funcs
 
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
@@ -31,7 +34,6 @@ mpi +single-precision sse2 test +threads xml zsh-completion"
 REQUIRED_USE="fkernels? ( !threads )"
 
 CDEPEND="
-	fkernels? ( virtual/fortran )
 	X? (
 		x11-libs/libX11
 		x11-libs/libSM
@@ -39,6 +41,7 @@ CDEPEND="
 		)
 	blas? ( virtual/blas )
 	fftw? ( sci-libs/fftw:3.0 )
+	fkernels? ( virtual/fortran )
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
 	mpi? ( virtual/mpi )
@@ -141,6 +144,7 @@ src_configure() {
 		$(cmake-utils_use xml GMX_XML)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_ACCELERATION="$acce"
+		-DGMXLIB="$(get_libdir)"
 	)
 
 	for x in ${GMX_DIRS}; do

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 4a98882..7ac7911 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -9,6 +9,9 @@ TEST_PV="4.0.4"
 EGIT_REPO_URI="git://git.gromacs.org/gromacs"
 EGIT_BRANCH="master"
 
+#to find external blas/lapack
+CMAKE_MIN_VERSION="2.8.5-r2"
+
 inherit bash-completion cmake-utils eutils fortran-2 git-2 multilib toolchain-funcs
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
@@ -23,7 +26,6 @@ mpi +single-precision sse2 test +threads xml zsh-completion"
 REQUIRED_USE="fkernels? ( !threads )"
 
 CDEPEND="
-	fkernels? ( virtual/fortran )
 	X? (
 		x11-libs/libX11
 		x11-libs/libSM
@@ -31,6 +33,7 @@ CDEPEND="
 		)
 	blas? ( virtual/blas )
 	fftw? ( sci-libs/fftw:3.0 )
+	fkernels? ( virtual/fortran )
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
 	mpi? ( virtual/mpi )
@@ -134,6 +137,7 @@ src_configure() {
 		$(cmake-utils_use xml GMX_XML)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_ACCELERATION="$acce"
+		-DGMXLIB="$(get_libdir)"
 	)
 
 	for x in ${GMX_DIRS}; do



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-09-10 14:52 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2011-09-10 14:52 UTC (permalink / raw
  To: gentoo-commits

commit:     37ca7e08ded85eceb402188309fd2feb4d4879e2
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 10 14:51:22 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sat Sep 10 14:51:51 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=37ca7e08

[sci-chemistry/gromacs] Migrate to the bash-completion-r1 eclass

(Portage version: 2.1.10.11/git/Linux i686, signed Manifest commit with key C2000586)

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |   25 +++++++++++--------------
 sci-chemistry/gromacs/gromacs-9999.ebuild     |   25 +++++++++++--------------
 3 files changed, 26 insertions(+), 28 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 07318f1..b7359bd 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  10 Sep 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-9999.ebuild:
+  Migrate to the bash-completion-r1 eclass
+
   18 Jul 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
   gromacs-9999.ebuild:
   sync with tree

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index 8235a5b..cfd9015 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -10,7 +10,7 @@ MANUAL_PV="4.5.4"
 #to find external blas/lapack
 CMAKE_MIN_VERSION="2.8.5-r2"
 
-inherit bash-completion cmake-utils eutils fortran-2 multilib toolchain-funcs
+inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
 
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
@@ -205,7 +205,7 @@ src_install() {
 	doenvd "${T}/80gromacs"
 	rm -f "${ED}"/usr/bin/GMXRC*
 
-	dobashcompletion "${ED}"/usr/bin/completion.bash ${PN}
+	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
 	if use zsh-completion ; then
 		insinto /usr/share/zsh/site-functions
 		newins "${ED}"/usr/bin/completion.zsh _${PN}
@@ -227,16 +227,13 @@ src_install() {
 
 pkg_postinst() {
 	env-update && source /etc/profile
-	elog
-	elog "Please read and cite:"
-	elog "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	elog "http://dx.doi.org/10.1021/ct700301q"
-	elog
-	bash-completion_pkg_postinst
-	elog
-	elog $(g_luck)
-	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
-	elog
-	elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
-	elog
+	einfo
+	einfo  "Please read and cite:"
+	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+	einfo  "http://dx.doi.org/10.1021/ct700301q"
+	einfo
+	einfo  $(g_luck)
+	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
+	einfo
+	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
 }

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 7ac7911..d87902f 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -12,7 +12,7 @@ EGIT_BRANCH="master"
 #to find external blas/lapack
 CMAKE_MIN_VERSION="2.8.5-r2"
 
-inherit bash-completion cmake-utils eutils fortran-2 git-2 multilib toolchain-funcs
+inherit bash-completion-r1 cmake-utils eutils fortran-2 git-2 multilib toolchain-funcs
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -198,7 +198,7 @@ src_install() {
 	doenvd "${T}/80gromacs"
 	rm -f "${ED}"/usr/bin/GMXRC*
 
-	dobashcompletion "${ED}"/usr/bin/completion.bash ${PN}
+	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
 	if use zsh-completion ; then
 		insinto /usr/share/zsh/site-functions
 		newins "${ED}"/usr/bin/completion.zsh _${PN}
@@ -223,16 +223,13 @@ src_install() {
 
 pkg_postinst() {
 	env-update && source /etc/profile
-	elog
-	elog "Please read and cite:"
-	elog "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	elog "http://dx.doi.org/10.1021/ct700301q"
-	elog
-	bash-completion_pkg_postinst
-	elog
-	elog $(g_luck)
-	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
-	elog
-	elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
-	elog
+	einfo
+	einfo  "Please read and cite:"
+	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+	einfo  "http://dx.doi.org/10.1021/ct700301q"
+	einfo
+	einfo  $(g_luck)
+	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
+	einfo
+	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
 }



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2011-09-28  7:32 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2011-09-28  7:32 UTC (permalink / raw
  To: gentoo-commits

commit:     447c6e1b7727d7f7a47f7e094de38879301d0ee7
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 28 07:32:11 2011 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Wed Sep 28 07:32:11 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=447c6e1b

[sci-chemistry/gromacs] added 4.6 live version

(Portage version: 2.1.10.11/git/Linux i686, signed Manifest commit with key C2000586)

---
 sci-chemistry/gromacs/ChangeLog               |    5 +
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |  239 +++++++++++++++++++++++++
 2 files changed, 244 insertions(+), 0 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index b7359bd..537e8c7 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*gromacs-4.6.9999 (28 Sep 2011)
+
+  28 Sep 2011; Christoph Junghans <ottxor@gentoo.org> +gromacs-4.6.9999.ebuild:
+  Added gromacs-4.6 live version
+
   10 Sep 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
   gromacs-9999.ebuild:
   Migrate to the bash-completion-r1 eclass

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
new file mode 100644
index 0000000..dab09b1
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -0,0 +1,239 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="4"
+
+TEST_PV="4.0.4"
+MANUAL_PV="4.5.4"
+
+#to find external blas/lapack
+CMAKE_MIN_VERSION="2.8.5-r2"
+
+inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
+
+SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
+
+if [ "${PV%9999}" != "${PV}" ]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
+	EGIT_BRANCH="release-4-6"
+	inherit git-2
+else
+	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
+fi
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
+mpi +single-precision sse2 test +threads xml zsh-completion"
+REQUIRED_USE="fkernels? ( !threads )"
+
+CDEPEND="
+	X? (
+		x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE
+		)
+	blas? ( virtual/blas )
+	fftw? ( sci-libs/fftw:3.0 )
+	fkernels? ( virtual/fortran )
+	gsl? ( sci-libs/gsl )
+	lapack? ( virtual/lapack )
+	mpi? ( virtual/mpi )
+	xml? ( dev-libs/libxml2:2 )"
+DEPEND="${CDEPEND}
+	dev-util/pkgconfig"
+RDEPEND="${CDEPEND}
+	app-shells/tcsh"
+
+RESTRICT="test"
+
+pkg_setup() {
+	use fkernels && fortran-2_pkg_setup
+}
+
+src_prepare() {
+	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
+	epatch_user
+
+	if use mpi && use threads; then
+		elog "mdrun uses only threads OR mpi, and gromacs favours the"
+		elog "use of mpi over threads, so a mpi-version of mdrun will"
+		elog "be compiled. If you want to run mdrun on shared memory"
+		elog "machines only, you can safely disable mpi"
+	fi
+
+	GMX_DIRS=""
+	use single-precision && GMX_DIRS+=" float"
+	use double-precision && GMX_DIRS+=" double"
+	#if neither single-precision nor double-precision is enabled
+	#build at least default (single)
+	[ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
+
+	for x in ${GMX_DIRS}; do
+		mkdir -p "${WORKDIR}/${P}_${x}" || die
+		use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
+	done
+}
+
+src_configure() {
+	local mycmakeargs_pre=( )
+	#from gromacs configure
+	if use fftw; then
+		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
+	else
+		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
+		ewarn "WARNING: The built-in FFTPACK routines are slow."
+		ewarn "Are you sure you don\'t want to use FFTW?"
+		ewarn "It is free and much faster..."
+	fi
+
+	if [[ $(gcc-version) == "4.1" ]]; then
+		eerror "gcc 4.1 is not supported by gromacs"
+		eerror "please run test suite"
+		die
+	fi
+
+	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
+
+	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
+	if use fkernels; then
+		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
+		ewarn "I hope, you know what are you doing..."
+	fi
+
+	if use double-precision ; then
+		#from gromacs manual
+		elog
+		elog "For most simulations single precision is accurate enough. In some"
+		elog "cases double precision is required to get reasonable results:"
+		elog
+		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
+		elog " and the calculation and diagonalization of the Hessian "
+		elog "-calculation of the constraint force between two large groups of	atoms"
+		elog "-energy conservation: this can only be done without temperature coupling and"
+		elog " without cutoffs"
+		elog
+	fi
+
+	if use mpi ; then
+		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
+		elog "we configure/compile gromacs twice (with and without mpi) and only"
+		elog "install mdrun with mpi support. In addtion you will get libgmx and"
+		elog "libmd with and without mpi support."
+	fi
+
+	#go from slowest to fasterest acceleration
+	local acce="none"
+	use fkernels && acce="fortran"
+	use altivec && acce="altivec"
+	use ia64 && acce="ia64"
+	use sse2 && acce="sse"
+
+	mycmakeargs_pre+=(
+		$(cmake-utils_use X GMX_X11)
+		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
+		$(cmake-utils_use gsl GMX_GSL)
+		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
+		$(cmake-utils_use threads GMX_THREADS)
+		$(cmake-utils_use xml GMX_XML)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_ACCELERATION="$acce"
+		-DGMXLIB="$(get_libdir)"
+	)
+
+	for x in ${GMX_DIRS}; do
+		einfo "Configuring for ${x} precision"
+		local suffix=""
+		#if we build single and double - double is suffixed
+		use double-precision && use single-precision && \
+			[ "${x}" = "double" ] && suffix="_d"
+		local p
+		[ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
+			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		use mpi || continue
+		einfo "Configuring for ${x} precision with mpi"
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
+			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		einfo "Compiling for ${x} precision"
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile
+		use mpi || continue
+		einfo "Compiling for ${x} precision with mpi"
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+			cmake-utils_src_compile mdrun
+	done
+}
+
+src_test() {
+	for x in ${GMX_DIRS}; do
+		local oldpath="${PATH}"
+		export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
+		cd "${WORKDIR}/${P}_${x}"
+		emake -j1 tests || die "${x} Precision test failed"
+		export PATH="${oldpath}"
+	done
+}
+
+src_install() {
+	for x in ${GMX_DIRS}; do
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \
+			cmake-utils_src_install
+		use mpi || continue
+		#cmake-utils_src_install does not support args
+		#using cmake-utils_src_compile instead
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+			cmake-utils_src_make install-mdrun DESTDIR="${D}"
+	done
+
+	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
+	echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
+
+	doenvd "${T}/80gromacs"
+	rm -f "${ED}"/usr/bin/GMXRC*
+
+	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
+	if use zsh-completion ; then
+		insinto /usr/share/zsh/site-functions
+		newins "${ED}"/usr/bin/completion.zsh _${PN}
+	fi
+	rm -f "${ED}"/usr/bin/completion.*
+
+	# Fix typos in a couple of files.
+	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
+		|| die "Failed to fixup demo script."
+
+	cd "${S}"
+	dodoc AUTHORS INSTALL* README*
+	if use doc; then
+		newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
+		dohtml -r "${ED}usr/share/gromacs/html/"
+	fi
+	rm -rf "${ED}usr/share/gromacs/html/"
+}
+
+pkg_postinst() {
+	env-update && source /etc/profile
+	einfo
+	einfo  "Please read and cite:"
+	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+	einfo  "http://dx.doi.org/10.1021/ct700301q"
+	einfo
+	einfo  $(g_luck)
+	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
+	einfo
+	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
+}



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-02-05  0:30 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-02-05  0:30 UTC (permalink / raw
  To: gentoo-commits

commit:     b34c72d1816ff04cb8d6556bf8a08392b96a01d1
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Feb  5 00:30:14 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sun Feb  5 00:30:14 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b34c72d1

added openmp support

(Portage version: 2.2.0_alpha84/git/Linux i686, unsigned Manifest commit)

---
 sci-chemistry/gromacs/ChangeLog               |    5 ++++-
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    5 +++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 537e8c7..424f26b 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-chemistry/gromacs
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 Feb 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  added openmp support
+
 *gromacs-4.6.9999 (28 Sep 2011)
 
   28 Sep 2011; Christoph Junghans <ottxor@gentoo.org> +gromacs-4.6.9999.ebuild:

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index dab09b1..2ce38b6 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -30,7 +30,7 @@ LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
 IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
-mpi +single-precision sse2 test +threads xml zsh-completion"
+mpi openmp +single-precision sse2 test +threads xml zsh-completion"
 REQUIRED_USE="fkernels? ( !threads )"
 
 CDEPEND="
@@ -141,6 +141,7 @@ src_configure() {
 		$(cmake-utils_use gsl GMX_GSL)
 		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
 		$(cmake-utils_use threads GMX_THREADS)
+		$(cmake-utils_use openmp GMX_OPENMP)
 		$(cmake-utils_use xml GMX_XML)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_ACCELERATION="$acce"



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-02-05 21:31 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-02-05 21:31 UTC (permalink / raw
  To: gentoo-commits

commit:     102b939a8f676888380ae1c02e7c96f11589022e
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Feb  5 21:30:29 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sun Feb  5 21:30:29 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=102b939a

handle new vmd detection

(Portage version: 2.2.0_alpha85/git/Linux i686, unsigned Manifest commit)

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    5 +----
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 424f26b..509854b 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   05 Feb 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  handle new vmd detection
+
+  05 Feb 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   added openmp support
 
 *gromacs-4.6.9999 (28 Sep 2011)

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 2ce38b6..99b5c2b 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -146,6 +146,7 @@ src_configure() {
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_ACCELERATION="$acce"
 		-DGMXLIB="$(get_libdir)"
+	    -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
 	)
 
 	for x in ${GMX_DIRS}; do
@@ -200,10 +201,6 @@ src_install() {
 			cmake-utils_src_make install-mdrun DESTDIR="${D}"
 	done
 
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
-
-	doenvd "${T}/80gromacs"
 	rm -f "${ED}"/usr/bin/GMXRC*
 
 	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-02-12  1:34 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-02-12  1:34 UTC (permalink / raw
  To: gentoo-commits

commit:     db7f1585143778adef558a34ae08cc157879d23f
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 12 01:31:15 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sun Feb 12 01:31:15 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=db7f1585

sci-chemistry/gromacs: fixed threads and mpi

(Portage version: 2.2.0_alpha85/git/Linux i686, unsigned Manifest commit)

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   11 +++++------
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 509854b..77af425 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  12 Feb 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  fixed threads and mpi
+
   05 Feb 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   handle new vmd detection
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 99b5c2b..0bd4bf3 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -73,7 +73,7 @@ src_prepare() {
 	use double-precision && GMX_DIRS+=" double"
 	#if neither single-precision nor double-precision is enabled
 	#build at least default (single)
-	[ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
+	[[ -z $GMX_DIRS ]] && GMX_DIRS+=" float"
 
 	for x in ${GMX_DIRS}; do
 		mkdir -p "${WORKDIR}/${P}_${x}" || die
@@ -140,7 +140,7 @@ src_configure() {
 		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
 		$(cmake-utils_use gsl GMX_GSL)
 		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use threads GMX_THREADS)
+		$(cmake-utils_use threads GMX_THREAD_MPI)
 		$(cmake-utils_use openmp GMX_OPENMP)
 		$(cmake-utils_use xml GMX_XML)
 		-DGMX_DEFAULT_SUFFIX=off
@@ -154,9 +154,9 @@ src_configure() {
 		local suffix=""
 		#if we build single and double - double is suffixed
 		use double-precision && use single-precision && \
-			[ "${x}" = "double" ] && suffix="_d"
+			[[ ${x} = "double" ]] && suffix="_d"
 		local p
-		[ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
 			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
@@ -164,7 +164,7 @@ src_configure() {
 		einfo "Configuring for ${x} precision with mpi"
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
 	done
 }
 
@@ -224,7 +224,6 @@ src_install() {
 }
 
 pkg_postinst() {
-	env-update && source /etc/profile
 	einfo
 	einfo  "Please read and cite:"
 	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-03-04  1:23 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-03-04  1:23 UTC (permalink / raw
  To: gentoo-commits

commit:     7bd36f7c9752fe04b58fdb1956bbcb3421711c22
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 12 20:49:33 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sun Feb 12 20:49:33 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7bd36f7c

sci-chemistry/gromacs: clean up

(Portage version: 2.2.0_alpha86/git/Linux i686, unsigned Manifest commit)

---
 sci-chemistry/gromacs/ChangeLog               |    3 +
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   52 +++---------------------
 2 files changed, 10 insertions(+), 45 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 77af425..c508a38 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   12 Feb 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  sci-chemistry/gromacs: clean up
+
+  12 Feb 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   fixed threads and mpi
 
   05 Feb 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 0bd4bf3..9ecb639 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -53,6 +53,10 @@ RDEPEND="${CDEPEND}
 
 RESTRICT="test"
 
+pkg_pretend() {
+	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
+}
+
 pkg_setup() {
 	use fkernels && fortran-2_pkg_setup
 }
@@ -61,13 +65,6 @@ src_prepare() {
 	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
 	epatch_user
 
-	if use mpi && use threads; then
-		elog "mdrun uses only threads OR mpi, and gromacs favours the"
-		elog "use of mpi over threads, so a mpi-version of mdrun will"
-		elog "be compiled. If you want to run mdrun on shared memory"
-		elog "machines only, you can safely disable mpi"
-	fi
-
 	GMX_DIRS=""
 	use single-precision && GMX_DIRS+=" float"
 	use double-precision && GMX_DIRS+=" double"
@@ -83,21 +80,6 @@ src_prepare() {
 
 src_configure() {
 	local mycmakeargs_pre=( )
-	#from gromacs configure
-	if use fftw; then
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
-	else
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
-		ewarn "WARNING: The built-in FFTPACK routines are slow."
-		ewarn "Are you sure you don\'t want to use FFTW?"
-		ewarn "It is free and much faster..."
-	fi
-
-	if [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
 
 	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
 
@@ -107,27 +89,6 @@ src_configure() {
 		ewarn "I hope, you know what are you doing..."
 	fi
 
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
-
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
-	fi
-
 	#go from slowest to fasterest acceleration
 	local acce="none"
 	use fkernels && acce="fortran"
@@ -136,11 +97,11 @@ src_configure() {
 	use sse2 && acce="sse"
 
 	mycmakeargs_pre+=(
+		-DGMX_FFT_LIBRARY=$(usex fftw fftw3 fftwpack)
 		$(cmake-utils_use X GMX_X11)
 		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
 		$(cmake-utils_use gsl GMX_GSL)
 		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use threads GMX_THREAD_MPI)
 		$(cmake-utils_use openmp GMX_OPENMP)
 		$(cmake-utils_use xml GMX_XML)
 		-DGMX_DEFAULT_SUFFIX=off
@@ -158,11 +119,12 @@ src_configure() {
 		local p
 		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
+			$(cmake-utils_use threads GMX_THREAD_MPI)
 			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF -DGMX_MPI=ON
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
 	done



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-03-04  1:23 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-03-04  1:23 UTC (permalink / raw
  To: gentoo-commits

commit:     91537132ed25844b2f45dce59670678d63600512
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  4 01:15:43 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sun Mar  4 01:15:43 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=91537132

removed obsolete call to env-update

(Portage version: 2.2.0_alpha89/git/Linux i686, unsigned Manifest commit)

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |    3 +--
 sci-chemistry/gromacs/gromacs-9999.ebuild     |    3 +--
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 62edd24..90f7e68 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  04 Mar 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-9999.ebuild:
+  removed obsolete call to env-update
+
   04 Mar 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   reworked fortran and openmp support
 

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index cfd9015..9a26c35 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -226,7 +226,6 @@ src_install() {
 }
 
 pkg_postinst() {
-	env-update && source /etc/profile
 	einfo
 	einfo  "Please read and cite:"
 	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index d87902f..ebe9a68 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -222,7 +222,6 @@ src_install() {
 }
 
 pkg_postinst() {
-	env-update && source /etc/profile
 	einfo
 	einfo  "Please read and cite:"
 	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-03-04  1:23 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-03-04  1:23 UTC (permalink / raw
  To: gentoo-commits

commit:     40d68f6aa3078ab6f35aa06be400a4d6ecffabf7
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  4 01:14:05 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sun Mar  4 01:14:05 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=40d68f6a

reworked fortran and openmp support

(Portage version: 2.2.0_alpha89/git/Linux i686, unsigned Manifest commit)

---
 sci-chemistry/gromacs/ChangeLog               |    3 ++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   36 +++++++++++++++---------
 2 files changed, 25 insertions(+), 14 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index c508a38..62edd24 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  04 Mar 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  reworked fortran and openmp support
+
   12 Feb 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   sci-chemistry/gromacs: clean up
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 9ecb639..a036dca 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -31,7 +31,6 @@ SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
 IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
 mpi openmp +single-precision sse2 test +threads xml zsh-completion"
-REQUIRED_USE="fkernels? ( !threads )"
 
 CDEPEND="
 	X? (
@@ -41,7 +40,7 @@ CDEPEND="
 		)
 	blas? ( virtual/blas )
 	fftw? ( sci-libs/fftw:3.0 )
-	fkernels? ( virtual/fortran )
+	fkernels? ( !threads? ( !altivec? ( !ia64? ( !sse2? ( virtual/fortran ) ) ) ) )
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
 	mpi? ( virtual/mpi )
@@ -55,10 +54,27 @@ RESTRICT="test"
 
 pkg_pretend() {
 	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
+	use openmp && ! tc-has-openmp && \
+		die "Please switch to an openmp compatible compiler"
 }
 
 pkg_setup() {
-	use fkernels && fortran-2_pkg_setup
+	#notes/todos
+	# -on apple: there is framework support
+	# -mkl support
+	# -there are power6 kernels
+	if use fkernels; then
+		if use altivec || use ia64 || use sse2; then
+			ewarn "Gromacs only supports one acceleration method, in your case"
+			ewarn "the fortran kernel will be overwritten by (altivec|ia64|sse2)"
+			ewarn "so it is save to disable fkernels use flag!"
+		elif use threads; then
+			ewarn "Fortran kernels and threads do not work together, disabling"
+			ewarn "fortran kernels"
+		else
+			fortran-2_pkg_setup
+		fi
+	fi
 }
 
 src_prepare() {
@@ -81,17 +97,9 @@ src_prepare() {
 src_configure() {
 	local mycmakeargs_pre=( )
 
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-	fi
-
-	#go from slowest to fasterest acceleration
+	#go from slowest to fastest acceleration
 	local acce="none"
-	use fkernels && acce="fortran"
+	use fkernels && use !threads && acce="fortran"
 	use altivec && acce="altivec"
 	use ia64 && acce="ia64"
 	use sse2 && acce="sse"
@@ -158,7 +166,7 @@ src_install() {
 			cmake-utils_src_install
 		use mpi || continue
 		#cmake-utils_src_install does not support args
-		#using cmake-utils_src_compile instead
+		#using cmake-utils_src_make instead
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
 			cmake-utils_src_make install-mdrun DESTDIR="${D}"
 	done



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-04-19 19:43 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2012-04-19 19:43 UTC (permalink / raw
  To: gentoo-commits

commit:     19b43c51fbb574570a8d034a0b93bde419a38447
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Thu Apr 19 19:42:30 2012 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Apr 19 19:42:30 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=19b43c51

[sci-chemistry/gromacs] Also add http mirror git uri

(Portage version: 2.2.0_alpha100/git/Linux x86_64, unsigned Manifest commit)

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |    2 +-
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    2 +-
 sci-chemistry/gromacs/gromacs-9999.ebuild     |    2 +-
 4 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 90f7e68..ad13bf2 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  19 Apr 2012; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-4.6.9999.ebuild, gromacs-9999.ebuild:
+  [sci-chemistry/gromacs] Also add http mirror git uri
+
   04 Mar 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
   gromacs-9999.ebuild:
   removed obsolete call to env-update

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index 9a26c35..d89ceb4 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -16,7 +16,7 @@ SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
 
 if [ "${PV%9999}" != "${PV}" ]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-4-5-patches"
 	inherit git-2
 else

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index a036dca..3bf2959 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -16,7 +16,7 @@ SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
 
 if [ "${PV%9999}" != "${PV}" ]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-4-6"
 	inherit git-2
 else

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index ebe9a68..24e0e14 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -6,7 +6,7 @@ EAPI="4"
 
 TEST_PV="4.0.4"
 
-EGIT_REPO_URI="git://git.gromacs.org/gromacs"
+EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git"
 EGIT_BRANCH="master"
 
 #to find external blas/lapack



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-04-28  1:21 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-04-28  1:21 UTC (permalink / raw
  To: gentoo-commits

commit:     a5a265d2d8e412c0786f3770d1c5f1ad2f5a8ad1
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Apr 28 01:16:55 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sat Apr 28 01:16:55 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a5a265d2

[sci-chemistry/gromacs] add more mirrors

(Portage version: 2.2.0_alpha101/git/Linux i686, unsigned Manifest commit)

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    5 ++++-
 2 files changed, 7 insertions(+), 1 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index ad13bf2..9310220 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  28 Apr 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  [sci-chemistry/gromacs] add more mirrors
+
   19 Apr 2012; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.5.9999.ebuild,
   gromacs-4.6.9999.ebuild, gromacs-9999.ebuild:
   [sci-chemistry/gromacs] Also add http mirror git uri

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 3bf2959..4d66fc3 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -16,7 +16,10 @@ SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
 
 if [ "${PV%9999}" != "${PV}" ]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git"
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+		https://gerrit.gromacs.org/gromacs.git
+		git://github.com/gromacs/gromacs.git
+		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-4-6"
 	inherit git-2
 else



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-06-11  2:15 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-06-11  2:15 UTC (permalink / raw
  To: gentoo-commits

commit:     f654c8c2fd1f9f0b0bc92727f72cd61132330cbd
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 11 02:14:37 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Mon Jun 11 02:14:37 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f654c8c2

add support for new hybrid kernels

(Portage version: 2.2.0_alpha110/git/Linux i686, unsigned Manifest commit)

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   21 +++++++++++++++++++--
 sci-chemistry/gromacs/metadata.xml            |    2 ++
 3 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 9310220..2395fef 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  11 Jun 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  metadata.xml:
+  add support for new hybrid kernels
+
   28 Apr 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   [sci-chemistry/gromacs] add more mirrors
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 4d66fc3..791d1c5 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -15,12 +15,13 @@ inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
 		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
 
-if [ "${PV%9999}" != "${PV}" ]; then
+if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
 		https://gerrit.gromacs.org/gromacs.git
 		git://github.com/gromacs/gromacs.git
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-4-6"
+	use hybrid && EGIT_BRANCH="nbnxn_hybrid_acc"
 	inherit git-2
 else
 	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
@@ -32,7 +33,7 @@ HOMEPAGE="http://www.gromacs.org/"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
+IUSE="X altivec blas cuda doc -double-precision +fftw fkernels gsl hybrid lapack
 mpi openmp +single-precision sse2 test +threads xml zsh-completion"
 
 CDEPEND="
@@ -42,6 +43,7 @@ CDEPEND="
 		x11-libs/libICE
 		)
 	blas? ( virtual/blas )
+	cuda? ( dev-util/nvidia-cuda-toolkit )
 	fftw? ( sci-libs/fftw:3.0 )
 	fkernels? ( !threads? ( !altivec? ( !ia64? ( !sse2? ( virtual/fortran ) ) ) ) )
 	gsl? ( sci-libs/gsl )
@@ -55,10 +57,16 @@ RDEPEND="${CDEPEND}
 
 RESTRICT="test"
 
+REQUIRED_USE="cuda? ( !double-precision hybrid )"
+
 pkg_pretend() {
 	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
 	use openmp && ! tc-has-openmp && \
 		die "Please switch to an openmp compatible compiler"
+	if use cuda && [[ $(( $(gcc-major-version) * 10 + $(gcc-minor-version) )) -gt 44 ]] ; then
+		eerror "gcc 4.5 and up are not supported for useflag cuda!"
+		die "gcc 4.5 and up are not supported for useflag cuda!"
+	fi
 }
 
 pkg_setup() {
@@ -107,10 +115,14 @@ src_configure() {
 	use ia64 && acce="ia64"
 	use sse2 && acce="sse"
 
+	#workaround for now
+	use sse2 && use hybrid && CFLAGS+=" -msse2"
+
 	mycmakeargs_pre+=(
 		-DGMX_FFT_LIBRARY=$(usex fftw fftw3 fftwpack)
 		$(cmake-utils_use X GMX_X11)
 		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
+		$(cmake-utils_use cuda GMX_GPU)
 		$(cmake-utils_use gsl GMX_GSL)
 		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
 		$(cmake-utils_use openmp GMX_OPENMP)
@@ -206,4 +218,9 @@ pkg_postinst() {
 	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
 	einfo
 	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
+	if use hybrid; then
+		elog "Cuda and hybrid acceleration is still experimental,"
+		elog "use 'cutoff-scheme = Verlet' in your mdp file and"
+		elog "report bugs: http://redmine.gromacs.org/issues"
+	fi
 }

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 3735fb7..444d47e 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -7,8 +7,10 @@
 		<name>Christoph Junghans</name>
 	</maintainer>
 	<use>
+		<flag name="cuda">Enable cuda non-bonded kernels</flag>
 		<flag name="double-precision">More precise calculations at the expense of speed</flag>
 		<flag name="fkernels">Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
+		<flag name="hybrid">Enable hybrid acceleration kernels</flag>
 		<flag name="single-precision">Single precision version of gromacs (default)</flag>
 	</use>
 </pkgmetadata>



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-06-19 14:10 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2012-06-19 14:10 UTC (permalink / raw
  To: gentoo-commits

commit:     b068ed3581fa74b2e1c3cc3519e8dcfd6afffe22
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 19 14:09:33 2012 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Tue Jun 19 14:09:33 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b068ed35

[sci-chemistry/gromacs] Add new acceleration use flags for gromacs

(Portage version: 2.2.0_alpha110/git/Linux x86_64, unsigned Manifest commit)

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   18 +++++++++++-------
 sci-chemistry/gromacs/gromacs-9999.ebuild     |   18 +++++++++++-------
 sci-chemistry/gromacs/metadata.xml            |    7 ++++++-
 4 files changed, 32 insertions(+), 15 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 2395fef..61418cf 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  19 Jun 2012; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-9999.ebuild, metadata.xml:
+  [sci-chemistry/gromacs] Add new acceleration use flags for gromacs
+
   11 Jun 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
   metadata.xml:
   add support for new hybrid kernels

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 791d1c5..752c56e 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -27,14 +27,16 @@ else
 	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
 fi
 
+ACCE_IUSE="fkernels power6 sse2 sse41 avx128fma avx256"
+
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
 
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X altivec blas cuda doc -double-precision +fftw fkernels gsl hybrid lapack
-mpi openmp +single-precision sse2 test +threads xml zsh-completion"
+IUSE="X blas cuda doc -double-precision +fftw gsl hybrid lapack
+mpi openmp +single-precision test +threads xml zsh-completion ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -109,11 +111,13 @@ src_configure() {
 	local mycmakeargs_pre=( )
 
 	#go from slowest to fastest acceleration
-	local acce="none"
-	use fkernels && use !threads && acce="fortran"
-	use altivec && acce="altivec"
-	use ia64 && acce="ia64"
-	use sse2 && acce="sse"
+	local acce="None"
+	use fkernels && use !threads && acce="Fortran"
+	use power6 && acce="Power6"
+	use sse2 && acce="SSE2"
+	use sse41 && acce="SSE4.1"
+	use avx128fma && acce="AVX_128_FMA"
+	use avx256 && acce="AVX_256"
 
 	#workaround for now
 	use sse2 && use hybrid && CFLAGS+=" -msse2"

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 24e0e14..f9891ea 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -9,6 +9,8 @@ TEST_PV="4.0.4"
 EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git"
 EGIT_BRANCH="master"
 
+ACCE_IUSE="fkernels power6 sse2 sse41 avx128fma avx256"
+
 #to find external blas/lapack
 CMAKE_MIN_VERSION="2.8.5-r2"
 
@@ -21,8 +23,8 @@ SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
-mpi +single-precision sse2 test +threads xml zsh-completion"
+IUSE="X blas doc -double-precision +fftw gsl lapack mpi +single-precision  test
++threads xml zsh-completion ${ACCE_IUSE}"
 REQUIRED_USE="fkernels? ( !threads )"
 
 CDEPEND="
@@ -122,11 +124,13 @@ src_configure() {
 	fi
 
 	#go from slowest to fasterest acceleration
-	local acce="none"
-	use fkernels && acce="fortran"
-	use altivec && acce="altivec"
-	use ia64 && acce="ia64"
-	use sse2 && acce="sse"
+	local acce="None"
+	use fkernels && use !threads && acce="Fortran"
+	use power6 && acce="Power6"
+	use sse2 && acce="SSE2"
+	use sse41 && acce="SSE4.1"
+	use avx128fma && acce="AVX_128_FMA"
+	use avx256 && acce="AVX_256"
 
 	mycmakeargs_pre+=(
 		$(cmake-utils_use X GMX_X11)

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 444d47e..dd3f082 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -9,8 +9,13 @@
 	<use>
 		<flag name="cuda">Enable cuda non-bonded kernels</flag>
 		<flag name="double-precision">More precise calculations at the expense of speed</flag>
-		<flag name="fkernels">Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
 		<flag name="hybrid">Enable hybrid acceleration kernels</flag>
 		<flag name="single-precision">Single precision version of gromacs (default)</flag>
+		<!-- acceleration optimization flags -->
+		<flag name="fkernels">Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
+		<flag name="sse41">Enable sse4.1 acceleration</flag>
+		<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
+		<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+		<flag name="power6">Enable Power6 optimizations</flag>
 	</use>
 </pkgmetadata>



^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-07-25  1:25 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-07-25  1:25 UTC (permalink / raw
  To: gentoo-commits

commit:     c299bcfc92f7743568f1f089f08abc0f0c05195b
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Jul 25 01:23:25 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Wed Jul 25 01:23:25 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c299bcfc

added ~x86-macos

(Portage version: 2.2.0_alpha120/git/Linux i686, unsigned Manifest commit)

---
 sci-chemistry/gromacs/ChangeLog               |    5 ++++-
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |    2 +-
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   11 ++++++++---
 sci-chemistry/gromacs/gromacs-9999.ebuild     |    2 +-
 4 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 61418cf..7af763e 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  25 Jul 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-4.6.9999.ebuild, gromacs-9999.ebuild:
+  added ~x86-macos
+
   19 Jun 2012; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild,
   gromacs-9999.ebuild, metadata.xml:
   [sci-chemistry/gromacs] Add new acceleration use flags for gromacs
@@ -305,4 +309,3 @@
   20 Jan 2009; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-3.3.3.ebuild,
   +gromacs-4.0.3.ebuild:
   Version bump
-

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index d89ceb4..a4a70d3 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -47,7 +47,7 @@ CDEPEND="
 	mpi? ( virtual/mpi )
 	xml? ( dev-libs/libxml2:2 )"
 DEPEND="${CDEPEND}
-	dev-util/pkgconfig"
+	virtual/pkgconfig"
 RDEPEND="${CDEPEND}
 	app-shells/tcsh"
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 752c56e..eac6265 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -34,7 +34,7 @@ HOMEPAGE="http://www.gromacs.org/"
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
 IUSE="X blas cuda doc -double-precision +fftw gsl hybrid lapack
 mpi openmp +single-precision test +threads xml zsh-completion ${ACCE_IUSE}"
 
@@ -53,7 +53,7 @@ CDEPEND="
 	mpi? ( virtual/mpi )
 	xml? ( dev-libs/libxml2:2 )"
 DEPEND="${CDEPEND}
-	dev-util/pkgconfig"
+	virtual/pkgconfig"
 RDEPEND="${CDEPEND}
 	app-shells/tcsh"
 
@@ -108,7 +108,7 @@ src_prepare() {
 }
 
 src_configure() {
-	local mycmakeargs_pre=( )
+	local mycmakeargs_pre=( ) extra
 
 	#go from slowest to fastest acceleration
 	local acce="None"
@@ -122,6 +122,10 @@ src_configure() {
 	#workaround for now
 	use sse2 && use hybrid && CFLAGS+=" -msse2"
 
+	#to create man pages, build tree binaries are executed (bug #398437)
+	[[ ${CHOST} = *-darwin* ]] && \
+		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
 	mycmakeargs_pre+=(
 		-DGMX_FFT_LIBRARY=$(usex fftw fftw3 fftwpack)
 		$(cmake-utils_use X GMX_X11)
@@ -135,6 +139,7 @@ src_configure() {
 		-DGMX_ACCELERATION="$acce"
 		-DGMXLIB="$(get_libdir)"
 	    -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+		${extra}
 	)
 
 	for x in ${GMX_DIRS}; do

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index f9891ea..d74f3cd 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -41,7 +41,7 @@ CDEPEND="
 	mpi? ( virtual/mpi )
 	xml? ( dev-libs/libxml2:2 )"
 DEPEND="${CDEPEND}
-	dev-util/pkgconfig"
+	virtual/pkgconfig"
 RDEPEND="${CDEPEND}
 	app-shells/tcsh"
 PDEPEND="doc? ( app-doc/gromacs-manual )"


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-08-09  5:15 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-08-09  5:15 UTC (permalink / raw
  To: gentoo-commits

commit:     755887d19235cb48a38de2e17eaefff1eb9d0a95
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Aug  9 05:15:08 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Thu Aug  9 05:15:35 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=755887d1

use ninja if available

(Portage version: 2.2.0_alpha120/git/Linux i686, unsigned Manifest commit)

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    8 +++-----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 7af763e..e597ab8 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  09 Aug 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  use ninja if available
+
   25 Jul 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
   gromacs-4.6.9999.ebuild, gromacs-9999.ebuild:
   added ~x86-macos

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index eac6265..f54af37 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -10,6 +10,8 @@ MANUAL_PV="4.5.4"
 #to find external blas/lapack
 CMAKE_MIN_VERSION="2.8.5-r2"
 
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
 inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
 
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
@@ -192,7 +194,7 @@ src_install() {
 		#cmake-utils_src_install does not support args
 		#using cmake-utils_src_make instead
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_make install-mdrun DESTDIR="${D}"
+			DESTDIR="${D}" cmake-utils_src_make install-mdrun
 	done
 
 	rm -f "${ED}"/usr/bin/GMXRC*
@@ -204,10 +206,6 @@ src_install() {
 	fi
 	rm -f "${ED}"/usr/bin/completion.*
 
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
 	cd "${S}"
 	dodoc AUTHORS INSTALL* README*
 	if use doc; then


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-10-03 14:54 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-10-03 14:54 UTC (permalink / raw
  To: gentoo-commits

commit:     6d54a8c0ae0936c3108a4c1d5ee96f2e93caba0e
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Oct  3 14:54:24 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Wed Oct  3 14:54:41 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6d54a8c0

hybrid stuff got merged

(Portage version: 2.2.0_alpha134/git/Linux i686, unsigned Manifest commit)

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   12 +++---------
 sci-chemistry/gromacs/metadata.xml            |    1 -
 3 files changed, 7 insertions(+), 10 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index e597ab8..47636de 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  03 Oct 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  metadata.xml:
+  hybrid stuff got merged
+
   09 Aug 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   use ninja if available
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index f54af37..bbf4161 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -23,7 +23,6 @@ if [[ $PV = *9999* ]]; then
 		git://github.com/gromacs/gromacs.git
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-4-6"
-	use hybrid && EGIT_BRANCH="nbnxn_hybrid_acc"
 	inherit git-2
 else
 	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
@@ -37,7 +36,7 @@ HOMEPAGE="http://www.gromacs.org/"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE="X blas cuda doc -double-precision +fftw gsl hybrid lapack
+IUSE="X blas cuda doc -double-precision +fftw gsl lapack
 mpi openmp +single-precision test +threads xml zsh-completion ${ACCE_IUSE}"
 
 CDEPEND="
@@ -61,7 +60,7 @@ RDEPEND="${CDEPEND}
 
 RESTRICT="test"
 
-REQUIRED_USE="cuda? ( !double-precision hybrid )"
+REQUIRED_USE="cuda? ( !double-precision )"
 
 pkg_pretend() {
 	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
@@ -122,7 +121,7 @@ src_configure() {
 	use avx256 && acce="AVX_256"
 
 	#workaround for now
-	use sse2 && use hybrid && CFLAGS+=" -msse2"
+	use sse2 && CFLAGS+=" -msse2"
 
 	#to create man pages, build tree binaries are executed (bug #398437)
 	[[ ${CHOST} = *-darwin* ]] && \
@@ -225,9 +224,4 @@ pkg_postinst() {
 	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
 	einfo
 	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
-	if use hybrid; then
-		elog "Cuda and hybrid acceleration is still experimental,"
-		elog "use 'cutoff-scheme = Verlet' in your mdp file and"
-		elog "report bugs: http://redmine.gromacs.org/issues"
-	fi
 }

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index dd3f082..acbcd53 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -9,7 +9,6 @@
 	<use>
 		<flag name="cuda">Enable cuda non-bonded kernels</flag>
 		<flag name="double-precision">More precise calculations at the expense of speed</flag>
-		<flag name="hybrid">Enable hybrid acceleration kernels</flag>
 		<flag name="single-precision">Single precision version of gromacs (default)</flag>
 		<!-- acceleration optimization flags -->
 		<flag name="fkernels">Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-10-04 14:39 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-10-04 14:39 UTC (permalink / raw
  To: gentoo-commits

commit:     ec696fcd94f02907ddb13c98daf18740f4097048
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Oct  4 14:38:19 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Thu Oct  4 14:38:19 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ec696fcd

live ebuild update

(Portage version: 2.2.0_alpha135/git/Linux i686, unsigned Manifest commit)

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   16 +++++++---------
 sci-chemistry/gromacs/gromacs-9999.ebuild     |    5 ++---
 3 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 47636de..197705f 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  04 Oct 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-9999.ebuild:
+  live ebuild update
+
   03 Oct 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
   metadata.xml:
   hybrid stuff got merged

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index bbf4161..d95a7cf 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -5,7 +5,6 @@
 EAPI="4"
 
 TEST_PV="4.0.4"
-MANUAL_PV="4.5.4"
 
 #to find external blas/lapack
 CMAKE_MIN_VERSION="2.8.5-r2"
@@ -14,8 +13,7 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
 
 inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
 
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
+SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
 
 if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -24,6 +22,7 @@ if [[ $PV = *9999* ]]; then
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-4-6"
 	inherit git-2
+	PDEPEND="doc? ( ~app-doc/gromacs-manual-${PV} )"
 else
 	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
 fi
@@ -55,8 +54,7 @@ CDEPEND="
 	xml? ( dev-libs/libxml2:2 )"
 DEPEND="${CDEPEND}
 	virtual/pkgconfig"
-RDEPEND="${CDEPEND}
-	app-shells/tcsh"
+RDEPEND="${CDEPEND}"
 
 RESTRICT="test"
 
@@ -120,9 +118,6 @@ src_configure() {
 	use avx128fma && acce="AVX_128_FMA"
 	use avx256 && acce="AVX_256"
 
-	#workaround for now
-	use sse2 && CFLAGS+=" -msse2"
-
 	#to create man pages, build tree binaries are executed (bug #398437)
 	[[ ${CHOST} = *-darwin* ]] && \
 		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
@@ -208,8 +203,11 @@ src_install() {
 	cd "${S}"
 	dodoc AUTHORS INSTALL* README*
 	if use doc; then
-		newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
 		dohtml -r "${ED}usr/share/gromacs/html/"
+		insinto /usr/share/gromacs
+		doins "admin/programs.txt"
+		ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list
+		doins "${T}"/programs.list
 	fi
 	rm -rf "${ED}usr/share/gromacs/html/"
 }

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index d74f3cd..1e7bf0c 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -42,9 +42,8 @@ CDEPEND="
 	xml? ( dev-libs/libxml2:2 )"
 DEPEND="${CDEPEND}
 	virtual/pkgconfig"
-RDEPEND="${CDEPEND}
-	app-shells/tcsh"
-PDEPEND="doc? ( app-doc/gromacs-manual )"
+RDEPEND="${CDEPEND}"
+PDEPEND="doc? ( ~app-doc/gromacs-manual-${PV} )"
 
 RESTRICT="test"
 


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-11-19  0:48 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-11-19  0:48 UTC (permalink / raw
  To: gentoo-commits

commit:     61dfc64a4cf8f53565b3959362ce0966f88a47f3
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 19 00:48:07 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Mon Nov 19 00:48:07 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=61dfc64a

live ebuild update

Package-Manager: portage-2.2.0_alpha142

---
 sci-chemistry/gromacs/ChangeLog               |    3 ++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   34 ++++++++++--------------
 2 files changed, 17 insertions(+), 20 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 197705f..afe6602 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  19 Nov 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  live ebuild update
+
   04 Oct 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
   gromacs-9999.ebuild:
   live ebuild update

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index d95a7cf..1ddd82a 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="4"
+EAPI=5
 
 TEST_PV="4.0.4"
 
@@ -33,10 +33,11 @@ DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
 
 LICENSE="GPL-2"
-SLOT="0"
+#every useflag combination and git commit could be binary different
+SLOT="0/$(date +%s)"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
 IUSE="X blas cuda doc -double-precision +fftw gsl lapack
-mpi openmp +single-precision test +threads xml zsh-completion ${ACCE_IUSE}"
+mpi openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -47,40 +48,32 @@ CDEPEND="
 	blas? ( virtual/blas )
 	cuda? ( dev-util/nvidia-cuda-toolkit )
 	fftw? ( sci-libs/fftw:3.0 )
-	fkernels? ( !threads? ( !altivec? ( !ia64? ( !sse2? ( virtual/fortran ) ) ) ) )
+	fkernels? ( !threads? ( !sse2? ( virtual/fortran ) ) )
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2:2 )"
+	mpi? ( virtual/mpi )"
 DEPEND="${CDEPEND}
 	virtual/pkgconfig"
 RDEPEND="${CDEPEND}"
 
 RESTRICT="test"
 
-REQUIRED_USE="cuda? ( !double-precision )"
+REQUIRED_USE="cuda? ( single-precision )"
 
 pkg_pretend() {
 	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
 	use openmp && ! tc-has-openmp && \
 		die "Please switch to an openmp compatible compiler"
-	if use cuda && [[ $(( $(gcc-major-version) * 10 + $(gcc-minor-version) )) -gt 44 ]] ; then
-		eerror "gcc 4.5 and up are not supported for useflag cuda!"
-		die "gcc 4.5 and up are not supported for useflag cuda!"
-	fi
 }
 
 pkg_setup() {
 	#notes/todos
 	# -on apple: there is framework support
 	# -mkl support
+	# -openmm support
 	# -there are power6 kernels
 	if use fkernels; then
-		if use altivec || use ia64 || use sse2; then
-			ewarn "Gromacs only supports one acceleration method, in your case"
-			ewarn "the fortran kernel will be overwritten by (altivec|ia64|sse2)"
-			ewarn "so it is save to disable fkernels use flag!"
-		elif use threads; then
+		if use threads; then
 			ewarn "Fortran kernels and threads do not work together, disabling"
 			ewarn "fortran kernels"
 		else
@@ -126,11 +119,9 @@ src_configure() {
 		-DGMX_FFT_LIBRARY=$(usex fftw fftw3 fftwpack)
 		$(cmake-utils_use X GMX_X11)
 		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use cuda GMX_GPU)
 		$(cmake-utils_use gsl GMX_GSL)
 		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
 		$(cmake-utils_use openmp GMX_OPENMP)
-		$(cmake-utils_use xml GMX_XML)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_ACCELERATION="$acce"
 		-DGMXLIB="$(get_libdir)"
@@ -146,13 +137,16 @@ src_configure() {
 			[[ ${x} = "double" ]] && suffix="_d"
 		local p
 		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+		local cuda=$(cmake-utils_use cuda GMX_GPU)
+		[[ ${x} = "double" ]] && use cuda && cuda="-DGMX_GPU=OFF"
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-			$(cmake-utils_use threads GMX_THREAD_MPI)
+			$(cmake-utils_use threads GMX_THREAD_MPI) ${cuda}
 			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF -DGMX_MPI=ON
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF
+			-DGMX_MPI=ON ${cuda}
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
 	done


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-11-27  5:43 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-11-27  5:43 UTC (permalink / raw
  To: gentoo-commits

commit:     7b59ade8bd1189a3300d561b64f2d4f945717003
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 27 05:28:09 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Tue Nov 27 05:28:48 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7b59ade8

added openmm support

Package-Manager: portage-2.2.0_alpha142

---
 sci-chemistry/gromacs/ChangeLog               |    4 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   30 ++++++++++++++++++------
 sci-chemistry/gromacs/metadata.xml            |    1 +
 3 files changed, 27 insertions(+), 8 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index afe6602..00923e8 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  27 Nov 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  metadata.xml:
+  added openmm support
+
   19 Nov 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   live ebuild update
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 1ddd82a..9b7b66f 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -33,11 +33,10 @@ DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
 
 LICENSE="GPL-2"
-#every useflag combination and git commit could be binary different
-SLOT="0/$(date +%s)"
+SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
 IUSE="X blas cuda doc -double-precision +fftw gsl lapack
-mpi openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
+mpi openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -51,14 +50,15 @@ CDEPEND="
 	fkernels? ( !threads? ( !sse2? ( virtual/fortran ) ) )
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )"
+	mpi? ( virtual/mpi )
+	openmm? ( sci-libs/openmm[cuda,opencl] )"
 DEPEND="${CDEPEND}
 	virtual/pkgconfig"
 RDEPEND="${CDEPEND}"
 
 RESTRICT="test"
 
-REQUIRED_USE="cuda? ( single-precision )"
+REQUIRED_USE="cuda? ( single-precision ) openmm? ( single-precision cuda )"
 
 pkg_pretend() {
 	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
@@ -70,7 +70,6 @@ pkg_setup() {
 	#notes/todos
 	# -on apple: there is framework support
 	# -mkl support
-	# -openmm support
 	# -there are power6 kernels
 	if use fkernels; then
 		if use threads; then
@@ -143,6 +142,14 @@ src_configure() {
 			$(cmake-utils_use threads GMX_THREAD_MPI) ${cuda}
 			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		if [[ ${x} = float ]] && use openmm; then
+			einfo "Configuring for openmm build"
+			mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
+				-DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON
+				-DGMX_BINARY_SUFFIX="openmm" -DGMX_LIBS_SUFFIX="openmm" )
+			CMAKE_BUILD_DIR="${WORKDIR}/${P}_openmm" \
+				OPENMM_ROOT_DIR="${EPREFIX}/usr" cmake-utils_src_configure
+		fi
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF
@@ -157,6 +164,11 @@ src_compile() {
 		einfo "Compiling for ${x} precision"
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\
 			cmake-utils_src_compile
+		if [[ ${x} = float ]] && use openmm; then
+			einfo "Compiling for openmm build"
+			CMAKE_BUILD_DIR="${WORKDIR}/${P}_openmm"\
+				cmake-utils_src_compile mdrun
+		fi
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
@@ -178,9 +190,11 @@ src_install() {
 	for x in ${GMX_DIRS}; do
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \
 			cmake-utils_src_install
+		if [[ ${x} = float ]] && use openmm; then
+			CMAKE_BUILD_DIR="${WORKDIR}/${P}_openmm" \
+				DESTDIR="${D}" cmake-utils_src_make install-mdrun
+		fi
 		use mpi || continue
-		#cmake-utils_src_install does not support args
-		#using cmake-utils_src_make instead
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
 			DESTDIR="${D}" cmake-utils_src_make install-mdrun
 	done

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index acbcd53..41931c0 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -15,6 +15,7 @@
 		<flag name="sse41">Enable sse4.1 acceleration</flag>
 		<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
 		<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+		<flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
 		<flag name="power6">Enable Power6 optimizations</flag>
 	</use>
 </pkgmetadata>


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-11-30 21:18 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-11-30 21:18 UTC (permalink / raw
  To: gentoo-commits

commit:     83882644554e19ff27159bbf60c8b0304c04724b
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Nov 30 21:00:31 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Fri Nov 30 21:00:31 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=83882644

sync with gx86

Package-Manager: portage-2.2.0_alpha143

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   17 ++++++++++++-----
 2 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 00923e8..2c90bf5 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  30 Nov 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  sync with gx86
+
   27 Nov 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
   metadata.xml:
   added openmm support

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 9b7b66f..f9efa61 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -5,6 +5,7 @@
 EAPI=5
 
 TEST_PV="4.0.4"
+MANUAL_PV="4.6-beta1"
 
 #to find external blas/lapack
 CMAKE_MIN_VERSION="2.8.5-r2"
@@ -24,7 +25,9 @@ if [[ $PV = *9999* ]]; then
 	inherit git-2
 	PDEPEND="doc? ( ~app-doc/gromacs-manual-${PV} )"
 else
-	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
+	S="${WORKDIR}/${P//_/-}"
+	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P//_/-}.tar.gz
+		doc? (  ftp://ftp.gromacs.org/pub/manual/gromacs-manual-${MANUAL_PV}.pdf )"
 fi
 
 ACCE_IUSE="fkernels power6 sse2 sse41 avx128fma avx256"
@@ -212,10 +215,14 @@ src_install() {
 	dodoc AUTHORS INSTALL* README*
 	if use doc; then
 		dohtml -r "${ED}usr/share/gromacs/html/"
-		insinto /usr/share/gromacs
-		doins "admin/programs.txt"
-		ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list
-		doins "${T}"/programs.list
+		if [[ $PV = *9999* ]]; then
+			insinto /usr/share/gromacs
+			doins "admin/programs.txt"
+			ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list
+			doins "${T}"/programs.list
+		else
+			dodoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf"
+		fi
 	fi
 	rm -rf "${ED}usr/share/gromacs/html/"
 }


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-12-08 22:15 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-12-08 22:15 UTC (permalink / raw
  To: gentoo-commits

commit:     07ad60ed3caadb2858e2d1575a14150234d4d2af
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Dec  8 22:12:44 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sat Dec  8 22:12:44 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=07ad60ed

CMAKE_BUILD_DIR -> BUILD_DIR

Package-Manager: portage-2.2.0_alpha145

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |   12 ++++++------
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   18 +++++++++---------
 sci-chemistry/gromacs/gromacs-9999.ebuild     |   12 ++++++------
 4 files changed, 25 insertions(+), 21 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 2c90bf5..11f1bf2 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  08 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-4.6.9999.ebuild, gromacs-9999.ebuild:
+  CMAKE_BUILD_DIR -> BUILD_DIR
+
   30 Nov 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   sync with gx86
 

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index a4a70d3..c1a0dd6 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -157,23 +157,23 @@ src_configure() {
 		[ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
 			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
 	done
 }
 
 src_compile() {
 	for x in ${GMX_DIRS}; do
 		einfo "Compiling for ${x} precision"
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
 			cmake-utils_src_compile
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
 			cmake-utils_src_compile mdrun
 	done
 }
@@ -190,12 +190,12 @@ src_test() {
 
 src_install() {
 	for x in ${GMX_DIRS}; do
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \
+		BUILD_DIR="${WORKDIR}/${P}_${x}" \
 			cmake-utils_src_install
 		use mpi || continue
 		#cmake-utils_src_install does not support args
 		#using cmake-utils_src_compile instead
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
 			cmake-utils_src_make install-mdrun DESTDIR="${D}"
 	done
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index f9efa61..5c84f85 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -144,13 +144,13 @@ src_configure() {
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
 			$(cmake-utils_use threads GMX_THREAD_MPI) ${cuda}
 			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
 		if [[ ${x} = float ]] && use openmm; then
 			einfo "Configuring for openmm build"
 			mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
 				-DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON
 				-DGMX_BINARY_SUFFIX="openmm" -DGMX_LIBS_SUFFIX="openmm" )
-			CMAKE_BUILD_DIR="${WORKDIR}/${P}_openmm" \
+			BUILD_DIR="${WORKDIR}/${P}_openmm" \
 				OPENMM_ROOT_DIR="${EPREFIX}/usr" cmake-utils_src_configure
 		fi
 		use mpi || continue
@@ -158,23 +158,23 @@ src_configure() {
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF
 			-DGMX_MPI=ON ${cuda}
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
 	done
 }
 
 src_compile() {
 	for x in ${GMX_DIRS}; do
 		einfo "Compiling for ${x} precision"
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
 			cmake-utils_src_compile
 		if [[ ${x} = float ]] && use openmm; then
 			einfo "Compiling for openmm build"
-			CMAKE_BUILD_DIR="${WORKDIR}/${P}_openmm"\
+			BUILD_DIR="${WORKDIR}/${P}_openmm"\
 				cmake-utils_src_compile mdrun
 		fi
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
 			cmake-utils_src_compile mdrun
 	done
 }
@@ -191,14 +191,14 @@ src_test() {
 
 src_install() {
 	for x in ${GMX_DIRS}; do
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \
+		BUILD_DIR="${WORKDIR}/${P}_${x}" \
 			cmake-utils_src_install
 		if [[ ${x} = float ]] && use openmm; then
-			CMAKE_BUILD_DIR="${WORKDIR}/${P}_openmm" \
+			BUILD_DIR="${WORKDIR}/${P}_openmm" \
 				DESTDIR="${D}" cmake-utils_src_make install-mdrun
 		fi
 		use mpi || continue
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
 			DESTDIR="${D}" cmake-utils_src_make install-mdrun
 	done
 

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 1e7bf0c..55770d0 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -153,23 +153,23 @@ src_configure() {
 		[ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
 			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
 	done
 }
 
 src_compile() {
 	for x in ${GMX_DIRS}; do
 		einfo "Compiling for ${x} precision"
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
 			cmake-utils_src_compile
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
 			cmake-utils_src_compile mdrun
 	done
 }
@@ -186,12 +186,12 @@ src_test() {
 
 src_install() {
 	for x in ${GMX_DIRS}; do
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \
+		BUILD_DIR="${WORKDIR}/${P}_${x}" \
 			cmake-utils_src_install
 		use mpi || continue
 		#cmake-utils_src_install does not support args
 		#using cmake-utils_src_compile instead
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
 			cmake-utils_src_make install-mdrun DESTDIR="${D}"
 	done
 


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-12-20  5:51 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-12-20  5:51 UTC (permalink / raw
  To: gentoo-commits

commit:     044ce28d3720d08f0c74848aebafc30575aa79fc
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 20 05:50:09 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Thu Dec 20 05:51:38 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=044ce28d

fortran is gone

Package-Manager: portage-2.2.0_alpha149

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   19 +++----------------
 2 files changed, 6 insertions(+), 16 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 11f1bf2..2f10b59 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  20 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  fortran is gone
+
   08 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
   gromacs-4.6.9999.ebuild, gromacs-9999.ebuild:
   CMAKE_BUILD_DIR -> BUILD_DIR

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 5c84f85..69a3d46 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -12,7 +12,7 @@ CMAKE_MIN_VERSION="2.8.5-r2"
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
+inherit bash-completion-r1 cmake-utils eutils multilib toolchain-funcs
 
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
 
@@ -30,7 +30,7 @@ else
 		doc? (  ftp://ftp.gromacs.org/pub/manual/gromacs-manual-${MANUAL_PV}.pdf )"
 fi
 
-ACCE_IUSE="fkernels power6 sse2 sse41 avx128fma avx256"
+ACCE_IUSE="sse2 sse41 avx128fma avx256"
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -50,7 +50,6 @@ CDEPEND="
 	blas? ( virtual/blas )
 	cuda? ( dev-util/nvidia-cuda-toolkit )
 	fftw? ( sci-libs/fftw:3.0 )
-	fkernels? ( !threads? ( !sse2? ( virtual/fortran ) ) )
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
 	mpi? ( virtual/mpi )
@@ -69,22 +68,11 @@ pkg_pretend() {
 		die "Please switch to an openmp compatible compiler"
 }
 
-pkg_setup() {
+src_prepare() {
 	#notes/todos
 	# -on apple: there is framework support
 	# -mkl support
-	# -there are power6 kernels
-	if use fkernels; then
-		if use threads; then
-			ewarn "Fortran kernels and threads do not work together, disabling"
-			ewarn "fortran kernels"
-		else
-			fortran-2_pkg_setup
-		fi
-	fi
-}
 
-src_prepare() {
 	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
 	epatch_user
 
@@ -106,7 +94,6 @@ src_configure() {
 
 	#go from slowest to fastest acceleration
 	local acce="None"
-	use fkernels && use !threads && acce="Fortran"
 	use power6 && acce="Power6"
 	use sse2 && acce="SSE2"
 	use sse41 && acce="SSE4.1"


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-12-22 19:46 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-12-22 19:46 UTC (permalink / raw
  To: gentoo-commits

commit:     085cbb1fbc4d10a7005d7bfee2617b7cd117dec1
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Dec 22 19:44:16 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sat Dec 22 19:44:16 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=085cbb1f

sync with gx86

Package-Manager: portage-2.2.0_alpha149

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   19 ++++++++++---------
 sci-chemistry/gromacs/gromacs-9999.ebuild     |   18 ++----------------
 sci-chemistry/gromacs/metadata.xml            |    2 +-
 4 files changed, 17 insertions(+), 26 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 2f10b59..92c7232 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  22 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-9999.ebuild, metadata.xml:
+  sync with gx86
+
   20 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   fortran is gone
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 69a3d46..a41494e 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -23,11 +23,11 @@ if [[ $PV = *9999* ]]; then
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-4-6"
 	inherit git-2
-	PDEPEND="doc? ( ~app-doc/gromacs-manual-${PV} )"
+	PDEPEND="doc? ( ~app-doc/${PN}-manual-${PV} )"
 else
 	S="${WORKDIR}/${P//_/-}"
 	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P//_/-}.tar.gz
-		doc? (  ftp://ftp.gromacs.org/pub/manual/gromacs-manual-${MANUAL_PV}.pdf )"
+		doc? (  ftp://ftp.gromacs.org/pub/manual/${PN}-manual-${MANUAL_PV}.pdf )"
 fi
 
 ACCE_IUSE="sse2 sse41 avx128fma avx256"
@@ -38,8 +38,7 @@ HOMEPAGE="http://www.gromacs.org/"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE="X blas cuda doc -double-precision +fftw gsl lapack
-mpi openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
+IUSE="X blas cuda doc -double-precision +fftw gsl lapack mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -94,7 +93,6 @@ src_configure() {
 
 	#go from slowest to fastest acceleration
 	local acce="None"
-	use power6 && acce="Power6"
 	use sse2 && acce="SSE2"
 	use sse41 && acce="SSE4.1"
 	use avx128fma && acce="AVX_128_FMA"
@@ -111,6 +109,7 @@ src_configure() {
 		$(cmake-utils_use gsl GMX_GSL)
 		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
 		$(cmake-utils_use openmp GMX_OPENMP)
+		$(cmake-utils_use !offensive GMX_NO_QUOTES)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_ACCELERATION="$acce"
 		-DGMXLIB="$(get_libdir)"
@@ -208,7 +207,7 @@ src_install() {
 			ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list
 			doins "${T}"/programs.list
 		else
-			dodoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf"
+			dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
 		fi
 	fi
 	rm -rf "${ED}usr/share/gromacs/html/"
@@ -219,9 +218,11 @@ pkg_postinst() {
 	einfo  "Please read and cite:"
 	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
 	einfo  "http://dx.doi.org/10.1021/ct700301q"
-	einfo
-	einfo  $(g_luck)
-	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
+	if use offensive; then
+		einfo
+		einfo  $(g_luck)
+		einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
+	fi
 	einfo
 	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
 }

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 55770d0..56187b0 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -9,12 +9,12 @@ TEST_PV="4.0.4"
 EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git"
 EGIT_BRANCH="master"
 
-ACCE_IUSE="fkernels power6 sse2 sse41 avx128fma avx256"
+ACCE_IUSE="sse2 sse41 avx128fma avx256"
 
 #to find external blas/lapack
 CMAKE_MIN_VERSION="2.8.5-r2"
 
-inherit bash-completion-r1 cmake-utils eutils fortran-2 git-2 multilib toolchain-funcs
+inherit bash-completion-r1 cmake-utils eutils git-2 multilib toolchain-funcs
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -25,7 +25,6 @@ SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
 IUSE="X blas doc -double-precision +fftw gsl lapack mpi +single-precision  test
 +threads xml zsh-completion ${ACCE_IUSE}"
-REQUIRED_USE="fkernels? ( !threads )"
 
 CDEPEND="
 	X? (
@@ -35,7 +34,6 @@ CDEPEND="
 		)
 	blas? ( virtual/blas )
 	fftw? ( sci-libs/fftw:3.0 )
-	fkernels? ( virtual/fortran )
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
 	mpi? ( virtual/mpi )
@@ -47,10 +45,6 @@ PDEPEND="doc? ( ~app-doc/gromacs-manual-${PV} )"
 
 RESTRICT="test"
 
-pkg_setup() {
-	use fkernels && fortran-2_pkg_setup
-}
-
 src_prepare() {
 	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
 	epatch_user
@@ -95,12 +89,6 @@ src_configure() {
 
 	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
 
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-	fi
-
 	if use double-precision ; then
 		#from gromacs manual
 		elog
@@ -124,8 +112,6 @@ src_configure() {
 
 	#go from slowest to fasterest acceleration
 	local acce="None"
-	use fkernels && use !threads && acce="Fortran"
-	use power6 && acce="Power6"
 	use sse2 && acce="SSE2"
 	use sse41 && acce="SSE4.1"
 	use avx128fma && acce="AVX_128_FMA"

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 41931c0..24ddf42 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -15,7 +15,7 @@
 		<flag name="sse41">Enable sse4.1 acceleration</flag>
 		<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
 		<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+		<flag name="offensive">Enable gromacs partly offensive quotes</flag>
 		<flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
-		<flag name="power6">Enable Power6 optimizations</flag>
 	</use>
 </pkgmetadata>


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-12-26  1:03 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-12-26  1:03 UTC (permalink / raw
  To: gentoo-commits

commit:     2b020ade5d2325a779e2d7662c5052122949d59b
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Dec 26 01:03:05 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Wed Dec 26 01:03:05 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2b020ade

Added mkl support

Package-Manager: portage-2.2.0_alpha149

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   24 +++++++++++++++++++-----
 sci-chemistry/gromacs/metadata.xml            |    1 +
 3 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 92c7232..c9d44fb 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  metadata.xml:
+  Added mkl support
+
   22 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
   gromacs-9999.ebuild, metadata.xml:
   sync with gx86

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index a41494e..cb9c0d4 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -38,7 +38,7 @@ HOMEPAGE="http://www.gromacs.org/"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE="X blas cuda doc -double-precision +fftw gsl lapack mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
+IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -51,6 +51,7 @@ CDEPEND="
 	fftw? ( sci-libs/fftw:3.0 )
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
+	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
 	openmm? ( sci-libs/openmm[cuda,opencl] )"
 DEPEND="${CDEPEND}
@@ -59,7 +60,10 @@ RDEPEND="${CDEPEND}"
 
 RESTRICT="test"
 
-REQUIRED_USE="cuda? ( single-precision ) openmm? ( single-precision cuda )"
+REQUIRED_USE="
+	cuda? ( single-precision )
+	openmm? ( single-precision )
+	mkl ( !blas !fftw !lapack )"
 
 pkg_pretend() {
 	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
@@ -70,7 +74,6 @@ pkg_pretend() {
 src_prepare() {
 	#notes/todos
 	# -on apple: there is framework support
-	# -mkl support
 
 	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
 	epatch_user
@@ -89,7 +92,7 @@ src_prepare() {
 }
 
 src_configure() {
-	local mycmakeargs_pre=( ) extra
+	local mycmakeargs_pre=( ) extra fft_opts=( )
 
 	#go from slowest to fastest acceleration
 	local acce="None"
@@ -102,8 +105,19 @@ src_configure() {
 	[[ ${CHOST} = *-darwin* ]] && \
 		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
 
+	if use fftw; then
+		fft_opts=( -DGMX_FFT_LIBRARY=ffw3 )
+	elif use mkl; then
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
+			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
+		)
+	else
+		fft_opts=( -DGMX_FFT_LIBRARY=fftwpack )
+	fi
+
 	mycmakeargs_pre+=(
-		-DGMX_FFT_LIBRARY=$(usex fftw fftw3 fftwpack)
+		"${fft_opts[@]}"
 		$(cmake-utils_use X GMX_X11)
 		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
 		$(cmake-utils_use gsl GMX_GSL)

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 24ddf42..1360fcb 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -17,5 +17,6 @@
 		<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
 		<flag name="offensive">Enable gromacs partly offensive quotes</flag>
 		<flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
+		<flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
 	</use>
 </pkgmetadata>


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-12-26  3:59 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-12-26  3:59 UTC (permalink / raw
  To: gentoo-commits

commit:     32899af849c88173cf81ef71d944ade72614f98a
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Dec 26 03:59:30 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Wed Dec 26 03:59:30 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=32899af8

fixed typo

Package-Manager: portage-2.2.0_alpha149

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    2 +-
 2 files changed, 4 insertions(+), 1 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index c9d44fb..e00cde9 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  fixed typo
+
   26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
   metadata.xml:
   Added mkl support

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index cb9c0d4..d253a1f 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -63,7 +63,7 @@ RESTRICT="test"
 REQUIRED_USE="
 	cuda? ( single-precision )
 	openmm? ( single-precision )
-	mkl ( !blas !fftw !lapack )"
+	mkl? ( !blas !fftw !lapack )"
 
 pkg_pretend() {
 	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-12-26 18:58 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-12-26 18:58 UTC (permalink / raw
  To: gentoo-commits

commit:     b8442ec858321bce2a64b476bb738e21865f1ffc
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Dec 26 18:58:46 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Wed Dec 26 18:58:46 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b8442ec8

fixed another typo

Package-Manager: portage-2.2.0_alpha149

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    4 ++--
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index e00cde9..7deeeef 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  fixed another typo
+
+  26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   fixed typo
 
   26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index d253a1f..362cb74 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -106,14 +106,14 @@ src_configure() {
 		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
 
 	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=ffw3 )
+		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
 	elif use mkl; then
 		fft_opts=( -DGMX_FFT_LIBRARY=mkl
 			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
 			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
 		)
 	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftwpack )
+		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
 	fi
 
 	mycmakeargs_pre+=(


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-12-26 22:36 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-12-26 22:36 UTC (permalink / raw
  To: gentoo-commits

commit:     847251fe1fa1e5e2ba7787320db860f5151262a6
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Dec 26 22:31:52 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Wed Dec 26 22:31:52 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=847251fe

fixed openmm suffix

Package-Manager: portage-2.2.0_alpha149

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    9 ++++++---
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 7deeeef..d371744 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  fixed openmm suffix
+
+  26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   fixed another typo
 
   26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 362cb74..4f7972b 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -53,7 +53,10 @@ CDEPEND="
 	lapack? ( virtual/lapack )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
-	openmm? ( sci-libs/openmm[cuda,opencl] )"
+	openmm? (
+		dev-util/nvidia-cuda-toolkit
+		sci-libs/openmm[cuda,opencl]
+	)"
 DEPEND="${CDEPEND}
 	virtual/pkgconfig"
 RDEPEND="${CDEPEND}"
@@ -127,7 +130,7 @@ src_configure() {
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_ACCELERATION="$acce"
 		-DGMXLIB="$(get_libdir)"
-	    -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
 		${extra}
 	)
 
@@ -149,7 +152,7 @@ src_configure() {
 			einfo "Configuring for openmm build"
 			mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
 				-DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON
-				-DGMX_BINARY_SUFFIX="openmm" -DGMX_LIBS_SUFFIX="openmm" )
+				-DGMX_BINARY_SUFFIX="_openmm" -DGMX_LIBS_SUFFIX="_openmm" )
 			BUILD_DIR="${WORKDIR}/${P}_openmm" \
 				OPENMM_ROOT_DIR="${EPREFIX}/usr" cmake-utils_src_configure
 		fi


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-12-27 21:44 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-12-27 21:44 UTC (permalink / raw
  To: gentoo-commits

commit:     7ea177472c26c6f91cb3f02720546c995623abd2
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 27 21:37:24 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Thu Dec 27 21:42:06 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7ea17747

sci-chemistry/gromacs: clean up

Package-Manager: portage-2.2.0_alpha149

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    7 +------
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index d371744..c2c3f21 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  27 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  sci-chemistry/gromacs: clean up
+
   26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   fixed openmm suffix
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 4f7972b..8e13d99 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -7,9 +7,6 @@ EAPI=5
 TEST_PV="4.0.4"
 MANUAL_PV="4.6-beta1"
 
-#to find external blas/lapack
-CMAKE_MIN_VERSION="2.8.5-r2"
-
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
 inherit bash-completion-r1 cmake-utils eutils multilib toolchain-funcs
@@ -64,6 +61,7 @@ RDEPEND="${CDEPEND}"
 RESTRICT="test"
 
 REQUIRED_USE="
+	|| ( single-precision double-precision )
 	cuda? ( single-precision )
 	openmm? ( single-precision )
 	mkl? ( !blas !fftw !lapack )"
@@ -84,9 +82,6 @@ src_prepare() {
 	GMX_DIRS=""
 	use single-precision && GMX_DIRS+=" float"
 	use double-precision && GMX_DIRS+=" double"
-	#if neither single-precision nor double-precision is enabled
-	#build at least default (single)
-	[[ -z $GMX_DIRS ]] && GMX_DIRS+=" float"
 
 	for x in ${GMX_DIRS}; do
 		mkdir -p "${WORKDIR}/${P}_${x}" || die


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-12-29 22:59 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-12-29 22:59 UTC (permalink / raw
  To: gentoo-commits

commit:     bccb1a9f8ddaa2dc32b48578280c0b10cc6a50ef
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Dec 29 22:54:14 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sat Dec 29 22:54:14 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bccb1a9f

fixed build with newer mkl

Package-Manager: portage-2.2.0_alpha149

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    8 +++++++-
 2 files changed, 10 insertions(+), 1 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index c2c3f21..2c7bfe2 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  29 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  fixed build with newer mkl
+
   27 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   sci-chemistry/gromacs: clean up
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 8e13d99..94dbbdd 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -105,11 +105,17 @@ src_configure() {
 
 	if use fftw; then
 		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl; then
+	elif use mkl && has_version "=sci-libs/mkl-10*"; then
 		fft_opts=( -DGMX_FFT_LIBRARY=mkl
 			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
 			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
 		)
+	elif use mkl; then
+		local bits=$(get_libdir)
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
+			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
+		)
 	else
 		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
 	fi


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2012-12-30 23:31 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2012-12-30 23:31 UTC (permalink / raw
  To: gentoo-commits

commit:     2841e25198ebdfa8a42a57d5de0f5289f9858a6f
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 30 23:29:53 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sun Dec 30 23:29:53 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2841e251

further clean up

Package-Manager: portage-2.2.0_alpha149

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    6 +++++-
 2 files changed, 8 insertions(+), 1 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 2c7bfe2..b932769 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  30 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  further clean up
+
   29 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   fixed build with newer mkl
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 94dbbdd..0b76b2f 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -32,7 +32,10 @@ ACCE_IUSE="sse2 sse41 avx128fma avx256"
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
 
-LICENSE="GPL-2"
+# see COPYING for details
+# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
 IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
@@ -132,6 +135,7 @@ src_configure() {
 		-DGMX_ACCELERATION="$acce"
 		-DGMXLIB="$(get_libdir)"
 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+		-DGMX_PREFIX_LIBMD=ON
 		${extra}
 	)
 


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-01-18  1:56 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2013-01-18  1:56 UTC (permalink / raw
  To: gentoo-commits

commit:     275925ee46146da754f89fbaace7fed19e769dde
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 18 01:55:36 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Jan 18 01:55:36 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=275925ee

live ebuild update

Package-Manager: portage-2.2.0_alpha154

---
 sci-chemistry/gromacs/ChangeLog               |    5 ++++-
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   13 +++++++++----
 2 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index b932769..6bc9948 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-chemistry/gromacs
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  18 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  live ebuild update
+
   30 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   further clean up
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 0b76b2f..4f26fd7 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -11,7 +11,7 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
 
 inherit bash-completion-r1 cmake-utils eutils multilib toolchain-funcs
 
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
+SRC_URI="test? ( http://${PN}.googlecode.com/files/regressiontests-master.tar.gz )"
 
 if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -88,8 +88,12 @@ src_prepare() {
 
 	for x in ${GMX_DIRS}; do
 		mkdir -p "${WORKDIR}/${P}_${x}" || die
-		use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
+		use test && cp -r "${WORKDIR}"/regressiontests-master "${WORKDIR}/${P}_${x}"
 	done
+
+	if use openmm; then
+		sed -i '/option.*GMX_OPENMM/s/^#//' src/contrib/CMakeLists.txt || die
+	fi
 }
 
 src_configure() {
@@ -130,7 +134,8 @@ src_configure() {
 		$(cmake-utils_use gsl GMX_GSL)
 		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
 		$(cmake-utils_use openmp GMX_OPENMP)
-		$(cmake-utils_use !offensive GMX_NO_QUOTES)
+		$(cmake-utils_use offensive GMX_COOL_QUOTES)
+		$(cmake-utils_use test BUILD_TESTING)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_ACCELERATION="$acce"
 		-DGMXLIB="$(get_libdir)"


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-01-18  2:58 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2013-01-18  2:58 UTC (permalink / raw
  To: gentoo-commits

commit:     58d3a3191fb7dab848d3f918778e2d58ee35250a
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 18 02:55:02 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Jan 18 02:55:02 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=58d3a319

yet another update for git

Package-Manager: portage-2.2.0_alpha154

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    4 ++--
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 6bc9948..cddca22 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   18 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  yet another update for git
+
+  18 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   live ebuild update
 
   30 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 4f26fd7..0e2a966 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -155,7 +155,7 @@ src_configure() {
 		local cuda=$(cmake-utils_use cuda GMX_GPU)
 		[[ ${x} = "double" ]] && use cuda && cuda="-DGMX_GPU=OFF"
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-			$(cmake-utils_use threads GMX_THREAD_MPI) ${cuda}
+			$(cmake-utils_use threads GMX_THREAD_MPI) ${cuda} -DGMX_OPENMM=OFF
 			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
 		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
 		if [[ ${x} = float ]] && use openmm; then
@@ -169,7 +169,7 @@ src_configure() {
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
+			-DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
 	done


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-01-21 14:00 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2013-01-21 14:00 UTC (permalink / raw
  To: gentoo-commits

commit:     e7ea430748b4b880d1150d1b2ba34f0a5338e4e1
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 21 14:00:01 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Mon Jan 21 14:00:01 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e7ea4307

[sci-chemistry/gromacs] Update 4.6 series ebuild

Package-Manager: portage-2.2.0_alpha158

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    6 +++---
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index cddca22..0481b25 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  21 Jan 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild:
+  [sci-chemistry/gromacs] Update 4.6 series ebuild
+
   18 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   yet another update for git
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 0e2a966..c7233cc 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -4,14 +4,14 @@
 
 EAPI=5
 
-TEST_PV="4.0.4"
-MANUAL_PV="4.6-beta1"
+TEST_PV="4.6"
+MANUAL_PV="4.6"
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
 inherit bash-completion-r1 cmake-utils eutils multilib toolchain-funcs
 
-SRC_URI="test? ( http://${PN}.googlecode.com/files/regressiontests-master.tar.gz )"
+SRC_URI="test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
 
 if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-01-21 14:33 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2013-01-21 14:33 UTC (permalink / raw
  To: gentoo-commits

commit:     23a00910c20889b890e1aa08b172dabd98053c90
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 21 14:31:42 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Mon Jan 21 14:31:42 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=23a00910

[sci-chemistry/gromacs] Drop restrict test for 4.6

Package-Manager: portage-2.2.0_alpha158

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    2 --
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 0481b25..9b0b7e4 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   21 Jan 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild:
+  [sci-chemistry/gromacs] Drop restrict test for 4.6
+
+  21 Jan 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild:
   [sci-chemistry/gromacs] Update 4.6 series ebuild
 
   18 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index c7233cc..60d3f85 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -61,8 +61,6 @@ DEPEND="${CDEPEND}
 	virtual/pkgconfig"
 RDEPEND="${CDEPEND}"
 
-RESTRICT="test"
-
 REQUIRED_USE="
 	|| ( single-precision double-precision )
 	cuda? ( single-precision )


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-01-21 19:19 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2013-01-21 19:19 UTC (permalink / raw
  To: gentoo-commits

commit:     9fb6a24873dd383c200a69cdf539828c3d4c853b
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 21 19:19:06 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jan 21 19:19:06 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9fb6a248

fixed sci-chemistry/gromacs[test]

Package-Manager: portage-2.2.0_alpha158

---
 sci-chemistry/gromacs/ChangeLog               |    3 ++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   46 ++++++++++++++++---------
 2 files changed, 33 insertions(+), 16 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 9b0b7e4..a4af5c4 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  21 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  fixed sci-chemistry/gromacs[test]
+
   21 Jan 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild:
   [sci-chemistry/gromacs] Drop restrict test for 4.6
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 60d3f85..9f12410 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -11,8 +11,6 @@ CMAKE_MAKEFILE_GENERATOR="ninja"
 
 inherit bash-completion-r1 cmake-utils eutils multilib toolchain-funcs
 
-SRC_URI="test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
-
 if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
 		https://gerrit.gromacs.org/gromacs.git
@@ -22,9 +20,9 @@ if [[ $PV = *9999* ]]; then
 	inherit git-2
 	PDEPEND="doc? ( ~app-doc/${PN}-manual-${PV} )"
 else
-	S="${WORKDIR}/${P//_/-}"
-	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P//_/-}.tar.gz
-		doc? (  ftp://ftp.gromacs.org/pub/manual/${PN}-manual-${MANUAL_PV}.pdf )"
+	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
+		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
 fi
 
 ACCE_IUSE="sse2 sse41 avx128fma avx256"
@@ -65,7 +63,8 @@ REQUIRED_USE="
 	|| ( single-precision double-precision )
 	cuda? ( single-precision )
 	openmm? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
+	mkl? ( !blas !fftw !lapack )
+	!openmm" #broken, but https://gerrit.gromacs.org/#/c/2087/
 
 pkg_pretend() {
 	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
@@ -73,6 +72,20 @@ pkg_pretend() {
 		die "Please switch to an openmp compatible compiler"
 }
 
+src_unpack() {
+	if [[ ${PV} != *9999 ]]; then
+		default
+	else
+		git-2_src_unpack
+		if use test; then
+			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
+			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
+				git-2_src_unpack
+		fi
+	fi
+}
+
 src_prepare() {
 	#notes/todos
 	# -on apple: there is framework support
@@ -84,10 +97,12 @@ src_prepare() {
 	use single-precision && GMX_DIRS+=" float"
 	use double-precision && GMX_DIRS+=" double"
 
-	for x in ${GMX_DIRS}; do
-		mkdir -p "${WORKDIR}/${P}_${x}" || die
-		use test && cp -r "${WORKDIR}"/regressiontests-master "${WORKDIR}/${P}_${x}"
-	done
+	if use test; then
+		for x in ${GMX_DIRS}; do
+			mkdir -p "${WORKDIR}/${P}_${x}" || die
+			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
+		done
+	fi
 
 	if use openmm; then
 		sed -i '/option.*GMX_OPENMM/s/^#//' src/contrib/CMakeLists.txt || die
@@ -133,12 +148,13 @@ src_configure() {
 		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
 		$(cmake-utils_use openmp GMX_OPENMP)
 		$(cmake-utils_use offensive GMX_COOL_QUOTES)
-		$(cmake-utils_use test BUILD_TESTING)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_ACCELERATION="$acce"
 		-DGMXLIB="$(get_libdir)"
 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
 		-DGMX_PREFIX_LIBMD=ON
+		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
+		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
 		${extra}
 	)
 
@@ -154,6 +170,7 @@ src_configure() {
 		[[ ${x} = "double" ]] && use cuda && cuda="-DGMX_GPU=OFF"
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
 			$(cmake-utils_use threads GMX_THREAD_MPI) ${cuda} -DGMX_OPENMM=OFF
+			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
 			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
 		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
 		if [[ ${x} = float ]] && use openmm; then
@@ -192,11 +209,8 @@ src_compile() {
 
 src_test() {
 	for x in ${GMX_DIRS}; do
-		local oldpath="${PATH}"
-		export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
-		cd "${WORKDIR}/${P}_${x}"
-		emake -j1 tests || die "${x} Precision test failed"
-		export PATH="${oldpath}"
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_make check
 	done
 }
 


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-01-21 20:30 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2013-01-21 20:30 UTC (permalink / raw
  To: gentoo-commits

commit:     3dd370c0dde951870d1cca039320e87452c1d8a8
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 21 20:29:42 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jan 21 20:29:42 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3dd370c0

sci-chemistry/gromacs: use cuda.eclass

Package-Manager: portage-2.2.0_alpha158

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    8 +++++---
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index a4af5c4..e8db884 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   21 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  sci-chemistry/gromacs: use cuda.eclass
+
+  21 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   fixed sci-chemistry/gromacs[test]
 
   21 Jan 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild:

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 9f12410..eae143b 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -9,7 +9,7 @@ MANUAL_PV="4.6"
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-inherit bash-completion-r1 cmake-utils eutils multilib toolchain-funcs
+inherit bash-completion-r1 cmake-utils cuda eutils multilib toolchain-funcs
 
 if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -45,14 +45,14 @@ CDEPEND="
 		x11-libs/libICE
 		)
 	blas? ( virtual/blas )
-	cuda? ( dev-util/nvidia-cuda-toolkit )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
 	fftw? ( sci-libs/fftw:3.0 )
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
 	openmm? (
-		dev-util/nvidia-cuda-toolkit
+		>=dev-util/nvidia-cuda-toolkit-4.2.9-r1
 		sci-libs/openmm[cuda,opencl]
 	)"
 DEPEND="${CDEPEND}
@@ -93,6 +93,8 @@ src_prepare() {
 	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
 	epatch_user
 
+	use cuda && cuda_src_prepare
+
 	GMX_DIRS=""
 	use single-precision && GMX_DIRS+=" float"
 	use double-precision && GMX_DIRS+=" double"


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-01-28  4:48 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2013-01-28  4:48 UTC (permalink / raw
  To: gentoo-commits

commit:     b40f4c4be3de95f231af23b9391be21788d02338
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 28 04:46:34 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jan 28 04:46:34 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b40f4c4b

added app-doc/gromacs-manual in here

Package-Manager: portage-2.2.0_alpha161

---
 sci-chemistry/gromacs/ChangeLog               |    3 ++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   40 ++++++++++++++++++------
 2 files changed, 33 insertions(+), 10 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index e8db884..4b96245 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  28 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  added app-doc/gromacs-manual in here
+
   21 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   sci-chemistry/gromacs: use cuda.eclass
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index eae143b..e808073 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -18,7 +18,6 @@ if [[ $PV = *9999* ]]; then
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-4-6"
 	inherit git-2
-	PDEPEND="doc? ( ~app-doc/${PN}-manual-${PV} )"
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
 		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
@@ -54,9 +53,15 @@ CDEPEND="
 	openmm? (
 		>=dev-util/nvidia-cuda-toolkit-4.2.9-r1
 		sci-libs/openmm[cuda,opencl]
-	)"
+	)
+	!app-doc/gromac-manual"
 DEPEND="${CDEPEND}
-	virtual/pkgconfig"
+	virtual/pkgconfig
+	doc? (
+		dev-texlive/texlive-latex
+		media-gfx/imagemagick
+		sys-apps/coreutils
+	)"
 RDEPEND="${CDEPEND}"
 
 REQUIRED_USE="
@@ -77,6 +82,12 @@ src_unpack() {
 		default
 	else
 		git-2_src_unpack
+		if use doc; then
+			EGIT_REPO_URI="git://git.gromacs.org/manual.git" \
+			EGIT_BRANCH="release-4-6" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \
+			EGIT_SOURCEDIR="${WORKDIR}/manual"\
+				git-2_src_unpack
+		fi
 		if use test; then
 			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
 			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
@@ -229,8 +240,6 @@ src_install() {
 			DESTDIR="${D}" cmake-utils_src_make install-mdrun
 	done
 
-	rm -f "${ED}"/usr/bin/GMXRC*
-
 	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
 	if use zsh-completion ; then
 		insinto /usr/share/zsh/site-functions
@@ -243,15 +252,26 @@ src_install() {
 	if use doc; then
 		dohtml -r "${ED}usr/share/gromacs/html/"
 		if [[ $PV = *9999* ]]; then
-			insinto /usr/share/gromacs
-			doins "admin/programs.txt"
-			ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list
-			doins "${T}"/programs.list
+			local progs
+			for x in "${ED}"/usr/bin/*; do
+				[[ $x = *_d ]] || progs+=" ${x##*/}"
+			done
+			sed -e "/^PROGRAMS=/s/=.*/='${progs## }'/" \
+				-e "/INSTALLED_OPTIONS_PROGRAM_NAME=/s:=.*:=${ED}/usr/bin/g_options:" \
+				-i "${WORKDIR}"/manual/mkman || die
+			mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )
+			BUILD_DIR="${WORKDIR}"/manual_build \
+				CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure
+			BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make
+			newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf"
 		else
 			dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
 		fi
 	fi
-	rm -rf "${ED}usr/share/gromacs/html/"
+	rm -rf "${ED}"/usr/share/gromacs/html/
+
+	rm -f "${ED}"/usr/bin/g_options*
+	rm -f "${ED}"/usr/bin/GMXRC*
 }
 
 pkg_postinst() {


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-01-30  3:29 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2013-01-30  3:29 UTC (permalink / raw
  To: gentoo-commits

commit:     f9733fe9af82bbed4e411475f14205f94e19727f
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 30 03:16:02 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Jan 30 03:16:02 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f9733fe9

added subslot, removed gromacs-manual blocker

Package-Manager: portage-2.2.0_alpha161

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    5 ++---
 sci-chemistry/gromacs/gromacs-9999.ebuild     |    7 +++----
 3 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index a991e3c..af4912d 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  30 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-9999.ebuild:
+  added subslot, removed gromacs-manual blocker
+
   30 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   clean up
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index c4e0088..5a4f573 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -33,7 +33,7 @@ HOMEPAGE="http://www.gromacs.org/"
 # http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0"
+SLOT="0/${PV}"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
 IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
 
@@ -53,8 +53,7 @@ CDEPEND="
 	openmm? (
 		>=dev-util/nvidia-cuda-toolkit-4.2.9-r1
 		sci-libs/openmm[cuda,opencl]
-	)
-	!app-doc/gromac-manual"
+	)"
 DEPEND="${CDEPEND}
 	virtual/pkgconfig
 	doc? (

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 56187b0..fdfa015 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="4"
+EAPI="5"
 
 TEST_PV="4.0.4"
 
@@ -21,7 +21,7 @@ HOMEPAGE="http://www.gromacs.org/"
 SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
 
 LICENSE="GPL-2"
-SLOT="0"
+SLOT="0/${PV}"
 KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
 IUSE="X blas doc -double-precision +fftw gsl lapack mpi +single-precision  test
 +threads xml zsh-completion ${ACCE_IUSE}"
@@ -41,7 +41,6 @@ CDEPEND="
 DEPEND="${CDEPEND}
 	virtual/pkgconfig"
 RDEPEND="${CDEPEND}"
-PDEPEND="doc? ( ~app-doc/gromacs-manual-${PV} )"
 
 RESTRICT="test"
 


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-01-30  3:29 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2013-01-30  3:29 UTC (permalink / raw
  To: gentoo-commits

commit:     e799b7383f93488ca50c10d8f12f1a13ad913f7a
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 30 02:52:30 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Jan 30 02:52:30 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e799b738

clean up

Package-Manager: portage-2.2.0_alpha161

---
 sci-chemistry/gromacs/ChangeLog               |    3 ++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   43 +++++++++---------------
 2 files changed, 19 insertions(+), 27 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 4b96245..a991e3c 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  30 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  clean up
+
   28 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   added app-doc/gromacs-manual in here
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index e808073..c4e0088 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -71,6 +71,9 @@ REQUIRED_USE="
 	mkl? ( !blas !fftw !lapack )
 	!openmm" #broken, but https://gerrit.gromacs.org/#/c/2087/
 
+DOCS=( AUTHORS INSTALL.cmake README )
+HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ )
+
 pkg_pretend() {
 	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
 	use openmp && ! tc-has-openmp && \
@@ -235,43 +238,29 @@ src_install() {
 			BUILD_DIR="${WORKDIR}/${P}_openmm" \
 				DESTDIR="${D}" cmake-utils_src_make install-mdrun
 		fi
+		#manual can only be build after gromacs was installed once in image
+		if use doc && [[ $PV = *9999*  && ! -d ${WORKDIR}/manual_build ]]; then
+			mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )
+			BUILD_DIR="${WORKDIR}"/manual_build \
+				CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure
+			BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make
+			newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf"
+		fi
 		use mpi || continue
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
 			DESTDIR="${D}" cmake-utils_src_make install-mdrun
 	done
 
+	use doc && [[ $PV != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
 	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
 	if use zsh-completion ; then
 		insinto /usr/share/zsh/site-functions
 		newins "${ED}"/usr/bin/completion.zsh _${PN}
 	fi
-	rm -f "${ED}"/usr/bin/completion.*
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL* README*
-	if use doc; then
-		dohtml -r "${ED}usr/share/gromacs/html/"
-		if [[ $PV = *9999* ]]; then
-			local progs
-			for x in "${ED}"/usr/bin/*; do
-				[[ $x = *_d ]] || progs+=" ${x##*/}"
-			done
-			sed -e "/^PROGRAMS=/s/=.*/='${progs## }'/" \
-				-e "/INSTALLED_OPTIONS_PROGRAM_NAME=/s:=.*:=${ED}/usr/bin/g_options:" \
-				-i "${WORKDIR}"/manual/mkman || die
-			mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )
-			BUILD_DIR="${WORKDIR}"/manual_build \
-				CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure
-			BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make
-			newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		else
-			dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
-		fi
-	fi
-	rm -rf "${ED}"/usr/share/gromacs/html/
-
-	rm -f "${ED}"/usr/bin/g_options*
-	rm -f "${ED}"/usr/bin/GMXRC*
+	rm -f "${ED}"usr/bin/completion.*
+	rm -rf "${ED}"usr/share/gromacs/html
+	rm -f "${ED}"usr/bin/g_options*
+	rm -f "${ED}"usr/bin/GMXRC*
 }
 
 pkg_postinst() {


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-02-12  4:21 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2013-02-12  4:21 UTC (permalink / raw
  To: gentoo-commits

commit:     b771bdf1df7e9b89773d419679fec77cdf9a9d3f
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Feb 12 04:21:18 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Feb 12 04:21:18 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b771bdf1

sse41 -> sse4_1 (bug #456886) + ninja has missing keywords

Package-Manager: portage-2.2.0_alpha161

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    6 ++----
 sci-chemistry/gromacs/gromacs-9999.ebuild     |    4 ++--
 sci-chemistry/gromacs/metadata.xml            |    2 +-
 4 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index af4912d..7672a1e 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  12 Feb 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-9999.ebuild, metadata.xml:
+  sse41 -> sse4_1 (bug #456886) + ninja has missing keywords
+
   30 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
   gromacs-9999.ebuild:
   added subslot, removed gromacs-manual blocker

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 5a4f573..5e52c9f 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -7,8 +7,6 @@ EAPI=5
 TEST_PV="4.6"
 MANUAL_PV="4.6"
 
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
 inherit bash-completion-r1 cmake-utils cuda eutils multilib toolchain-funcs
 
 if [[ $PV = *9999* ]]; then
@@ -24,7 +22,7 @@ else
 		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
 fi
 
-ACCE_IUSE="sse2 sse41 avx128fma avx256"
+ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -130,7 +128,7 @@ src_configure() {
 	#go from slowest to fastest acceleration
 	local acce="None"
 	use sse2 && acce="SSE2"
-	use sse41 && acce="SSE4.1"
+	use sse4_1 && acce="SSE4.1"
 	use avx128fma && acce="AVX_128_FMA"
 	use avx256 && acce="AVX_256"
 

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index fdfa015..b9af3c0 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -9,7 +9,7 @@ TEST_PV="4.0.4"
 EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git"
 EGIT_BRANCH="master"
 
-ACCE_IUSE="sse2 sse41 avx128fma avx256"
+ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
 
 #to find external blas/lapack
 CMAKE_MIN_VERSION="2.8.5-r2"
@@ -112,7 +112,7 @@ src_configure() {
 	#go from slowest to fasterest acceleration
 	local acce="None"
 	use sse2 && acce="SSE2"
-	use sse41 && acce="SSE4.1"
+	use sse4_1 && acce="SSE4.1"
 	use avx128fma && acce="AVX_128_FMA"
 	use avx256 && acce="AVX_256"
 

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 1360fcb..8a88d53 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -12,7 +12,7 @@
 		<flag name="single-precision">Single precision version of gromacs (default)</flag>
 		<!-- acceleration optimization flags -->
 		<flag name="fkernels">Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
-		<flag name="sse41">Enable sse4.1 acceleration</flag>
+		<flag name="sse4_1">Enable sse4.1 acceleration</flag>
 		<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
 		<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
 		<flag name="offensive">Enable gromacs partly offensive quotes</flag>


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-03-06  2:04 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2013-03-06  2:04 UTC (permalink / raw
  To: gentoo-commits

commit:     d641b77cf7e5b677eea55c8b689c6945961ed8e8
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Mar  6 02:03:56 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Mar  6 02:03:56 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d641b77c

sync with gx86 + clean up

Package-Manager: portage-2.2.0_alpha165

---
 sci-chemistry/gromacs/ChangeLog               |    5 +
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |  238 -------------------------
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   36 ++--
 sci-chemistry/gromacs/gromacs-9999.ebuild     |    1 -
 sci-chemistry/gromacs/metadata.xml            |    1 -
 5 files changed, 25 insertions(+), 256 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 7672a1e..45159e4 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  06 Mar 2013; Christoph Junghans <ottxor@gentoo.org> -Manifest,
+  -gromacs-4.5.9999.ebuild, gromacs-4.6.9999.ebuild, gromacs-9999.ebuild,
+  metadata.xml:
+  sync with gx86 + clean up
+
   12 Feb 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
   gromacs-9999.ebuild, metadata.xml:
   sse41 -> sse4_1 (bug #456886) + ninja has missing keywords

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
deleted file mode 100644
index c1a0dd6..0000000
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ /dev/null
@@ -1,238 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="4"
-
-TEST_PV="4.0.4"
-MANUAL_PV="4.5.4"
-
-#to find external blas/lapack
-CMAKE_MIN_VERSION="2.8.5-r2"
-
-inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
-
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
-
-if [ "${PV%9999}" != "${PV}" ]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-4-5-patches"
-	inherit git-2
-else
-	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
-fi
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
-mpi +single-precision sse2 test +threads xml zsh-completion"
-REQUIRED_USE="fkernels? ( !threads )"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	fkernels? ( virtual/fortran )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2:2 )"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig"
-RDEPEND="${CDEPEND}
-	app-shells/tcsh"
-
-RESTRICT="test"
-
-pkg_setup() {
-	use fkernels && fortran-2_pkg_setup
-}
-
-src_prepare() {
-	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
-	epatch_user
-
-	if use mpi && use threads; then
-		elog "mdrun uses only threads OR mpi, and gromacs favours the"
-		elog "use of mpi over threads, so a mpi-version of mdrun will"
-		elog "be compiled. If you want to run mdrun on shared memory"
-		elog "machines only, you can safely disable mpi"
-	fi
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-	#if neither single-precision nor double-precision is enabled
-	#build at least default (single)
-	[ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
-
-	for x in ${GMX_DIRS}; do
-		mkdir -p "${WORKDIR}/${P}_${x}" || die
-		use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
-	done
-}
-
-src_configure() {
-	local mycmakeargs_pre=( )
-	#from gromacs configure
-	if use fftw; then
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
-	else
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
-		ewarn "WARNING: The built-in FFTPACK routines are slow."
-		ewarn "Are you sure you don\'t want to use FFTW?"
-		ewarn "It is free and much faster..."
-	fi
-
-	if [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
-
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-	fi
-
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
-
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
-	fi
-
-	#go from slowest to fasterest acceleration
-	local acce="none"
-	use fkernels && acce="fortran"
-	use altivec && acce="altivec"
-	use ia64 && acce="ia64"
-	use sse2 && acce="sse"
-
-	mycmakeargs_pre+=(
-		$(cmake-utils_use X GMX_X11)
-		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use gsl GMX_GSL)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use threads GMX_THREADS)
-		$(cmake-utils_use xml GMX_XML)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_ACCELERATION="$acce"
-		-DGMXLIB="$(get_libdir)"
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[ "${x}" = "double" ] && suffix="_d"
-		local p
-		[ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile mdrun
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		local oldpath="${PATH}"
-		export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
-		cd "${WORKDIR}/${P}_${x}"
-		emake -j1 tests || die "${x} Precision test failed"
-		export PATH="${oldpath}"
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		use mpi || continue
-		#cmake-utils_src_install does not support args
-		#using cmake-utils_src_compile instead
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_make install-mdrun DESTDIR="${D}"
-	done
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
-
-	doenvd "${T}/80gromacs"
-	rm -f "${ED}"/usr/bin/GMXRC*
-
-	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${ED}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -f "${ED}"/usr/bin/completion.*
-
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL* README*
-	if use doc; then
-		newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
-		dohtml -r "${ED}usr/share/gromacs/html/"
-	fi
-	rm -rf "${ED}usr/share/gromacs/html/"
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "http://dx.doi.org/10.1021/ct700301q"
-	einfo
-	einfo  $(g_luck)
-	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
-	einfo
-	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
-}

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 5e52c9f..8bd98be 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -4,10 +4,12 @@
 
 EAPI=5
 
-TEST_PV="4.6"
-MANUAL_PV="4.6"
+TEST_PV="4.6.1"
+MANUAL_PV="4.6.1"
 
-inherit bash-completion-r1 cmake-utils cuda eutils multilib toolchain-funcs
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
 
 if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -16,10 +18,16 @@ if [[ $PV = *9999* ]]; then
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-4-6"
 	inherit git-2
+	LIVE_DEPEND="doc? (
+		dev-texlive/texlive-latex
+		media-gfx/imagemagick
+		sys-apps/coreutils
+	)"
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
 		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
 		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
+	LIVE_DEPEND=""
 fi
 
 ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
@@ -32,7 +40,7 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
 IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
 
 CDEPEND="
@@ -54,11 +62,7 @@ CDEPEND="
 	)"
 DEPEND="${CDEPEND}
 	virtual/pkgconfig
-	doc? (
-		dev-texlive/texlive-latex
-		media-gfx/imagemagick
-		sys-apps/coreutils
-	)"
+	${LIVE_DEPEND}"
 RDEPEND="${CDEPEND}"
 
 REQUIRED_USE="
@@ -68,7 +72,7 @@ REQUIRED_USE="
 	mkl? ( !blas !fftw !lapack )
 	!openmm" #broken, but https://gerrit.gromacs.org/#/c/2087/
 
-DOCS=( AUTHORS INSTALL.cmake README )
+DOCS=( AUTHORS README )
 HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ )
 
 pkg_pretend() {
@@ -101,8 +105,7 @@ src_prepare() {
 	#notes/todos
 	# -on apple: there is framework support
 
-	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
-	epatch_user
+	cmake-utils_src_prepare
 
 	use cuda && cuda_src_prepare
 
@@ -117,9 +120,7 @@ src_prepare() {
 		done
 	fi
 
-	if use openmm; then
-		sed -i '/option.*GMX_OPENMM/s/^#//' src/contrib/CMakeLists.txt || die
-	fi
+	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
 }
 
 src_configure() {
@@ -190,6 +191,7 @@ src_configure() {
 			einfo "Configuring for openmm build"
 			mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
 				-DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON
+				-DOpenMM_PLUGIN_DIR="${EPREFIX}/usr/$(get_libdir)/plugins"
 				-DGMX_BINARY_SUFFIX="_openmm" -DGMX_LIBS_SUFFIX="_openmm" )
 			BUILD_DIR="${WORKDIR}/${P}_openmm" \
 				OPENMM_ROOT_DIR="${EPREFIX}/usr" cmake-utils_src_configure
@@ -258,6 +260,8 @@ src_install() {
 	rm -rf "${ED}"usr/share/gromacs/html
 	rm -f "${ED}"usr/bin/g_options*
 	rm -f "${ED}"usr/bin/GMXRC*
+
+	readme.gentoo_create_doc
 }
 
 pkg_postinst() {
@@ -271,5 +275,5 @@ pkg_postinst() {
 		einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
 	fi
 	einfo
-	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
+	readme.gentoo_print_elog
 }

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index b9af3c0..36a6d2d 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -18,7 +18,6 @@ inherit bash-completion-r1 cmake-utils eutils git-2 multilib toolchain-funcs
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
 
 LICENSE="GPL-2"
 SLOT="0/${PV}"

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 8a88d53..880233e 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -11,7 +11,6 @@
 		<flag name="double-precision">More precise calculations at the expense of speed</flag>
 		<flag name="single-precision">Single precision version of gromacs (default)</flag>
 		<!-- acceleration optimization flags -->
-		<flag name="fkernels">Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
 		<flag name="sse4_1">Enable sse4.1 acceleration</flag>
 		<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
 		<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-03-09  1:48 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2013-03-09  1:48 UTC (permalink / raw
  To: gentoo-commits

commit:     574832e9da7138e51ef957c0a02b61b07a8983dd
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Mar  9 01:46:43 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Mar  9 01:46:43 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=574832e9

fixed deps + doc build on darwin

Package-Manager: portage-2.2.0_alpha166

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    4 ++++
 2 files changed, 7 insertions(+), 0 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 45159e4..89d1580 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  09 Mar 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  fixed deps + doc build on darwin
+
   06 Mar 2013; Christoph Junghans <ottxor@gentoo.org> -Manifest,
   -gromacs-4.5.9999.ebuild, gromacs-4.6.9999.ebuild, gromacs-9999.ebuild,
   metadata.xml:

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 8bd98be..4d79e52 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -20,6 +20,7 @@ if [[ $PV = *9999* ]]; then
 	inherit git-2
 	LIVE_DEPEND="doc? (
 		dev-texlive/texlive-latex
+		dev-texlive/texlive-latexextra
 		media-gfx/imagemagick
 		sys-apps/coreutils
 	)"
@@ -242,7 +243,10 @@ src_install() {
 			mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )
 			BUILD_DIR="${WORKDIR}"/manual_build \
 				CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure
+			[[ ${CHOST} = *-darwin* ]] && \
+				export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)"
 			BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make
+			[[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)"
 			newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf"
 		fi
 		use mpi || continue


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-03-10  1:04 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2013-03-10  1:04 UTC (permalink / raw
  To: gentoo-commits

commit:     c3db2a4a04c738a9f4c18b00688e384b4ec3f741
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 10 01:04:41 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Mar 10 01:04:41 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c3db2a4a

added cuda build fix from gx86

Package-Manager: portage-2.2.0_alpha166

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    7 ++++---
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 89d1580..bc0c784 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  10 Mar 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  added cuda build fix from gx86
+
   09 Mar 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   fixed deps + doc build on darwin
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 4d79e52..ca14997 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -181,10 +181,11 @@ src_configure() {
 			[[ ${x} = "double" ]] && suffix="_d"
 		local p
 		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=$(cmake-utils_use cuda GMX_GPU)
-		[[ ${x} = "double" ]] && use cuda && cuda="-DGMX_GPU=OFF"
+		local cuda=( "-DGMX_GPU=OFF" )
+		[[ ${x} = "single" ]] && use cuda && \
+			cuda=( -DGMX_GPU=ON -DCUDA_HOST_COMPILER_OPTIONS="${NVCCFLAGS}" )
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-			$(cmake-utils_use threads GMX_THREAD_MPI) ${cuda} -DGMX_OPENMM=OFF
+			$(cmake-utils_use threads GMX_THREAD_MPI) "${cuda[@]}" -DGMX_OPENMM=OFF
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
 			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
 		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-03-15  9:30 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2013-03-15  9:30 UTC (permalink / raw
  To: gentoo-commits

commit:     fa1afc31593c42a91ff3cbc04edbadf77c3568b6
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 15 09:29:55 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri Mar 15 09:29:55 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fa1afc31

Fix build with cuda enabled

Package-Manager: portage-2.2.0_alpha166

---
 sci-chemistry/gromacs/ChangeLog               |    4 ++++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    2 +-
 2 files changed, 5 insertions(+), 1 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index bc0c784..f9bd96e 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  15 Mar 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-9999.ebuild:
+  Fix build with cuda enabled
+
   10 Mar 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   added cuda build fix from gx86
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index ca14997..552ffca 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -182,7 +182,7 @@ src_configure() {
 		local p
 		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
 		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "single" ]] && use cuda && \
+		[[ ${x} = "float" ]] && use cuda && \
 			cuda=( -DGMX_GPU=ON -DCUDA_HOST_COMPILER_OPTIONS="${NVCCFLAGS}" )
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
 			$(cmake-utils_use threads GMX_THREAD_MPI) "${cuda[@]}" -DGMX_OPENMM=OFF


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-03-15  9:34 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2013-03-15  9:34 UTC (permalink / raw
  To: gentoo-commits

commit:     b62368cd6c1141a9584eff5eea145b0a6430812a
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 15 09:34:03 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri Mar 15 09:34:03 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b62368cd

nvcc flags dont needed anymore here

Package-Manager: portage-2.2.0_alpha166

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |    2 +-
 2 files changed, 4 insertions(+), 1 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index f9bd96e..1cba1c5 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  15 Mar 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild:
+  nvcc flags dont needed anymore here
+
   15 Mar 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild,
   gromacs-9999.ebuild:
   Fix build with cuda enabled

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 552ffca..7babac6 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -183,7 +183,7 @@ src_configure() {
 		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
 		local cuda=( "-DGMX_GPU=OFF" )
 		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON -DCUDA_HOST_COMPILER_OPTIONS="${NVCCFLAGS}" )
+			cuda=( -DGMX_GPU=ON )
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
 			$(cmake-utils_use threads GMX_THREAD_MPI) "${cuda[@]}" -DGMX_OPENMM=OFF
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-05-05 17:34 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2013-05-05 17:34 UTC (permalink / raw
  To: gentoo-commits

commit:     d53ca58988e9ddedffc5b0141b91ac22e7ff4043
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun May  5 17:33:13 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun May  5 17:33:49 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d53ca589

sync with gx86

Package-Manager: portage-2.2.0_alpha174

---
 sci-chemistry/gromacs/ChangeLog               |    3 +++
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |   12 +++---------
 2 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 1344590..e91c85a 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 May 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild:
+  sync with gx86
+
 *gromacs-4.5.9999 (03 May 2013)
 
   03 May 2013; Christoph Junghans <ottxor@gentoo.org>

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
index 697033f..b5ed085 100644
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -1,14 +1,13 @@
 # Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.7.ebuild,v 1.2 2013/05/05 17:31:09 ottxor Exp $
 
 EAPI="4"
 
 TEST_PV="4.0.4"
 MANUAL_PV="4.5.6"
 
-#to find external blas/lapack
-CMAKE_MIN_VERSION="2.8.5-r2"
+FORTRAN_NEEDED=fkernels
 
 inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
 
@@ -30,7 +29,7 @@ HOMEPAGE="http://www.gromacs.org/"
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
 IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
 mpi +single-precision sse2 test +threads xml zsh-completion"
 REQUIRED_USE="fkernels? ( !threads )"
@@ -43,7 +42,6 @@ CDEPEND="
 		)
 	blas? ( virtual/blas )
 	fftw? ( sci-libs/fftw:3.0 )
-	fkernels? ( virtual/fortran )
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
 	mpi? ( virtual/mpi )
@@ -55,10 +53,6 @@ RDEPEND="${CDEPEND}
 
 RESTRICT="test"
 
-pkg_setup() {
-	use fkernels && fortran-2_pkg_setup
-}
-
 src_prepare() {
 	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
 	epatch_user


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-06-02 17:40 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2013-06-02 17:40 UTC (permalink / raw
  To: gentoo-commits

commit:     f29955289db5fa42abcec73547a096293eb882a3
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Jun  1 21:38:06 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Jun  2 17:40:26 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f2995528

sync with gx86

Package-Manager: portage-2.2.0_alpha177

---
 sci-chemistry/gromacs/ChangeLog               | 3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild | 7 +++----
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index e91c85a..9a16c48 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  01 Jun 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  sync with gx86
+
   05 May 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild:
   sync with gx86
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 7babac6..2382893 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -4,8 +4,8 @@
 
 EAPI=5
 
-TEST_PV="4.6.1"
-MANUAL_PV="4.6.1"
+TEST_PV="4.6.2"
+MANUAL_PV="4.6.2"
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
@@ -70,8 +70,7 @@ REQUIRED_USE="
 	|| ( single-precision double-precision )
 	cuda? ( single-precision )
 	openmm? ( single-precision )
-	mkl? ( !blas !fftw !lapack )
-	!openmm" #broken, but https://gerrit.gromacs.org/#/c/2087/
+	mkl? ( !blas !fftw !lapack )"
 
 DOCS=( AUTHORS README )
 HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ )


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-12-03  4:00 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2013-12-03  4:00 UTC (permalink / raw
  To: gentoo-commits

commit:     ec5a4f359119a8d3bd186f4f3a24481a0089f98c
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Tue Dec  3 03:59:38 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Tue Dec  3 03:59:38 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ec5a4f35

Slightly update live ebuild for master branch

Package-Manager: portage-2.2.7

---
 sci-chemistry/gromacs/ChangeLog           |   3 +
 sci-chemistry/gromacs/gromacs-9999.ebuild | 280 ++++++++++++++++++------------
 2 files changed, 172 insertions(+), 111 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 9a16c48..fc03b04 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  Slightly update live ebuild for master branch
+
   01 Jun 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   sync with gx86
 

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 36a6d2d..706734c 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -2,28 +2,47 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="5"
+EAPI=5
 
-TEST_PV="4.0.4"
+TEST_PV="5.0-beta1"
+MANUAL_PV="5.0-beta1"
 
-EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git"
-EGIT_BRANCH="master"
+CMAKE_MAKEFILE_GENERATOR="ninja"
 
-ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
 
-#to find external blas/lapack
-CMAKE_MIN_VERSION="2.8.5-r2"
+if [[ $PV = *9999* ]]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+		https://gerrit.gromacs.org/gromacs.git
+		git://github.com/gromacs/gromacs.git
+		http://repo.or.cz/r/gromacs.git"
+	EGIT_BRANCH="master"
+	inherit git-2
+	LIVE_DEPEND="doc? (
+		dev-texlive/texlive-latex
+		dev-texlive/texlive-latexextra
+		media-gfx/imagemagick
+		sys-apps/coreutils
+	)"
+else
+	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
+		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
+	LIVE_DEPEND=""
+fi
 
-inherit bash-completion-r1 cmake-utils eutils git-2 multilib toolchain-funcs
+ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
 
-LICENSE="GPL-2"
+# see COPYING for details
+# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X blas doc -double-precision +fftw gsl lapack mpi +single-precision  test
-+threads xml zsh-completion ${ACCE_IUSE}"
+KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -32,99 +51,121 @@ CDEPEND="
 		x11-libs/libICE
 		)
 	blas? ( virtual/blas )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
 	fftw? ( sci-libs/fftw:3.0 )
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
+	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2:2 )"
+	"
 DEPEND="${CDEPEND}
-	virtual/pkgconfig"
+	virtual/pkgconfig
+	${LIVE_DEPEND}"
 RDEPEND="${CDEPEND}"
 
-RESTRICT="test"
-
-src_prepare() {
-	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
-	epatch_user
-
-	if use mpi && use threads; then
-		elog "mdrun uses only threads OR mpi, and gromacs favours the"
-		elog "use of mpi over threads, so a mpi-version of mdrun will"
-		elog "be compiled. If you want to run mdrun on shared memory"
-		elog "machines only, you can safely disable mpi"
-	fi
+REQUIRED_USE="
+	|| ( single-precision double-precision )
+	cuda? ( single-precision )
+	mkl? ( !blas !fftw !lapack )"
 
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-	#if neither single-precision nor double-precision is enabled
-	#build at least default (single)
-	[ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
+DOCS=( AUTHORS README )
+HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ )
 
-	for x in ${GMX_DIRS}; do
-		mkdir -p "${WORKDIR}/${P}_${x}" || die
-		use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
-	done
+pkg_pretend() {
+	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
+	use openmp && ! tc-has-openmp && \
+		die "Please switch to an openmp compatible compiler"
 }
 
-src_configure() {
-	local mycmakeargs_pre=( )
-	#from gromacs configure
-	if use fftw; then
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
+src_unpack() {
+	if [[ ${PV} != *9999 ]]; then
+		default
 	else
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
-		ewarn "WARNING: The built-in FFTPACK routines are slow."
-		ewarn "Are you sure you don\'t want to use FFTW?"
-		ewarn "It is free and much faster..."
+		git-2_src_unpack
+		if use doc; then
+			EGIT_REPO_URI="git://git.gromacs.org/manual.git" \
+			EGIT_BRANCH="release-4-6" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \
+			EGIT_SOURCEDIR="${WORKDIR}/manual"\
+				git-2_src_unpack
+		fi
+		if use test; then
+			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
+			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
+				git-2_src_unpack
+		fi
 	fi
+}
 
-	if [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
+src_prepare() {
+	#notes/todos
+	# -on apple: there is framework support
 
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
+	cmake-utils_src_prepare
+
+	use cuda && cuda_src_prepare
 
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
+	GMX_DIRS=""
+	use single-precision && GMX_DIRS+=" float"
+	use double-precision && GMX_DIRS+=" double"
+
+	if use test; then
+		for x in ${GMX_DIRS}; do
+			mkdir -p "${WORKDIR}/${P}_${x}" || die
+			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
+		done
 	fi
 
-	#go from slowest to fasterest acceleration
+	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
+}
+
+src_configure() {
+	local mycmakeargs_pre=( ) extra fft_opts=( )
+
+	#go from slowest to fastest acceleration
 	local acce="None"
 	use sse2 && acce="SSE2"
 	use sse4_1 && acce="SSE4.1"
 	use avx128fma && acce="AVX_128_FMA"
 	use avx256 && acce="AVX_256"
 
+	#to create man pages, build tree binaries are executed (bug #398437)
+	[[ ${CHOST} = *-darwin* ]] && \
+		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
+	if use fftw; then
+		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
+	elif use mkl && has_version "=sci-libs/mkl-10*"; then
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
+			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
+		)
+	elif use mkl; then
+		local bits=$(get_libdir)
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
+			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
+		)
+	else
+		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
+	fi
+
 	mycmakeargs_pre+=(
+		"${fft_opts[@]}"
 		$(cmake-utils_use X GMX_X11)
 		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
 		$(cmake-utils_use gsl GMX_GSL)
 		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use threads GMX_THREADS)
-		$(cmake-utils_use xml GMX_XML)
+		$(cmake-utils_use openmp GMX_OPENMP)
+		$(cmake-utils_use offensive GMX_COOL_QUOTES)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_ACCELERATION="$acce"
 		-DGMXLIB="$(get_libdir)"
+		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+		-DGMX_PREFIX_LIBMD=ON
+		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
+		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
+		${extra}
 	)
 
 	for x in ${GMX_DIRS}; do
@@ -132,17 +173,32 @@ src_configure() {
 		local suffix=""
 		#if we build single and double - double is suffixed
 		use double-precision && use single-precision && \
-			[ "${x}" = "double" ] && suffix="_d"
+			[[ ${x} = "double" ]] && suffix="_d"
 		local p
-		[ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+		local cuda=( "-DGMX_GPU=OFF" )
+		[[ ${x} = "float" ]] && use cuda && \
+			cuda=( -DGMX_GPU=ON )
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
+			$(cmake-utils_use threads GMX_THREAD_MPI) "${cuda[@]}" -DGMX_OPENMM=OFF
+			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
 			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
 		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		if [[ ${x} = float ]] && use openmm; then
+			einfo "Configuring for openmm build"
+			mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
+				-DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON
+				-DOpenMM_PLUGIN_DIR="${EPREFIX}/usr/$(get_libdir)/plugins"
+				-DGMX_BINARY_SUFFIX="_openmm" -DGMX_LIBS_SUFFIX="_openmm" )
+			BUILD_DIR="${WORKDIR}/${P}_openmm" \
+				OPENMM_ROOT_DIR="${EPREFIX}/usr" cmake-utils_src_configure
+		fi
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF
+			-DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
 	done
 }
 
@@ -151,6 +207,11 @@ src_compile() {
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
 			cmake-utils_src_compile
+		if [[ ${x} = float ]] && use openmm; then
+			einfo "Compiling for openmm build"
+			BUILD_DIR="${WORKDIR}/${P}_openmm"\
+				cmake-utils_src_compile mdrun
+		fi
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
@@ -160,11 +221,8 @@ src_compile() {
 
 src_test() {
 	for x in ${GMX_DIRS}; do
-		local oldpath="${PATH}"
-		export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
-		cd "${WORKDIR}/${P}_${x}"
-		emake -j1 tests || die "${x} Precision test failed"
-		export PATH="${oldpath}"
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_make check
 	done
 }
 
@@ -172,40 +230,38 @@ src_install() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}" \
 			cmake-utils_src_install
+		if [[ ${x} = float ]] && use openmm; then
+			BUILD_DIR="${WORKDIR}/${P}_openmm" \
+				DESTDIR="${D}" cmake-utils_src_make install-mdrun
+		fi
+		#manual can only be build after gromacs was installed once in image
+		if use doc && [[ $PV = *9999*  && ! -d ${WORKDIR}/manual_build ]]; then
+			mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )
+			BUILD_DIR="${WORKDIR}"/manual_build \
+				CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure
+			[[ ${CHOST} = *-darwin* ]] && \
+				export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)"
+			BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make
+			[[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)"
+			newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf"
+		fi
 		use mpi || continue
-		#cmake-utils_src_install does not support args
-		#using cmake-utils_src_compile instead
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_make install-mdrun DESTDIR="${D}"
+			DESTDIR="${D}" cmake-utils_src_make install-mdrun
 	done
 
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
-
-	doenvd "${T}/80gromacs"
-	rm -f "${ED}"/usr/bin/GMXRC*
-
+	use doc && [[ $PV != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
 	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
 	if use zsh-completion ; then
 		insinto /usr/share/zsh/site-functions
 		newins "${ED}"/usr/bin/completion.zsh _${PN}
 	fi
-	rm -f "${ED}"/usr/bin/completion.*
-
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL* README*
-	if use doc; then
-		dohtml -r "${ED}usr/share/gromacs/html/"
-		insinto /usr/share/gromacs
-		doins "admin/programs.txt"
-		ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list
-		doins "${T}"/programs.list
-	fi
-	rm -rf "${ED}usr/share/gromacs/html/"
+	rm -f "${ED}"usr/bin/completion.*
+	rm -rf "${ED}"usr/share/gromacs/html
+	rm -f "${ED}"usr/bin/g_options*
+	rm -f "${ED}"usr/bin/GMXRC*
+
+	readme.gentoo_create_doc
 }
 
 pkg_postinst() {
@@ -213,9 +269,11 @@ pkg_postinst() {
 	einfo  "Please read and cite:"
 	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
 	einfo  "http://dx.doi.org/10.1021/ct700301q"
+	if use offensive; then
+		einfo
+		einfo  $(g_luck)
+		einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
+	fi
 	einfo
-	einfo  $(g_luck)
-	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
-	einfo
-	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
+	readme.gentoo_print_elog
 }


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-12-03  4:06 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2013-12-03  4:06 UTC (permalink / raw
  To: gentoo-commits

commit:     59ceeaad78fce1fcc8d452177b0fa64eb3b517c6
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Tue Dec  3 04:04:32 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Tue Dec  3 04:04:32 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=59ceeaad

More updates to gmx live

Package-Manager: portage-2.2.7

---
 sci-chemistry/gromacs/ChangeLog           | 3 +++
 sci-chemistry/gromacs/gromacs-9999.ebuild | 9 ---------
 2 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index fc03b04..60e7d86 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  More updates to gmx live
+
+  03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
   Slightly update live ebuild for master branch
 
   01 Jun 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 706734c..f14bba5 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -184,15 +184,6 @@ src_configure() {
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
 			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
 		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		if [[ ${x} = float ]] && use openmm; then
-			einfo "Configuring for openmm build"
-			mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-				-DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON
-				-DOpenMM_PLUGIN_DIR="${EPREFIX}/usr/$(get_libdir)/plugins"
-				-DGMX_BINARY_SUFFIX="_openmm" -DGMX_LIBS_SUFFIX="_openmm" )
-			BUILD_DIR="${WORKDIR}/${P}_openmm" \
-				OPENMM_ROOT_DIR="${EPREFIX}/usr" cmake-utils_src_configure
-		fi
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-12-03  4:16 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2013-12-03  4:16 UTC (permalink / raw
  To: gentoo-commits

commit:     e32399020c4bb115091b08e106c67f2241ba4bc7
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Tue Dec  3 04:15:53 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Tue Dec  3 04:15:53 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e3239902

More updates #2 to gmx live

Package-Manager: portage-2.2.7

---
 sci-chemistry/gromacs/ChangeLog           | 3 +++
 sci-chemistry/gromacs/gromacs-9999.ebuild | 9 ---------
 2 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 60e7d86..e4f8243 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  More updates #2 to gmx live
+
+  03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
   More updates to gmx live
 
   03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index f14bba5..02ecef6 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -198,11 +198,6 @@ src_compile() {
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
 			cmake-utils_src_compile
-		if [[ ${x} = float ]] && use openmm; then
-			einfo "Compiling for openmm build"
-			BUILD_DIR="${WORKDIR}/${P}_openmm"\
-				cmake-utils_src_compile mdrun
-		fi
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
@@ -221,10 +216,6 @@ src_install() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}" \
 			cmake-utils_src_install
-		if [[ ${x} = float ]] && use openmm; then
-			BUILD_DIR="${WORKDIR}/${P}_openmm" \
-				DESTDIR="${D}" cmake-utils_src_make install-mdrun
-		fi
 		#manual can only be build after gromacs was installed once in image
 		if use doc && [[ $PV = *9999*  && ! -d ${WORKDIR}/manual_build ]]; then
 			mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-12-03  4:47 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2013-12-03  4:47 UTC (permalink / raw
  To: gentoo-commits

commit:     d7eafeaa9dc3c544754f9ca3f8426d1a4b40faaa
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Tue Dec  3 04:47:04 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Tue Dec  3 04:47:04 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d7eafeaa

make mdrun target work for gmx live

Package-Manager: portage-2.2.7

---
 sci-chemistry/gromacs/ChangeLog           | 3 +++
 sci-chemistry/gromacs/gromacs-9999.ebuild | 6 +++---
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index e4f8243..eb2cc95 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  make mdrun target work for gmx live
+
+  03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
   More updates #2 to gmx live
 
   03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 02ecef6..1a6d1ef 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -187,7 +187,7 @@ src_configure() {
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF
+			-DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF -DGMX_BUILD_MDRUN_ONLY=ON
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
 	done
@@ -201,7 +201,7 @@ src_compile() {
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile mdrun
+			cmake-utils_src_compile
 	done
 }
 
@@ -229,7 +229,7 @@ src_install() {
 		fi
 		use mpi || continue
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			DESTDIR="${D}" cmake-utils_src_make install-mdrun
+			cmake-utils_src_install
 	done
 
 	use doc && [[ $PV != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-12-05  3:40 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2013-12-05  3:40 UTC (permalink / raw
  To: gentoo-commits

commit:     4aecc817114c313401f89857baf12b4b5959d6cd
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Thu Dec  5 03:39:46 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Dec  5 03:39:46 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4aecc817

Update live ebuild to current state

Package-Manager: portage-2.2.7

---
 sci-chemistry/gromacs/ChangeLog           |  3 ++
 sci-chemistry/gromacs/gromacs-9999.ebuild | 62 +++++++++++++++----------------
 2 files changed, 33 insertions(+), 32 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index eb2cc95..732b917 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  Update live ebuild to current state
+
   03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
   make mdrun target work for gmx live
 

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 1a6d1ef..080c1cb 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -18,17 +18,10 @@ if [[ $PV = *9999* ]]; then
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="master"
 	inherit git-2
-	LIVE_DEPEND="doc? (
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-		sys-apps/coreutils
-	)"
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
 		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
 		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
-	LIVE_DEPEND=""
 fi
 
 ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
@@ -42,7 +35,7 @@ HOMEPAGE="http://www.gromacs.org/"
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
 KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
+IUSE="X blas cuda +doc -double-precision +fftw gsl lapack mkl mpi +offensive openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -60,7 +53,11 @@ CDEPEND="
 	"
 DEPEND="${CDEPEND}
 	virtual/pkgconfig
-	${LIVE_DEPEND}"
+	doc? (
+		dev-texlive/texlive-latex
+		dev-texlive/texlive-latexextra
+		media-gfx/imagemagick
+	)"
 RDEPEND="${CDEPEND}"
 
 REQUIRED_USE="
@@ -82,12 +79,6 @@ src_unpack() {
 		default
 	else
 		git-2_src_unpack
-		if use doc; then
-			EGIT_REPO_URI="git://git.gromacs.org/manual.git" \
-			EGIT_BRANCH="release-4-6" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \
-			EGIT_SOURCEDIR="${WORKDIR}/manual"\
-				git-2_src_unpack
-		fi
 		if use test; then
 			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
 			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
@@ -158,6 +149,7 @@ src_configure() {
 		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
 		$(cmake-utils_use openmp GMX_OPENMP)
 		$(cmake-utils_use offensive GMX_COOL_QUOTES)
+		$(cmake-utils_use doc GMX_BUILD_MANUAL)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_ACCELERATION="$acce"
 		-DGMXLIB="$(get_libdir)"
@@ -165,6 +157,8 @@ src_configure() {
 		-DGMX_PREFIX_LIBMD=ON
 		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
 		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
+		-DBUILD_TESTING=OFF
+		-DGMX_BUILD_UNITTESTS=OFF
 		${extra}
 	)
 
@@ -179,16 +173,29 @@ src_configure() {
 		local cuda=( "-DGMX_GPU=OFF" )
 		[[ ${x} = "float" ]] && use cuda && \
 			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-			$(cmake-utils_use threads GMX_THREAD_MPI) "${cuda[@]}" -DGMX_OPENMM=OFF
+		mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_MPI=OFF
+			$(cmake-utils_use threads GMX_THREAD_MPI)
+			"${cuda[@]}"
+			-DGMX_OPENMM=OFF
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
+			-DGMX_BINARY_SUFFIX="${suffix}"
+			-DGMX_LIBS_SUFFIX="${suffix}"
+			)
 		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF -DGMX_BUILD_MDRUN_ONLY=ON
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
+		mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_THREAD_MPI=OFF
+			-DGMX_MPI=ON ${cuda}
+			-DGMX_OPENMM=OFF
+			-DGMX_BUILD_MDRUN_ONLY=ON
+			-DGMX_BUILD_MANUAL=OFF
+			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
+			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
+			)
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
 	done
 }
@@ -216,23 +223,14 @@ src_install() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}" \
 			cmake-utils_src_install
-		#manual can only be build after gromacs was installed once in image
-		if use doc && [[ $PV = *9999*  && ! -d ${WORKDIR}/manual_build ]]; then
-			mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )
-			BUILD_DIR="${WORKDIR}"/manual_build \
-				CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure
-			[[ ${CHOST} = *-darwin* ]] && \
-				export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)"
-			BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make
-			[[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)"
-			newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf"
+		if use doc; then
+			newdoc "${WORKDIR}"/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
 		fi
 		use mpi || continue
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
 			cmake-utils_src_install
 	done
 
-	use doc && [[ $PV != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
 	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
 	if use zsh-completion ; then
 		insinto /usr/share/zsh/site-functions


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-12-05  3:41 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2013-12-05  3:41 UTC (permalink / raw
  To: gentoo-commits

commit:     3b3b3c81eb3f813d2d1de5ad5894121a04f04e6d
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Thu Dec  5 03:41:07 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Dec  5 03:41:07 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3b3b3c81

Drop 4.5

Package-Manager: portage-2.2.7

---
 sci-chemistry/gromacs/ChangeLog               |   4 +
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild | 242 --------------------------
 sci-chemistry/gromacs/metadata.xml            |   1 -
 3 files changed, 4 insertions(+), 243 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 732b917..996e1d9 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> -Manifest,
+  -gromacs-4.5.9999.ebuild, metadata.xml:
+  Drop 4.5
+
   05 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
   Update live ebuild to current state
 

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
deleted file mode 100644
index b5ed085..0000000
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ /dev/null
@@ -1,242 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.7.ebuild,v 1.2 2013/05/05 17:31:09 ottxor Exp $
-
-EAPI="4"
-
-TEST_PV="4.0.4"
-MANUAL_PV="4.5.6"
-
-FORTRAN_NEEDED=fkernels
-
-inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
-
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
-
-if [ "${PV%9999}" != "${PV}" ]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-4-5-patches"
-	inherit git-2
-else
-	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
-		sse2? ( http://dev.gentoo.org/~alexxy/gromacs/0001-Make-stack-non-executable-for-GAS-assembly.patch.gz )
-		sse2? ( http://dev.gentoo.org/~alexxy/gromacs/0002-Make-stack-non-executable-for-ATT-assembly.patch.gz )"
-fi
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
-mpi +single-precision sse2 test +threads xml zsh-completion"
-REQUIRED_USE="fkernels? ( !threads )"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2:2 )"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig"
-RDEPEND="${CDEPEND}
-	app-shells/tcsh"
-
-RESTRICT="test"
-
-src_prepare() {
-	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
-	epatch_user
-
-	if use mpi && use threads; then
-		elog "mdrun uses only threads OR mpi, and gromacs favours the"
-		elog "use of mpi over threads, so a mpi-version of mdrun will"
-		elog "be compiled. If you want to run mdrun on shared memory"
-		elog "machines only, you can safely disable mpi"
-	fi
-
-	if [[ ${PV} != *9999 ]] && use sse2; then
-		# Add patches for non-exec stack - qa issue
-		epatch "${WORKDIR}/0001-Make-stack-non-executable-for-GAS-assembly.patch"
-		epatch "${WORKDIR}/0002-Make-stack-non-executable-for-ATT-assembly.patch"
-		#alexxy patches, renamve kernel from .s to .S
-		epatch "${FILESDIR}/${P}-cmake-cpp-asm.patch"
-	fi
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-	#if neither single-precision nor double-precision is enabled
-	#build at least default (single)
-	[ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
-
-	for x in ${GMX_DIRS}; do
-		mkdir -p "${WORKDIR}/${P}_${x}" || die
-		use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
-	done
-}
-
-src_configure() {
-	local mycmakeargs_pre=( )
-	#from gromacs configure
-	if use fftw; then
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
-	else
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
-		ewarn "WARNING: The built-in FFTPACK routines are slow."
-		ewarn "Are you sure you don\'t want to use FFTW?"
-		ewarn "It is free and much faster..."
-	fi
-
-	if [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
-
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-	fi
-
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
-
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
-	fi
-
-	#go from slowest to fasterest acceleration
-	local acce="none"
-	use fkernels && acce="fortran"
-	use altivec && acce="altivec"
-	use ia64 && acce="ia64"
-	use sse2 && acce="sse"
-
-	mycmakeargs_pre+=(
-		$(cmake-utils_use X GMX_X11)
-		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use gsl GMX_GSL)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use threads GMX_THREADS)
-		$(cmake-utils_use xml GMX_XML)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_ACCELERATION="$acce"
-		-DGMXLIB="$(get_libdir)"
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[ "${x}" = "double" ] && suffix="_d"
-		local p
-		[ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile mdrun
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		local oldpath="${PATH}"
-		export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
-		cd "${WORKDIR}/${P}_${x}"
-		emake -j1 tests || die "${x} Precision test failed"
-		export PATH="${oldpath}"
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		use mpi || continue
-		#cmake-utils_src_install does not support args
-		#using cmake-utils_src_compile instead
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_make install-mdrun DESTDIR="${D}"
-	done
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
-
-	doenvd "${T}/80gromacs"
-	rm -f "${ED}"/usr/bin/GMXRC*
-
-	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${ED}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -f "${ED}"/usr/bin/completion.*
-
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL* README*
-	if use doc; then
-		newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
-		dohtml -r "${ED}usr/share/gromacs/html/"
-	fi
-	rm -rf "${ED}usr/share/gromacs/html/"
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "http://dx.doi.org/10.1021/ct700301q"
-	einfo
-	einfo  $(g_luck)
-	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
-	einfo
-	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
-}

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 8a88d53..880233e 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -11,7 +11,6 @@
 		<flag name="double-precision">More precise calculations at the expense of speed</flag>
 		<flag name="single-precision">Single precision version of gromacs (default)</flag>
 		<!-- acceleration optimization flags -->
-		<flag name="fkernels">Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
 		<flag name="sse4_1">Enable sse4.1 acceleration</flag>
 		<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
 		<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-12-05  6:00 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2013-12-05  6:00 UTC (permalink / raw
  To: gentoo-commits

commit:     41b0fdf9c8d699a403d9513dea566510c29b4b66
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Thu Dec  5 05:59:42 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Dec  5 05:59:42 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=41b0fdf9

Make gromacs 9999 build manual again

Package-Manager: portage-2.2.7

---
 sci-chemistry/gromacs/ChangeLog           | 3 +++
 sci-chemistry/gromacs/gromacs-9999.ebuild | 8 +++++---
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 996e1d9..781b354 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  Make gromacs 9999 build manual again
+
   05 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> -Manifest,
   -gromacs-4.5.9999.ebuild, metadata.xml:
   Drop 4.5

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 080c1cb..20a16c6 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -66,7 +66,6 @@ REQUIRED_USE="
 	mkl? ( !blas !fftw !lapack )"
 
 DOCS=( AUTHORS README )
-HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ )
 
 pkg_pretend() {
 	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
@@ -205,6 +204,10 @@ src_compile() {
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
 			cmake-utils_src_compile
+		if use doc; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}"\
+				cmake-utils_src_compile manual
+		fi
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
@@ -224,7 +227,7 @@ src_install() {
 		BUILD_DIR="${WORKDIR}/${P}_${x}" \
 			cmake-utils_src_install
 		if use doc; then
-			newdoc "${WORKDIR}"/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+			newdoc "${WORKDIR}/${P}_${x}"/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
 		fi
 		use mpi || continue
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
@@ -237,7 +240,6 @@ src_install() {
 		newins "${ED}"/usr/bin/completion.zsh _${PN}
 	fi
 	rm -f "${ED}"usr/bin/completion.*
-	rm -rf "${ED}"usr/share/gromacs/html
 	rm -f "${ED}"usr/bin/g_options*
 	rm -f "${ED}"usr/bin/GMXRC*
 


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-12-06  9:34 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2013-12-06  9:34 UTC (permalink / raw
  To: gentoo-commits

commit:     48ddd384fe8e96a4e904b8ccb1da1fc86087b1e3
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Fri Dec  6 09:34:20 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri Dec  6 09:34:20 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=48ddd384

Add 5.0-beta1 release

Package-Manager: portage-2.2.7

---
 sci-chemistry/gromacs/ChangeLog                             |  6 ++++++
 .../{gromacs-9999.ebuild => gromacs-5.0_beta1.ebuild}       | 13 +++++--------
 sci-chemistry/gromacs/gromacs-9999.ebuild                   | 13 +++++--------
 3 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 781b354..4c5ac13 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*gromacs-5.0_beta1 (06 Dec 2013)
+
+  06 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-5.0_beta1.ebuild,
+  gromacs-9999.ebuild:
+  Add 5.0-beta1 release
+
   05 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
   Make gromacs 9999 build manual again
 

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild
similarity index 95%
copy from sci-chemistry/gromacs/gromacs-9999.ebuild
copy to sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild
index 20a16c6..81ed0cc 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild
@@ -5,7 +5,6 @@
 EAPI=5
 
 TEST_PV="5.0-beta1"
-MANUAL_PV="5.0-beta1"
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
@@ -19,8 +18,7 @@ if [[ $PV = *9999* ]]; then
 	EGIT_BRANCH="master"
 	inherit git-2
 else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
+	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
 fi
 
@@ -67,6 +65,10 @@ REQUIRED_USE="
 
 DOCS=( AUTHORS README )
 
+if [[ ${PV} != *9999 ]]; then
+	S="${WORKDIR}/${PN}-${PV/_/-}"
+fi
+
 pkg_pretend() {
 	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
 	use openmp && ! tc-has-openmp && \
@@ -251,11 +253,6 @@ pkg_postinst() {
 	einfo  "Please read and cite:"
 	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
 	einfo  "http://dx.doi.org/10.1021/ct700301q"
-	if use offensive; then
-		einfo
-		einfo  $(g_luck)
-		einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
-	fi
 	einfo
 	readme.gentoo_print_elog
 }

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 20a16c6..81ed0cc 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -5,7 +5,6 @@
 EAPI=5
 
 TEST_PV="5.0-beta1"
-MANUAL_PV="5.0-beta1"
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
@@ -19,8 +18,7 @@ if [[ $PV = *9999* ]]; then
 	EGIT_BRANCH="master"
 	inherit git-2
 else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
+	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
 fi
 
@@ -67,6 +65,10 @@ REQUIRED_USE="
 
 DOCS=( AUTHORS README )
 
+if [[ ${PV} != *9999 ]]; then
+	S="${WORKDIR}/${PN}-${PV/_/-}"
+fi
+
 pkg_pretend() {
 	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
 	use openmp && ! tc-has-openmp && \
@@ -251,11 +253,6 @@ pkg_postinst() {
 	einfo  "Please read and cite:"
 	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
 	einfo  "http://dx.doi.org/10.1021/ct700301q"
-	if use offensive; then
-		einfo
-		einfo  $(g_luck)
-		einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
-	fi
 	einfo
 	readme.gentoo_print_elog
 }


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2013-12-07 16:22 Justin Lecher
  0 siblings, 0 replies; 102+ messages in thread
From: Justin Lecher @ 2013-12-07 16:22 UTC (permalink / raw
  To: gentoo-commits

commit:     bf9b101c4cffb2f90ca820beba0a16b069250198
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Dec  7 16:21:59 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Dec  7 16:21:59 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bf9b101c

sci-chemistry/gromacs: Fix multilib-strict problems

Package-Manager: portage-2.2.7

---
 sci-chemistry/gromacs/ChangeLog                |  4 +++
 sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild | 11 +++++----
 sci-chemistry/gromacs/metadata.xml             | 34 +++++++++++++-------------
 3 files changed, 27 insertions(+), 22 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 4c5ac13..0688eb6 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  07 Dec 2013; Justin Lecher <jlec@gentoo.org> gromacs-5.0_beta1.ebuild,
+  metadata.xml:
+  Fix multilib-strict problems
+
 *gromacs-5.0_beta1 (06 Dec 2013)
 
   06 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-5.0_beta1.ebuild,

diff --git a/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild b/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild
index 81ed0cc..a60490f 100644
--- a/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild
@@ -160,6 +160,7 @@ src_configure() {
 		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
 		-DBUILD_TESTING=OFF
 		-DGMX_BUILD_UNITTESTS=OFF
+		-DGMX_LIB_INSTALL_DIR=$(get_libdir)
 		${extra}
 	)
 
@@ -241,18 +242,18 @@ src_install() {
 		insinto /usr/share/zsh/site-functions
 		newins "${ED}"/usr/bin/completion.zsh _${PN}
 	fi
-	rm -f "${ED}"usr/bin/completion.*
-	rm -f "${ED}"usr/bin/g_options*
-	rm -f "${ED}"usr/bin/GMXRC*
+	rm -f "${ED}"usr/bin/completion.* || die
+	rm -f "${ED}"usr/bin/g_options* || die
+	rm -f "${ED}"usr/bin/GMXRC* || die
 
 	readme.gentoo_create_doc
 }
 
 pkg_postinst() {
-	einfo
+	echo
 	einfo  "Please read and cite:"
 	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
 	einfo  "http://dx.doi.org/10.1021/ct700301q"
-	einfo
+	echo
 	readme.gentoo_print_elog
 }

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 880233e..49684a9 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -1,21 +1,21 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-chemistry</herd>
-	<maintainer>
-		<email>ottxor@gentoo.org</email>
-		<name>Christoph Junghans</name>
-	</maintainer>
-	<use>
-		<flag name="cuda">Enable cuda non-bonded kernels</flag>
-		<flag name="double-precision">More precise calculations at the expense of speed</flag>
-		<flag name="single-precision">Single precision version of gromacs (default)</flag>
-		<!-- acceleration optimization flags -->
-		<flag name="sse4_1">Enable sse4.1 acceleration</flag>
-		<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
-		<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
-		<flag name="offensive">Enable gromacs partly offensive quotes</flag>
-		<flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
-		<flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
-	</use>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>ottxor@gentoo.org</email>
+    <name>Christoph Junghans</name>
+  </maintainer>
+  <use>
+    <flag name="cuda">Enable cuda non-bonded kernels</flag>
+    <flag name="double-precision">More precise calculations at the expense of speed</flag>
+    <flag name="single-precision">Single precision version of gromacs (default)</flag>
+    <!-- acceleration optimization flags -->
+    <flag name="sse4_1">Enable sse4.1 acceleration</flag>
+    <flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
+    <flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+    <flag name="offensive">Enable gromacs partly offensive quotes</flag>
+    <flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
+    <flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
+  </use>
 </pkgmetadata>


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-01-06 18:48 Justin Lecher
  0 siblings, 0 replies; 102+ messages in thread
From: Justin Lecher @ 2014-01-06 18:48 UTC (permalink / raw
  To: gentoo-commits

commit:     a7eb933ed6697e4ec0ceb368a8bdeec7dda67526
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan  6 18:41:36 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan  6 18:41:36 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a7eb933e

sci-chemistry/gromacs: Switch from git-2 to git-r3

Package-Manager: portage-2.2.8

---
 sci-chemistry/gromacs/ChangeLog                | 6 +++++-
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild  | 4 ++--
 sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild | 4 ++--
 sci-chemistry/gromacs/gromacs-9999.ebuild      | 4 ++--
 4 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 0688eb6..9cb3670 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-chemistry/gromacs
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  06 Jan 2014; Justin Lecher <jlec@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild:
+  Switch from git-2 to git-r3
+
   07 Dec 2013; Justin Lecher <jlec@gentoo.org> gromacs-5.0_beta1.ebuild,
   metadata.xml:
   Fix multilib-strict problems

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 2382893..b9e3acf 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -17,7 +17,7 @@ if [[ $PV = *9999* ]]; then
 		git://github.com/gromacs/gromacs.git
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-4-6"
-	inherit git-2
+	inherit git-r3
 	LIVE_DEPEND="doc? (
 		dev-texlive/texlive-latex
 		dev-texlive/texlive-latexextra

diff --git a/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild b/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild
index a60490f..ec8d01c 100644
--- a/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -16,7 +16,7 @@ if [[ $PV = *9999* ]]; then
 		git://github.com/gromacs/gromacs.git
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="master"
-	inherit git-2
+	inherit git-r3
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 81ed0cc..18e8b04 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -16,7 +16,7 @@ if [[ $PV = *9999* ]]; then
 		git://github.com/gromacs/gromacs.git
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="master"
-	inherit git-2
+	inherit git-r3
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-01-06 19:27 Justin Lecher
  0 siblings, 0 replies; 102+ messages in thread
From: Justin Lecher @ 2014-01-06 19:27 UTC (permalink / raw
  To: gentoo-commits

commit:     5b20639cd73d9b5238221c359c2edebbb1d38600
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan  6 19:17:45 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan  6 19:17:45 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5b20639c

sci-chemistry/gromacs: Switch from git-2 to git-r3

Package-Manager: portage-2.2.8

---
 sci-chemistry/gromacs/ChangeLog                | 4 ++++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild  | 6 +++---
 sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild | 4 ++--
 sci-chemistry/gromacs/gromacs-9999.ebuild      | 4 ++--
 4 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 9cb3670..6c1a34a 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -6,6 +6,10 @@
   gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild:
   Switch from git-2 to git-r3
 
+  06 Jan 2014; Justin Lecher <jlec@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild:
+  Switch from git-2 to git-r3
+
   07 Dec 2013; Justin Lecher <jlec@gentoo.org> gromacs-5.0_beta1.ebuild,
   metadata.xml:
   Fix multilib-strict problems

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index b9e3acf..604df80 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -85,18 +85,18 @@ src_unpack() {
 	if [[ ${PV} != *9999 ]]; then
 		default
 	else
-		git-2_src_unpack
+		git-r3_src_unpack
 		if use doc; then
 			EGIT_REPO_URI="git://git.gromacs.org/manual.git" \
 			EGIT_BRANCH="release-4-6" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \
 			EGIT_SOURCEDIR="${WORKDIR}/manual"\
-				git-2_src_unpack
+				git-r3_src_unpack
 		fi
 		if use test; then
 			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
 			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
 			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
-				git-2_src_unpack
+				git-r3_src_unpack
 		fi
 	fi
 }

diff --git a/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild b/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild
index ec8d01c..14e9c85 100644
--- a/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild
@@ -79,12 +79,12 @@ src_unpack() {
 	if [[ ${PV} != *9999 ]]; then
 		default
 	else
-		git-2_src_unpack
+		git-r3_src_unpack
 		if use test; then
 			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
 			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
 			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
-				git-2_src_unpack
+				git-r3_src_unpack
 		fi
 	fi
 }

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 18e8b04..15e97ca 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -79,12 +79,12 @@ src_unpack() {
 	if [[ ${PV} != *9999 ]]; then
 		default
 	else
-		git-2_src_unpack
+		git-r3_src_unpack
 		if use test; then
 			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
 			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
 			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
-				git-2_src_unpack
+				git-r3_src_unpack
 		fi
 	fi
 }


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-01-28  7:55 Justin Lecher
  0 siblings, 0 replies; 102+ messages in thread
From: Justin Lecher @ 2014-01-28  7:55 UTC (permalink / raw
  To: gentoo-commits

commit:     e05f720094eb00f349aaf18828b1626c48eeb083
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 25 16:05:14 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan 27 06:37:50 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e05f7200

sci-chemistry/gromacs: Add missing dep for USE=doc

Package-Manager: portage-2.2.8-r1

---
 sci-chemistry/gromacs/ChangeLog                | 4 ++++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild  | 4 +++-
 sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild | 1 +
 sci-chemistry/gromacs/gromacs-9999.ebuild      | 1 +
 4 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 6c1a34a..9176712 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  25 Jan 2014; Justin Lecher <jlec@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild:
+  Add missing dep for USE=doc
+
   06 Jan 2014; Justin Lecher <jlec@gentoo.org> gromacs-4.6.9999.ebuild,
   gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild:
   Switch from git-2 to git-r3

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 604df80..c2f3435 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -19,6 +19,7 @@ if [[ $PV = *9999* ]]; then
 	EGIT_BRANCH="release-4-6"
 	inherit git-r3
 	LIVE_DEPEND="doc? (
+		app-doc/doxygen
 		dev-texlive/texlive-latex
 		dev-texlive/texlive-latexextra
 		media-gfx/imagemagick
@@ -63,7 +64,8 @@ CDEPEND="
 	)"
 DEPEND="${CDEPEND}
 	virtual/pkgconfig
-	${LIVE_DEPEND}"
+	${LIVE_DEPEND}
+	doc? ( app-doc/doxygen )"
 RDEPEND="${CDEPEND}"
 
 REQUIRED_USE="

diff --git a/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild b/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild
index 14e9c85..a3eb16e 100644
--- a/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild
@@ -52,6 +52,7 @@ CDEPEND="
 DEPEND="${CDEPEND}
 	virtual/pkgconfig
 	doc? (
+		app-doc/doxygen
 		dev-texlive/texlive-latex
 		dev-texlive/texlive-latexextra
 		media-gfx/imagemagick

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 15e97ca..e0c2d4a 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -52,6 +52,7 @@ CDEPEND="
 DEPEND="${CDEPEND}
 	virtual/pkgconfig
 	doc? (
+		app-doc/doxygen
 		dev-texlive/texlive-latex
 		dev-texlive/texlive-latexextra
 		media-gfx/imagemagick


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-02-05 12:02 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2014-02-05 12:02 UTC (permalink / raw
  To: gentoo-commits

commit:     13087fa51659f80616b2be37ba352856535ee402
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Wed Feb  5 12:04:44 2014 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Wed Feb  5 12:04:44 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=13087fa5

Revert back to git-2 since git-r2  gives problems

Package-Manager: portage-2.2.8-r1

---
 sci-chemistry/gromacs/ChangeLog           | 3 +++
 sci-chemistry/gromacs/gromacs-9999.ebuild | 6 +++---
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 9176712..ed2b685 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 Feb 2014; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  Revert back to git-2 since git-r2  gives problems
+
   25 Jan 2014; Justin Lecher <jlec@gentoo.org> gromacs-4.6.9999.ebuild,
   gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild:
   Add missing dep for USE=doc

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index e0c2d4a..cc7ac90 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -16,7 +16,7 @@ if [[ $PV = *9999* ]]; then
 		git://github.com/gromacs/gromacs.git
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="master"
-	inherit git-r3
+	inherit git-2
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
@@ -80,12 +80,12 @@ src_unpack() {
 	if [[ ${PV} != *9999 ]]; then
 		default
 	else
-		git-r3_src_unpack
+		git-2_src_unpack
 		if use test; then
 			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
 			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
 			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
+				git-2_src_unpack
 		fi
 	fi
 }


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-02-05 12:09 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2014-02-05 12:09 UTC (permalink / raw
  To: gentoo-commits

commit:     ba6ba542dda0ec8ec140dce44b56f1655e04cc40
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Wed Feb  5 12:12:06 2014 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Wed Feb  5 12:12:06 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ba6ba542

Bash completion changes are comming =D

Package-Manager: portage-2.2.8-r1

---
 sci-chemistry/gromacs/ChangeLog           |  3 +++
 sci-chemistry/gromacs/gromacs-9999.ebuild | 12 ++++++------
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index ed2b685..0d3f2b0 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   05 Feb 2014; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  Bash completion changes are comming =D
+
+  05 Feb 2014; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
   Revert back to git-2 since git-r2  gives problems
 
   25 Jan 2014; Justin Lecher <jlec@gentoo.org> gromacs-4.6.9999.ebuild,

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index cc7ac90..949e30d 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -237,12 +237,12 @@ src_install() {
 			cmake-utils_src_install
 	done
 
-	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${ED}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -f "${ED}"usr/bin/completion.*
+	#newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
+	#if use zsh-completion ; then
+	#	insinto /usr/share/zsh/site-functions
+	#	newins "${ED}"/usr/bin/completion.zsh _${PN}
+	#fi
+	#rm -f "${ED}"usr/bin/completion.*
 	rm -f "${ED}"usr/bin/g_options*
 	rm -f "${ED}"usr/bin/GMXRC*
 


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-02-16 23:04 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2014-02-16 23:04 UTC (permalink / raw
  To: gentoo-commits

commit:     3870ba06f784b6f55712c08db6e7f75ba403426a
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 16 23:00:01 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Feb 16 23:00:01 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3870ba06

git-r3 too smart, migrate back to git-2

Package-Manager: portage-2.2.7

---
 sci-chemistry/gromacs/ChangeLog               |  3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild | 10 +++++-----
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 0d3f2b0..ed1841b 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Feb 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  git-r3 too smart, migrate back to git-2
+
   05 Feb 2014; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
   Bash completion changes are comming =D
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index c2f3435..73e8445 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -17,7 +17,7 @@ if [[ $PV = *9999* ]]; then
 		git://github.com/gromacs/gromacs.git
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-4-6"
-	inherit git-r3
+	inherit git-2
 	LIVE_DEPEND="doc? (
 		app-doc/doxygen
 		dev-texlive/texlive-latex
@@ -87,18 +87,18 @@ src_unpack() {
 	if [[ ${PV} != *9999 ]]; then
 		default
 	else
-		git-r3_src_unpack
+		git-2_src_unpack
 		if use doc; then
 			EGIT_REPO_URI="git://git.gromacs.org/manual.git" \
 			EGIT_BRANCH="release-4-6" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \
 			EGIT_SOURCEDIR="${WORKDIR}/manual"\
-				git-r3_src_unpack
+				git-2_src_unpack
 		fi
 		if use test; then
 			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
+			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \
 			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
+				git-2_src_unpack
 		fi
 	fi
 }


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-02-20 13:26 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2014-02-20 13:26 UTC (permalink / raw
  To: gentoo-commits

commit:     3f5f99c1134bfa97bb493d3f56e2a002f6783adf
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Thu Feb 20 13:27:50 2014 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Feb 20 13:27:50 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3f5f99c1

Update gromacs 5.0

Package-Manager: portage-2.2.8-r1

---
 sci-chemistry/gromacs/ChangeLog           | 3 +++
 sci-chemistry/gromacs/gromacs-9999.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index ed1841b..259ba45 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  20 Feb 2014; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  Update gromacs 5.0
+
   16 Feb 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
   git-r3 too smart, migrate back to git-2
 

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 949e30d..ad9d1e3 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -153,7 +153,7 @@ src_configure() {
 		$(cmake-utils_use offensive GMX_COOL_QUOTES)
 		$(cmake-utils_use doc GMX_BUILD_MANUAL)
 		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_ACCELERATION="$acce"
+		-DGMX_SIMD="$acce"
 		-DGMXLIB="$(get_libdir)"
 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
 		-DGMX_PREFIX_LIBMD=ON


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-03-05  0:44 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2014-03-05  0:44 UTC (permalink / raw
  To: gentoo-commits

commit:     ce9c528657493939f1ce77303db86a5d1dbf8ee0
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Mar  5 00:41:50 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Mar  5 00:43:58 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ce9c5286

fix multilib-strict

Package-Manager: portage-2.2.7

---
 sci-chemistry/gromacs/ChangeLog           | 3 +++
 sci-chemistry/gromacs/gromacs-9999.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 259ba45..299e5b1 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 Mar 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-9999.ebuild:
+  fix multilib-strict
+
   20 Feb 2014; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
   Update gromacs 5.0
 

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index e28b75e..11be99e 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -154,7 +154,7 @@ src_configure() {
 		$(cmake-utils_use doc GMX_BUILD_MANUAL)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
-		-DGMXLIB="$(get_libdir)"
+		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
 		-DGMX_PREFIX_LIBMD=ON
 		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-04-08  8:14 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2014-04-08  8:14 UTC (permalink / raw
  To: gentoo-commits

commit:     2346e75d6ac38cfa981829bbb4efc2ad2bc043b2
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Tue Apr  8 08:13:50 2014 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Tue Apr  8 08:13:50 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2346e75d

[sci-chemistry/gromacs] New ebuilds

Package-Manager: portage-2.2.10

---
 sci-chemistry/gromacs/ChangeLog                    |  8 ++++
 ...cs-5.0_beta1.ebuild => gromacs-5.0.9999.ebuild} | 50 +++++++++++-----------
 ...{gromacs-9999.ebuild => gromacs-5.0_rc1.ebuild} | 43 ++++++++++---------
 sci-chemistry/gromacs/gromacs-9999.ebuild          | 39 +++++++++--------
 sci-chemistry/gromacs/metadata.xml                 | 11 +++--
 5 files changed, 83 insertions(+), 68 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 299e5b1..502a133 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*gromacs-5.0.9999 (08 Apr 2014)
+*gromacs-5.0_rc1 (08 Apr 2014)
+
+  08 Apr 2014; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-5.0.9999.ebuild,
+  +gromacs-5.0_rc1.ebuild, -gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild,
+  metadata.xml:
+  [sci-chemistry/gromacs] New ebuilds
+
   05 Mar 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-9999.ebuild:
   fix multilib-strict
 

diff --git a/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
similarity index 86%
rename from sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild
rename to sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
index a3eb16e..6445042 100644
--- a/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-TEST_PV="5.0-beta1"
+TEST_PV="5.0-rc1"
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
@@ -15,14 +15,14 @@ if [[ $PV = *9999* ]]; then
 		https://gerrit.gromacs.org/gromacs.git
 		git://github.com/gromacs/gromacs.git
 		http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="master"
+	EGIT_BRANCH="release-5-0"
 	inherit git-r3
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
+		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
 fi
 
-ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
+ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256"
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -32,8 +32,8 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE="X blas cuda +doc -double-precision +fftw gsl lapack mkl mpi +offensive openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
+KEYWORDS=""
+IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -42,9 +42,9 @@ CDEPEND="
 		x11-libs/libICE
 		)
 	blas? ( virtual/blas )
+	boost? ( >=dev-libs/boost-1.55 )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
 	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
@@ -119,8 +119,9 @@ src_configure() {
 	local acce="None"
 	use sse2 && acce="SSE2"
 	use sse4_1 && acce="SSE4.1"
-	use avx128fma && acce="AVX_128_FMA"
-	use avx256 && acce="AVX_256"
+	use avx_128_fma && acce="AVX_128_FMA"
+	use avx_256 && acce="AVX_256"
+	use avx2_256 && acee="AVX2_256"
 
 	#to create man pages, build tree binaries are executed (bug #398437)
 	[[ ${CHOST} = *-darwin* ]] && \
@@ -147,21 +148,20 @@ src_configure() {
 		"${fft_opts[@]}"
 		$(cmake-utils_use X GMX_X11)
 		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use gsl GMX_GSL)
 		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
 		$(cmake-utils_use openmp GMX_OPENMP)
 		$(cmake-utils_use offensive GMX_COOL_QUOTES)
+		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
+		$(cmake-utils_use tng GMX_USE_TNG)
 		$(cmake-utils_use doc GMX_BUILD_MANUAL)
 		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_ACCELERATION="$acce"
-		-DGMXLIB="$(get_libdir)"
+		-DGMX_SIMD="$acce"
+		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_PREFIX_LIBMD=ON
 		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
 		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
 		-DBUILD_TESTING=OFF
 		-DGMX_BUILD_UNITTESTS=OFF
-		-DGMX_LIB_INSTALL_DIR=$(get_libdir)
 		${extra}
 	)
 
@@ -195,6 +195,7 @@ src_configure() {
 			-DGMX_MPI=ON ${cuda}
 			-DGMX_OPENMM=OFF
 			-DGMX_BUILD_MDRUN_ONLY=ON
+			-DBUILD_SHARED_LIBS=OFF
 			-DGMX_BUILD_MANUAL=OFF
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
 			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
@@ -208,6 +209,9 @@ src_compile() {
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
 			cmake-utils_src_compile
+		# generate bash completion
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile completion
 		if use doc; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}"\
 				cmake-utils_src_compile manual
@@ -233,28 +237,24 @@ src_install() {
 		if use doc; then
 			newdoc "${WORKDIR}/${P}_${x}"/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
 		fi
+		newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs
 		use mpi || continue
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
 			cmake-utils_src_install
 	done
-
-	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${ED}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -f "${ED}"usr/bin/completion.* || die
-	rm -f "${ED}"usr/bin/g_options* || die
-	rm -f "${ED}"usr/bin/GMXRC* || die
+	# drop non needed staff
+	rm -f "${ED}"usr/bin/gmx-completion*
+	rm -f "${ED}"usr/bin/g_options*
+	rm -f "${ED}"usr/bin/GMXRC*
 
 	readme.gentoo_create_doc
 }
 
 pkg_postinst() {
-	echo
+	einfo
 	einfo  "Please read and cite:"
 	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
 	einfo  "http://dx.doi.org/10.1021/ct700301q"
-	echo
+	einfo
 	readme.gentoo_print_elog
 }

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild
similarity index 87%
copy from sci-chemistry/gromacs/gromacs-9999.ebuild
copy to sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild
index 11be99e..350910c 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-TEST_PV="5.0-beta1"
+TEST_PV="5.0-rc1"
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
@@ -15,14 +15,14 @@ if [[ $PV = *9999* ]]; then
 		https://gerrit.gromacs.org/gromacs.git
 		git://github.com/gromacs/gromacs.git
 		http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="master"
-	inherit git-2
+	EGIT_BRANCH="release-5-0"
+	inherit git-r3
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
+		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
 fi
 
-ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
+ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256"
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -32,8 +32,8 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-KEYWORDS=""
-IUSE="X blas cuda +doc -double-precision +fftw gsl lapack mkl mpi +offensive openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -42,9 +42,9 @@ CDEPEND="
 		x11-libs/libICE
 		)
 	blas? ( virtual/blas )
+	boost? ( >=dev-libs/boost-1.55 )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
 	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
@@ -80,12 +80,12 @@ src_unpack() {
 	if [[ ${PV} != *9999 ]]; then
 		default
 	else
-		git-2_src_unpack
+		git-r3_src_unpack
 		if use test; then
 			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
 			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
 			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
-				git-2_src_unpack
+				git-r3_src_unpack
 		fi
 	fi
 }
@@ -119,8 +119,9 @@ src_configure() {
 	local acce="None"
 	use sse2 && acce="SSE2"
 	use sse4_1 && acce="SSE4.1"
-	use avx128fma && acce="AVX_128_FMA"
-	use avx256 && acce="AVX_256"
+	use avx_128_fma && acce="AVX_128_FMA"
+	use avx_256 && acce="AVX_256"
+	use avx2_256 && acee="AVX2_256"
 
 	#to create man pages, build tree binaries are executed (bug #398437)
 	[[ ${CHOST} = *-darwin* ]] && \
@@ -147,16 +148,16 @@ src_configure() {
 		"${fft_opts[@]}"
 		$(cmake-utils_use X GMX_X11)
 		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use gsl GMX_GSL)
 		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
 		$(cmake-utils_use openmp GMX_OPENMP)
 		$(cmake-utils_use offensive GMX_COOL_QUOTES)
+		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
+		$(cmake-utils_use tng GMX_USE_TNG)
 		$(cmake-utils_use doc GMX_BUILD_MANUAL)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
 		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_PREFIX_LIBMD=ON
 		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
 		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
 		-DBUILD_TESTING=OFF
@@ -194,6 +195,7 @@ src_configure() {
 			-DGMX_MPI=ON ${cuda}
 			-DGMX_OPENMM=OFF
 			-DGMX_BUILD_MDRUN_ONLY=ON
+			-DBUILD_SHARED_LIBS=OFF
 			-DGMX_BUILD_MANUAL=OFF
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
 			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
@@ -207,6 +209,9 @@ src_compile() {
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
 			cmake-utils_src_compile
+		# generate bash completion
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile completion
 		if use doc; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}"\
 				cmake-utils_src_compile manual
@@ -232,17 +237,13 @@ src_install() {
 		if use doc; then
 			newdoc "${WORKDIR}/${P}_${x}"/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
 		fi
+		newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs
 		use mpi || continue
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
 			cmake-utils_src_install
 	done
-
-	#newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
-	#if use zsh-completion ; then
-	#	insinto /usr/share/zsh/site-functions
-	#	newins "${ED}"/usr/bin/completion.zsh _${PN}
-	#fi
-	#rm -f "${ED}"usr/bin/completion.*
+	# drop non needed staff
+	rm -f "${ED}"usr/bin/gmx-completion*
 	rm -f "${ED}"usr/bin/g_options*
 	rm -f "${ED}"usr/bin/GMXRC*
 

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 11be99e..6ccbd8e 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-TEST_PV="5.0-beta1"
+TEST_PV="5.0-rc1"
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
@@ -16,13 +16,13 @@ if [[ $PV = *9999* ]]; then
 		git://github.com/gromacs/gromacs.git
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="master"
-	inherit git-2
+	inherit git-r3
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
+		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
 fi
 
-ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
+ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256"
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -33,7 +33,7 @@ HOMEPAGE="http://www.gromacs.org/"
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
 KEYWORDS=""
-IUSE="X blas cuda +doc -double-precision +fftw gsl lapack mkl mpi +offensive openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
+IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -42,9 +42,9 @@ CDEPEND="
 		x11-libs/libICE
 		)
 	blas? ( virtual/blas )
+	boost? ( >=dev-libs/boost-1.55 )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
 	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
@@ -80,12 +80,12 @@ src_unpack() {
 	if [[ ${PV} != *9999 ]]; then
 		default
 	else
-		git-2_src_unpack
+		git-r3_src_unpack
 		if use test; then
 			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
 			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
 			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
-				git-2_src_unpack
+				git-r3_src_unpack
 		fi
 	fi
 }
@@ -119,8 +119,9 @@ src_configure() {
 	local acce="None"
 	use sse2 && acce="SSE2"
 	use sse4_1 && acce="SSE4.1"
-	use avx128fma && acce="AVX_128_FMA"
-	use avx256 && acce="AVX_256"
+	use avx_128_fma && acce="AVX_128_FMA"
+	use avx_256 && acce="AVX_256"
+	use avx2_256 && acee="AVX2_256"
 
 	#to create man pages, build tree binaries are executed (bug #398437)
 	[[ ${CHOST} = *-darwin* ]] && \
@@ -147,16 +148,16 @@ src_configure() {
 		"${fft_opts[@]}"
 		$(cmake-utils_use X GMX_X11)
 		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use gsl GMX_GSL)
 		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
 		$(cmake-utils_use openmp GMX_OPENMP)
 		$(cmake-utils_use offensive GMX_COOL_QUOTES)
+		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
+		$(cmake-utils_use tng GMX_USE_TNG)
 		$(cmake-utils_use doc GMX_BUILD_MANUAL)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
 		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_PREFIX_LIBMD=ON
 		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
 		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
 		-DBUILD_TESTING=OFF
@@ -194,6 +195,7 @@ src_configure() {
 			-DGMX_MPI=ON ${cuda}
 			-DGMX_OPENMM=OFF
 			-DGMX_BUILD_MDRUN_ONLY=ON
+			-DBUILD_SHARED_LIBS=OFF
 			-DGMX_BUILD_MANUAL=OFF
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
 			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
@@ -207,6 +209,9 @@ src_compile() {
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
 			cmake-utils_src_compile
+		# generate bash completion
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile completion
 		if use doc; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}"\
 				cmake-utils_src_compile manual
@@ -232,17 +237,13 @@ src_install() {
 		if use doc; then
 			newdoc "${WORKDIR}/${P}_${x}"/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
 		fi
+		newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs
 		use mpi || continue
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
 			cmake-utils_src_install
 	done
-
-	#newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
-	#if use zsh-completion ; then
-	#	insinto /usr/share/zsh/site-functions
-	#	newins "${ED}"/usr/bin/completion.zsh _${PN}
-	#fi
-	#rm -f "${ED}"usr/bin/completion.*
+	# drop non needed staff
+	rm -f "${ED}"usr/bin/gmx-completion*
 	rm -f "${ED}"usr/bin/g_options*
 	rm -f "${ED}"usr/bin/GMXRC*
 

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 49684a9..c3bf63e 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -9,11 +9,16 @@
   <use>
     <flag name="cuda">Enable cuda non-bonded kernels</flag>
     <flag name="double-precision">More precise calculations at the expense of speed</flag>
-    <flag name="single-precision">Single precision version of gromacs (default)</flag>
+	<flag name="single-precision">Single precision version of gromacs (default)</flag>
+	<flag name="boost">Enable external boost library</flag>
+	<flag name="tng">Enable new trajectory format - tng</flag>
     <!-- acceleration optimization flags -->
     <flag name="sse4_1">Enable sse4.1 acceleration</flag>
-    <flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
-    <flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+	<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
+	<flag name="avx_128_fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
+	<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+	<flag name="avx_256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+	<flag name="avx2_256">Enable 256bit avx2 (e.g. Intel Haswell)</flag>
     <flag name="offensive">Enable gromacs partly offensive quotes</flag>
     <flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
     <flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-04-14 23:59 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2014-04-14 23:59 UTC (permalink / raw
  To: gentoo-commits

commit:     ec73f9addaa0ce06739c8bf62ee1001392ffae30
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 14 23:59:00 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Apr 14 23:59:00 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ec73f9ad

added make-symlinks use flag, multilib-strict fix

Package-Manager: portage-2.2.8-r1

---
 sci-chemistry/gromacs/ChangeLog               |  4 ++++
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild | 12 ++++++++++--
 sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild  | 12 ++++++++++--
 sci-chemistry/gromacs/gromacs-9999.ebuild     | 12 ++++++++++--
 sci-chemistry/gromacs/metadata.xml            |  1 +
 5 files changed, 35 insertions(+), 6 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 502a133..03c55c5 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  14 Apr 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild,
+  gromacs-5.0_rc1.ebuild, gromacs-9999.ebuild, metadata.xml:
+  added make-symlinks use flag, multilib-strict fix
+
 *gromacs-5.0.9999 (08 Apr 2014)
 *gromacs-5.0_rc1 (08 Apr 2014)
 

diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
index 6445042..b6be22e 100644
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
@@ -33,7 +33,7 @@ HOMEPAGE="http://www.gromacs.org/"
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
 KEYWORDS=""
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -154,6 +154,7 @@ src_configure() {
 		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
 		$(cmake-utils_use tng GMX_USE_TNG)
 		$(cmake-utils_use doc GMX_BUILD_MANUAL)
+		$(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
 		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
@@ -242,10 +243,17 @@ src_install() {
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
 			cmake-utils_src_install
 	done
-	# drop non needed staff
+	# drop unneeded stuff
 	rm -f "${ED}"usr/bin/gmx-completion*
 	rm -f "${ED}"usr/bin/g_options*
 	rm -f "${ED}"usr/bin/GMXRC*
+	rm -f "${ED}"usr/lib*/libtng*.a
+
+	#workaround for libtng
+	if [[ $(get_libdir) != lib ]]; then
+		mv "${ED}"usr/lib/libtng* "${ED}usr/$(get_libdir)" || die
+		rmdir "${ED}"usr/lib || die
+	fi
 
 	readme.gentoo_create_doc
 }

diff --git a/sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild b/sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild
index 350910c..34e34f4 100644
--- a/sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild
@@ -33,7 +33,7 @@ HOMEPAGE="http://www.gromacs.org/"
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -154,6 +154,7 @@ src_configure() {
 		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
 		$(cmake-utils_use tng GMX_USE_TNG)
 		$(cmake-utils_use doc GMX_BUILD_MANUAL)
+		$(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
 		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
@@ -242,10 +243,17 @@ src_install() {
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
 			cmake-utils_src_install
 	done
-	# drop non needed staff
+	# drop unneeded stuff
 	rm -f "${ED}"usr/bin/gmx-completion*
 	rm -f "${ED}"usr/bin/g_options*
 	rm -f "${ED}"usr/bin/GMXRC*
+	rm -f "${ED}"usr/lib*/libtng*.a
+
+	#workaround for libtng
+	if [[ $(get_libdir) != lib ]]; then
+		mv "${ED}"usr/lib/libtng* "${ED}usr/$(get_libdir)" || die
+		rmdir "${ED}"usr/lib || die
+	fi
 
 	readme.gentoo_create_doc
 }

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 6ccbd8e..9f86383 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -33,7 +33,7 @@ HOMEPAGE="http://www.gromacs.org/"
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
 KEYWORDS=""
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -154,6 +154,7 @@ src_configure() {
 		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
 		$(cmake-utils_use tng GMX_USE_TNG)
 		$(cmake-utils_use doc GMX_BUILD_MANUAL)
+		$(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
 		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
@@ -242,10 +243,17 @@ src_install() {
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
 			cmake-utils_src_install
 	done
-	# drop non needed staff
+	# drop unneeded stuff
 	rm -f "${ED}"usr/bin/gmx-completion*
 	rm -f "${ED}"usr/bin/g_options*
 	rm -f "${ED}"usr/bin/GMXRC*
+	rm -f "${ED}"usr/lib*/libtng*.a
+
+	#workaround for libtng
+	if [[ $(get_libdir) != lib ]]; then
+		mv "${ED}"usr/lib/libtng* "${ED}usr/$(get_libdir)" || die
+		rmdir "${ED}"usr/lib || die
+	fi
 
 	readme.gentoo_create_doc
 }

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index c3bf63e..87e0f0a 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -12,6 +12,7 @@
 	<flag name="single-precision">Single precision version of gromacs (default)</flag>
 	<flag name="boost">Enable external boost library</flag>
 	<flag name="tng">Enable new trajectory format - tng</flag>
+	<flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag>
     <!-- acceleration optimization flags -->
     <flag name="sse4_1">Enable sse4.1 acceleration</flag>
 	<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-06-26  5:36 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2014-06-26  5:36 UTC (permalink / raw
  To: gentoo-commits

commit:     bba716734f23364fa41165ad369d8e8d29fd327e
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Jun 26 05:35:48 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Jun 26 05:35:48 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bba71673

live ebuild update

Package-Manager: portage-2.2.8-r1

---
 sci-chemistry/gromacs/ChangeLog               | 3 +++
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild | 8 +-------
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 03c55c5..e98a9ec 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  26 Jun 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+  live ebuild update
+
   14 Apr 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild,
   gromacs-5.0_rc1.ebuild, gromacs-9999.ebuild, metadata.xml:
   added make-symlinks use flag, multilib-strict fix

diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
index b6be22e..6488bd5 100644
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
@@ -247,13 +247,7 @@ src_install() {
 	rm -f "${ED}"usr/bin/gmx-completion*
 	rm -f "${ED}"usr/bin/g_options*
 	rm -f "${ED}"usr/bin/GMXRC*
-	rm -f "${ED}"usr/lib*/libtng*.a
-
-	#workaround for libtng
-	if [[ $(get_libdir) != lib ]]; then
-		mv "${ED}"usr/lib/libtng* "${ED}usr/$(get_libdir)" || die
-		rmdir "${ED}"usr/lib || die
-	fi
+	rm -f "${ED}"usr/$(get_libdir)/libtng*.a
 
 	readme.gentoo_create_doc
 }


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-07-07 19:57 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2014-07-07 19:57 UTC (permalink / raw
  To: gentoo-commits

commit:     868f040035e235b89ddcc524706cc64c93ebde92
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Jul  7 19:56:50 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jul  7 19:56:50 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=868f0400

sync with gx86, fix FEATURES=test

Package-Manager: portage-2.2.8-r1

---
 sci-chemistry/gromacs/ChangeLog               |  4 ++++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild | 25 +++++++++++++------------
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild |  7 ++++---
 3 files changed, 21 insertions(+), 15 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index e98a9ec..fa5fa26 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  07 Jul 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-5.0.9999.ebuild:
+  sync with gx86, fix FEATURES=test
+
   26 Jun 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
   live ebuild update
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 37018ba..2865833 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -4,8 +4,8 @@
 
 EAPI=5
 
-TEST_PV="4.6.2"
-MANUAL_PV="4.6.2"
+TEST_PV="4.6.6"
+MANUAL_PV="4.6.6"
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
@@ -17,7 +17,7 @@ if [[ $PV = *9999* ]]; then
 		git://github.com/gromacs/gromacs.git
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-4-6"
-	inherit git-2
+	inherit git-r3
 	LIVE_DEPEND="doc? (
 		app-doc/doxygen
 		dev-texlive/texlive-latex
@@ -25,11 +25,13 @@ if [[ $PV = *9999* ]]; then
 		media-gfx/imagemagick
 		sys-apps/coreutils
 	)"
+	KEYWORDS=""
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
 		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
-		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
+		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
 	LIVE_DEPEND=""
+	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
 fi
 
 ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
@@ -42,7 +44,6 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-KEYWORDS=""
 IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
 
 CDEPEND="
@@ -87,18 +88,18 @@ src_unpack() {
 	if [[ ${PV} != *9999 ]]; then
 		default
 	else
-		git-2_src_unpack
+		git-r3_src_unpack
 		if use doc; then
 			EGIT_REPO_URI="git://git.gromacs.org/manual.git" \
-			EGIT_BRANCH="release-4-6" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \
-			EGIT_SOURCEDIR="${WORKDIR}/manual"\
-				git-2_src_unpack
+			EGIT_BRANCH="release-4-6" EGIT_COMMIT="release-4-6" \
+			EGIT_CHECKOUT_DIR="${WORKDIR}/manual"\
+				git-r3_src_unpack
 		fi
 		if use test; then
 			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \
-			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
-				git-2_src_unpack
+			EGIT_BRANCH="release-4-6" EGIT_COMMIT="release-4-6" \
+			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
+				git-r3_src_unpack
 		fi
 	fi
 }

diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
index 6488bd5..88169b2 100644
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
@@ -17,9 +17,11 @@ if [[ $PV = *9999* ]]; then
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-5-0"
 	inherit git-r3
+	KEYWORDS=""
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
+	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
 fi
 
 ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256"
@@ -32,7 +34,6 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-KEYWORDS=""
 IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
@@ -83,8 +84,8 @@ src_unpack() {
 		git-r3_src_unpack
 		if use test; then
 			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
-			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
+			EGIT_BRANCH="master" EGIT_COMMIT="master" \
+			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
 				git-r3_src_unpack
 		fi
 	fi


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-09-03 22:53 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2014-09-03 22:53 UTC (permalink / raw
  To: gentoo-commits

commit:     6c21e41bbd14c03b35ff24c4dc253ccedf6173a6
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Sep  3 22:53:28 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Sep  3 22:53:40 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6c21e41b

drop old

Package-Manager: portage-2.2.8-r1

---
 sci-chemistry/gromacs/ChangeLog              |   4 +
 sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild | 268 ---------------------------
 2 files changed, 4 insertions(+), 268 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index b89772c..2b74e15 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  03 Sep 2014; Christoph Junghans <ottxor@gentoo.org> -Manifest,
+  -gromacs-5.0_rc1.ebuild:
+  drop old
+
   03 Sep 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
   live update
 

diff --git a/sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild b/sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild
deleted file mode 100644
index 34e34f4..0000000
--- a/sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild
+++ /dev/null
@@ -1,268 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-TEST_PV="5.0-rc1"
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		git://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-5-0"
-	inherit git-r3
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
-fi
-
-ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	boost? ( >=dev-libs/boost-1.55 )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
-	use openmp && ! tc-has-openmp && \
-		die "Please switch to an openmp compatible compiler"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
-			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use sse2 && acce="SSE2"
-	use sse4_1 && acce="SSE4.1"
-	use avx_128_fma && acce="AVX_128_FMA"
-	use avx_256 && acce="AVX_256"
-	use avx2_256 && acee="AVX2_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		$(cmake-utils_use X GMX_X11)
-		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use openmp GMX_OPENMP)
-		$(cmake-utils_use offensive GMX_COOL_QUOTES)
-		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
-		$(cmake-utils_use tng GMX_USE_TNG)
-		$(cmake-utils_use doc GMX_BUILD_MANUAL)
-		$(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
-		-DBUILD_TESTING=OFF
-		-DGMX_BUILD_UNITTESTS=OFF
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=OFF
-			$(cmake-utils_use threads GMX_THREAD_MPI)
-			"${cuda[@]}"
-			-DGMX_OPENMM=OFF
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
-			-DGMX_OPENMM=OFF
-			-DGMX_BUILD_MDRUN_ONLY=ON
-			-DBUILD_SHARED_LIBS=OFF
-			-DGMX_BUILD_MANUAL=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		# generate bash completion
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile completion
-		if use doc; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
-	done
-	# drop unneeded stuff
-	rm -f "${ED}"usr/bin/gmx-completion*
-	rm -f "${ED}"usr/bin/g_options*
-	rm -f "${ED}"usr/bin/GMXRC*
-	rm -f "${ED}"usr/lib*/libtng*.a
-
-	#workaround for libtng
-	if [[ $(get_libdir) != lib ]]; then
-		mv "${ED}"usr/lib/libtng* "${ED}usr/$(get_libdir)" || die
-		rmdir "${ED}"usr/lib || die
-	fi
-
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "http://dx.doi.org/10.1021/ct700301q"
-	einfo
-	readme.gentoo_print_elog
-}


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-09-03 22:53 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2014-09-03 22:53 UTC (permalink / raw
  To: gentoo-commits

commit:     748ef46fde8eb29578b2e350288a791b8fd64ca9
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Sep  3 22:52:52 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Sep  3 22:53:40 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=748ef46f

live update

Package-Manager: portage-2.2.8-r1

---
 sci-chemistry/gromacs/ChangeLog               | 3 +++
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index fa5fa26..b89772c 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  03 Sep 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+  live update
+
   07 Jul 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
   gromacs-5.0.9999.ebuild:
   sync with gx86, fix FEATURES=test

diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
index 88169b2..92152a3 100644
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
@@ -237,7 +237,7 @@ src_install() {
 		BUILD_DIR="${WORKDIR}/${P}_${x}" \
 			cmake-utils_src_install
 		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
 		fi
 		newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs
 		use mpi || continue


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-09-04 15:06 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2014-09-04 15:06 UTC (permalink / raw
  To: gentoo-commits

commit:     e1bd57c95dd8f13b3e2fea99dec893f853decdbc
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Sep  4 15:05:34 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Sep  4 15:05:34 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e1bd57c9

sync with gx86

Package-Manager: portage-2.2.8-r1

---
 sci-chemistry/gromacs/ChangeLog               | 3 +++
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild | 6 +++++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 2b74e15..dbc7446 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  04 Sep 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+  sync with gx86
+
   03 Sep 2014; Christoph Junghans <ottxor@gentoo.org> -Manifest,
   -gromacs-5.0_rc1.ebuild:
   drop old

diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
index 92152a3..042eb28 100644
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
@@ -21,7 +21,7 @@ if [[ $PV = *9999* ]]; then
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
 ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256"
@@ -189,6 +189,8 @@ src_configure() {
 			-DGMX_LIBS_SUFFIX="${suffix}"
 			)
 		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
 		mycmakeargs=(
@@ -203,6 +205,8 @@ src_configure() {
 			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
 			)
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
 	done
 }
 


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-09-06 18:45 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2014-09-06 18:45 UTC (permalink / raw
  To: gentoo-commits

commit:     f7cc0c793b88498555f37010cccf2a303945d942
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Sep  6 18:44:59 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Sep  6 18:44:59 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f7cc0c79

sync with gx86

Package-Manager: portage-2.2.8-r1

---
 sci-chemistry/gromacs/ChangeLog               | 3 +++
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild | 9 ++-------
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index dbc7446..bc8af30 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  06 Sep 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+  sync with gx86
+
   04 Sep 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
   sync with gx86
 

diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
index 042eb28..a30abac 100644
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
@@ -4,8 +4,6 @@
 
 EAPI=5
 
-TEST_PV="5.0-rc1"
-
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
 inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
@@ -20,7 +18,7 @@ if [[ $PV = *9999* ]]; then
 	KEYWORDS=""
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
+		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
 	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
@@ -249,10 +247,7 @@ src_install() {
 			cmake-utils_src_install
 	done
 	# drop unneeded stuff
-	rm -f "${ED}"usr/bin/gmx-completion*
-	rm -f "${ED}"usr/bin/g_options*
-	rm -f "${ED}"usr/bin/GMXRC*
-	rm -f "${ED}"usr/$(get_libdir)/libtng*.a
+	rm "${ED}"usr/bin/GMXRC* || die
 
 	readme.gentoo_create_doc
 }


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-09-07 18:49 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2014-09-07 18:49 UTC (permalink / raw
  To: gentoo-commits

commit:     db4c48705c9059b1b3ce9d65f88dd5b5d0b86aea
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Sep  7 18:49:16 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Sep  7 18:49:28 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=db4c4870

fix completion install

Package-Manager: portage-2.2.8-r1

---
 sci-chemistry/gromacs/ChangeLog               |  3 +++
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild | 17 +++++++++++++++--
 2 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index bc8af30..baff1c7 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  07 Sep 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+  fix completion install
+
   06 Sep 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
   sync with gx86
 

diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
index a30abac..7c341a7 100644
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
@@ -213,9 +213,11 @@ src_compile() {
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
 			cmake-utils_src_compile
-		# generate bash completion
+		# generate bash completion, not 100% necessary for
+		# rel ebuilds as bundled
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
 			cmake-utils_src_compile completion
+		# not 100% necessary for rel ebuilds as available from website
 		if use doc; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}"\
 				cmake-utils_src_compile manual
@@ -241,13 +243,24 @@ src_install() {
 		if use doc; then
 			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
 		fi
-		newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs
+		#release ebuild does this automatically
+		if [[ $PV = *9999* ]]; then
+			cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die
+			echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die
+		fi
 		use mpi || continue
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
 			cmake-utils_src_install
 	done
 	# drop unneeded stuff
 	rm "${ED}"usr/bin/GMXRC* || die
+	#concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs)
+	#little hacckery as some gmx-completion* newlines ,so cat won't work
+	for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do
+		echo $(<${x})
+	done > "${T}"/gmx-bashcomp || die
+	newbashcomp "${T}"/gmx-bashcomp gromacs
+	rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die
 
 	readme.gentoo_create_doc
 }


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-10-09  9:32 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2014-10-09  9:32 UTC (permalink / raw
  To: gentoo-commits

commit:     eb14cedcd76a03df5a1732d81225c2951ac04a83
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Thu Oct  9 09:32:07 2014 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Oct  9 09:32:07 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=eb14cedc

Fix doc install

Package-Manager: portage-2.2.14_rc1

---
 sci-chemistry/gromacs/ChangeLog           | 3 +++
 sci-chemistry/gromacs/gromacs-9999.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index baff1c7..303fbd8 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  09 Oct 2014; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  Fix doc install
+
   07 Sep 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
   fix completion install
 

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 9f86383..cfaf1a7 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -236,7 +236,7 @@ src_install() {
 		BUILD_DIR="${WORKDIR}/${P}_${x}" \
 			cmake-utils_src_install
 		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
 		fi
 		newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs
 		use mpi || continue


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-11-25 16:05 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2014-11-25 16:05 UTC (permalink / raw
  To: gentoo-commits

commit:     498fd9bde15c43643b86f892afd0d742017e4361
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 25 16:03:00 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Nov 25 16:03:00 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=498fd9bd

fixed a typo preventing AVX2 support (bug #530454)

Package-Manager: portage-2.2.8-r2

---
 sci-chemistry/gromacs/ChangeLog               | 4 ++++
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild | 2 +-
 sci-chemistry/gromacs/gromacs-9999.ebuild     | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 303fbd8..fb02018 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  25 Nov 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-5.0.9999.ebuild, gromacs-9999.ebuild:
+  fixed a typo preventing AVX2 support (bug #530454)
+
   09 Oct 2014; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
   Fix doc install
 

diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
index 7c341a7..e869042 100644
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
@@ -120,7 +120,7 @@ src_configure() {
 	use sse4_1 && acce="SSE4.1"
 	use avx_128_fma && acce="AVX_128_FMA"
 	use avx_256 && acce="AVX_256"
-	use avx2_256 && acee="AVX2_256"
+	use avx2_256 && acce="AVX2_256"
 
 	#to create man pages, build tree binaries are executed (bug #398437)
 	[[ ${CHOST} = *-darwin* ]] && \

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index cfaf1a7..2c3fbe7 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -121,7 +121,7 @@ src_configure() {
 	use sse4_1 && acce="SSE4.1"
 	use avx_128_fma && acce="AVX_128_FMA"
 	use avx_256 && acce="AVX_256"
-	use avx2_256 && acee="AVX2_256"
+	use avx2_256 && acce="AVX2_256"
 
 	#to create man pages, build tree binaries are executed (bug #398437)
 	[[ ${CHOST} = *-darwin* ]] && \


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2014-12-21 23:12 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2014-12-21 23:12 UTC (permalink / raw
  To: gentoo-commits

commit:     b257930db621ae3983cfc53353af0db4eddac014
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 21 23:12:35 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Dec 21 23:12:35 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b257930d

sync with gx86

Package-Manager: portage-2.2.14

---
 sci-chemistry/gromacs/ChangeLog               | 3 +++
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild | 8 ++++++--
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index fb02018..da2baae 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  21 Dec 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+  sync with gx86
+
   25 Nov 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
   gromacs-5.0.9999.ebuild, gromacs-9999.ebuild:
   fixed a typo preventing AVX2 support (bug #530454)

diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
index e869042..210ceef 100644
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
@@ -259,9 +259,13 @@ src_install() {
 	for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do
 		echo $(<${x})
 	done > "${T}"/gmx-bashcomp || die
-	newbashcomp "${T}"/gmx-bashcomp gromacs
+	newbashcomp "${T}"/gmx-bashcomp gmx
+	bashcomp_alias gmx mdrun
 	rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die
-
+	if use double-precision && use single-precision; then
+		bashcomp_alias gmx gmx_d
+		bashcomp_alias gmx mdrun_d
+	fi
 	readme.gentoo_create_doc
 }
 


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2015-01-31 20:19 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2015-01-31 20:19 UTC (permalink / raw
  To: gentoo-commits

commit:     4bb4e72ee1217167a37c0f89e51d0df4f90ab94e
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 31 20:17:02 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Jan 31 20:17:02 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4bb4e72e

Switch to CPU_FLAGS_X86 (bug #538268)

Package-Manager: portage-2.2.14

---
 sci-chemistry/gromacs/ChangeLog               |  6 +++++-
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild | 12 ++++++------
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild | 14 +++++++-------
 sci-chemistry/gromacs/gromacs-9999.ebuild     | 14 +++++++-------
 sci-chemistry/gromacs/metadata.xml            |  6 ------
 5 files changed, 25 insertions(+), 27 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index da2baae..5acf30f 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-chemistry/gromacs
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  31 Jan 2015; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-5.0.9999.ebuild, gromacs-9999.ebuild, metadata.xml:
+  Switch to CPU_FLAGS_X86 (bug #538268)
+
   21 Dec 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
   sync with gx86
 

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 2865833..e8ac17c 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -34,7 +34,7 @@ else
 	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
 fi
 
-ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx"
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -131,10 +131,10 @@ src_configure() {
 
 	#go from slowest to fastest acceleration
 	local acce="None"
-	use sse2 && acce="SSE2"
-	use sse4_1 && acce="SSE4.1"
-	use avx128fma && acce="AVX_128_FMA"
-	use avx256 && acce="AVX_256"
+	use cpu_flags_x86_sse2 && acce="SSE2"
+	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+	use cpu_flags_x86_avx && acce="AVX_256"
 
 	#to create man pages, build tree binaries are executed (bug #398437)
 	[[ ${CHOST} = *-darwin* ]] && \

diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
index 210ceef..f338fd5 100644
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -22,7 +22,7 @@ else
 	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
-ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256"
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -116,11 +116,11 @@ src_configure() {
 
 	#go from slowest to fastest acceleration
 	local acce="None"
-	use sse2 && acce="SSE2"
-	use sse4_1 && acce="SSE4.1"
-	use avx_128_fma && acce="AVX_128_FMA"
-	use avx_256 && acce="AVX_256"
-	use avx2_256 && acce="AVX2_256"
+	use cpu_flags_x86_sse2 && acce="SSE2"
+	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+	use cpu_flags_x86_avx && acce="AVX_256"
+	use cpu_flags_x86_avx2 && acce="AVX2_256"
 
 	#to create man pages, build tree binaries are executed (bug #398437)
 	[[ ${CHOST} = *-darwin* ]] && \

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 2c3fbe7..b50184a 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -22,7 +22,7 @@ else
 		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
 fi
 
-ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256"
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
@@ -117,11 +117,11 @@ src_configure() {
 
 	#go from slowest to fastest acceleration
 	local acce="None"
-	use sse2 && acce="SSE2"
-	use sse4_1 && acce="SSE4.1"
-	use avx_128_fma && acce="AVX_128_FMA"
-	use avx_256 && acce="AVX_256"
-	use avx2_256 && acce="AVX2_256"
+	use cpu_flags_x86_sse2 && acce="SSE2"
+	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+	use cpu_flags_x86_avx && acce="AVX_256"
+	use cpu_flags_x86_avx2 && acce="AVX2_256"
 
 	#to create man pages, build tree binaries are executed (bug #398437)
 	[[ ${CHOST} = *-darwin* ]] && \

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 87e0f0a..8a5c745 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -14,12 +14,6 @@
 	<flag name="tng">Enable new trajectory format - tng</flag>
 	<flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag>
     <!-- acceleration optimization flags -->
-    <flag name="sse4_1">Enable sse4.1 acceleration</flag>
-	<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
-	<flag name="avx_128_fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
-	<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
-	<flag name="avx_256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
-	<flag name="avx2_256">Enable 256bit avx2 (e.g. Intel Haswell)</flag>
     <flag name="offensive">Enable gromacs partly offensive quotes</flag>
     <flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
     <flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2015-03-08  0:06 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2015-03-08  0:06 UTC (permalink / raw
  To: gentoo-commits

commit:     622cca8abb489eef26c6142f5ed663d707fde6b9
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  8 00:06:35 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Mar  8 00:06:35 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=622cca8a

removed openmm build

Package-Manager: portage-2.2.14

 sci-chemistry/gromacs/ChangeLog               |  4 ++++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild | 27 ++-------------------------
 sci-chemistry/gromacs/metadata.xml            |  1 -
 3 files changed, 6 insertions(+), 26 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 5acf30f..1e2a646 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  08 Mar 2015; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  metadata.xml:
+  removed openmm build
+
   31 Jan 2015; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
   gromacs-5.0.9999.ebuild, gromacs-9999.ebuild, metadata.xml:
   Switch to CPU_FLAGS_X86 (bug #538268)

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index e8ac17c..3b8475a 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -44,7 +44,7 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
+IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -58,11 +58,7 @@ CDEPEND="
 	gsl? ( sci-libs/gsl )
 	lapack? ( virtual/lapack )
 	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	openmm? (
-		>=dev-util/nvidia-cuda-toolkit-4.2.9-r1
-		sci-libs/openmm[cuda,opencl]
-	)"
+	mpi? ( virtual/mpi )"
 DEPEND="${CDEPEND}
 	virtual/pkgconfig
 	${LIVE_DEPEND}
@@ -72,7 +68,6 @@ RDEPEND="${CDEPEND}"
 REQUIRED_USE="
 	|| ( single-precision double-precision )
 	cuda? ( single-precision )
-	openmm? ( single-precision )
 	mkl? ( !blas !fftw !lapack )"
 
 DOCS=( AUTHORS README )
@@ -191,15 +186,6 @@ src_configure() {
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
 			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
 		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		if [[ ${x} = float ]] && use openmm; then
-			einfo "Configuring for openmm build"
-			mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-				-DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON
-				-DOpenMM_PLUGIN_DIR="${EPREFIX}/usr/$(get_libdir)/plugins"
-				-DGMX_BINARY_SUFFIX="_openmm" -DGMX_LIBS_SUFFIX="_openmm" )
-			BUILD_DIR="${WORKDIR}/${P}_openmm" \
-				OPENMM_ROOT_DIR="${EPREFIX}/usr" cmake-utils_src_configure
-		fi
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF
@@ -214,11 +200,6 @@ src_compile() {
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
 			cmake-utils_src_compile
-		if [[ ${x} = float ]] && use openmm; then
-			einfo "Compiling for openmm build"
-			BUILD_DIR="${WORKDIR}/${P}_openmm"\
-				cmake-utils_src_compile mdrun
-		fi
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
@@ -237,10 +218,6 @@ src_install() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}" \
 			cmake-utils_src_install
-		if [[ ${x} = float ]] && use openmm; then
-			BUILD_DIR="${WORKDIR}/${P}_openmm" \
-				DESTDIR="${D}" cmake-utils_src_make install-mdrun
-		fi
 		#manual can only be build after gromacs was installed once in image
 		if use doc && [[ $PV = *9999*  && ! -d ${WORKDIR}/manual_build ]]; then
 			mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 8a5c745..30ce22a 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -15,7 +15,6 @@
 	<flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag>
     <!-- acceleration optimization flags -->
     <flag name="offensive">Enable gromacs partly offensive quotes</flag>
-    <flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
     <flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
   </use>
 </pkgmetadata>


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2015-06-16 17:53 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2015-06-16 17:53 UTC (permalink / raw
  To: gentoo-commits

commit:     e0920dd70e4d0bf9b701380ed28e30504b451f8e
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 16 17:53:10 2015 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Tue Jun 16 17:53:10 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e0920dd7

Drop unneeded hack

Package-Manager: portage-2.2.19

 sci-chemistry/gromacs/ChangeLog           | 3 +++
 sci-chemistry/gromacs/gromacs-9999.ebuild | 7 -------
 2 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 1e2a646..c7bcab9 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2015; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  Drop unneeded hack
+
   08 Mar 2015; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
   metadata.xml:
   removed openmm build

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index b50184a..9b8bf86 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -247,13 +247,6 @@ src_install() {
 	rm -f "${ED}"usr/bin/gmx-completion*
 	rm -f "${ED}"usr/bin/g_options*
 	rm -f "${ED}"usr/bin/GMXRC*
-	rm -f "${ED}"usr/lib*/libtng*.a
-
-	#workaround for libtng
-	if [[ $(get_libdir) != lib ]]; then
-		mv "${ED}"usr/lib/libtng* "${ED}usr/$(get_libdir)" || die
-		rmdir "${ED}"usr/lib || die
-	fi
 
 	readme.gentoo_create_doc
 }


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2015-06-21 13:01 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2015-06-21 13:01 UTC (permalink / raw
  To: gentoo-commits

commit:     c2f021e443ab214f718b402fd3dba6083a4acbb4
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 21 13:00:52 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Jun 21 13:00:52 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c2f021e4

sync with gx86

Package-Manager: portage-2.2.18

 sci-chemistry/gromacs/ChangeLog               | 3 +++
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild | 5 +++++
 2 files changed, 8 insertions(+)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index c7bcab9..87c6faf 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  21 Jun 2015; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+  sync with gx86
+
   16 Jun 2015; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
   Drop unneeded hack
 

diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
index f338fd5..10703bc 100644
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
@@ -252,6 +252,11 @@ src_install() {
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
 			cmake-utils_src_install
 	done
+
+	if use tng; then
+		insinto /usr/include/tng
+		doins src/external/tng_io/include/tng/*h
+	fi
 	# drop unneeded stuff
 	rm "${ED}"usr/bin/GMXRC* || die
 	#concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs)


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2015-08-20 23:28 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2015-08-20 23:28 UTC (permalink / raw
  To: gentoo-commits

commit:     f74483584e681fc56f71e67d3e0c151ca37c5331
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Aug 20 23:28:27 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Aug 20 23:28:27 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f7448358

sci-chemistry/gromacs: version bump

Package-Manager: portage-2.2.20.1

 sci-chemistry/gromacs/ChangeLog               |   5 +
 sci-chemistry/gromacs/gromacs-5.1.9999.ebuild | 269 ++++++++++++++++++++++++++
 2 files changed, 274 insertions(+)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 320428f..5248d93 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+*gromacs-5.1.9999 (20 Aug 2015)
+
+  20 Aug 2015; Christoph Junghans <ottxor@gentoo.org> +gromacs-5.1.9999.ebuild:
+  sci-chemistry/gromacs: version bump
+
   21 Jun 2015; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
   sync with gx86
 

diff --git a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild
new file mode 100644
index 0000000..031dfca
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild
@@ -0,0 +1,269 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
+
+if [[ $PV = *9999* ]]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+		https://gerrit.gromacs.org/gromacs.git
+		git://github.com/gromacs/gromacs.git
+		http://repo.or.cz/r/gromacs.git"
+	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}"
+	inherit git-r3
+	KEYWORDS=""
+else
+	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
+		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
+	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+fi
+
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+# see COPYING for details
+# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
+SLOT="0/${PV}"
+IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+	X? (
+		x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE
+		)
+	blas? ( virtual/blas )
+	boost? ( >=dev-libs/boost-1.55 )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+	fftw? ( sci-libs/fftw:3.0 )
+	lapack? ( virtual/lapack )
+	mkl? ( sci-libs/mkl )
+	mpi? ( virtual/mpi )
+	"
+DEPEND="${CDEPEND}
+	virtual/pkgconfig
+	doc? (
+		app-doc/doxygen
+		dev-texlive/texlive-latex
+		dev-texlive/texlive-latexextra
+		media-gfx/imagemagick
+	)"
+RDEPEND="${CDEPEND}"
+
+REQUIRED_USE="
+	|| ( single-precision double-precision )
+	cuda? ( single-precision )
+	mkl? ( !blas !fftw !lapack )"
+
+DOCS=( AUTHORS README )
+
+if [[ ${PV} != *9999 ]]; then
+	S="${WORKDIR}/${PN}-${PV/_/-}"
+fi
+
+pkg_pretend() {
+	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
+	use openmp && ! tc-has-openmp && \
+		die "Please switch to an openmp compatible compiler"
+}
+
+src_unpack() {
+	if [[ ${PV} != *9999 ]]; then
+		default
+	else
+		git-r3_src_unpack
+		if use test; then
+			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+			EGIT_BRANCH="${EGIT_BRANCH}" \
+			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
+				git-r3_src_unpack
+		fi
+	fi
+}
+
+src_prepare() {
+	#notes/todos
+	# -on apple: there is framework support
+
+	cmake-utils_src_prepare
+
+	use cuda && cuda_src_prepare
+
+	GMX_DIRS=""
+	use single-precision && GMX_DIRS+=" float"
+	use double-precision && GMX_DIRS+=" double"
+
+	if use test; then
+		for x in ${GMX_DIRS}; do
+			mkdir -p "${WORKDIR}/${P}_${x}" || die
+			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
+		done
+	fi
+
+	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
+}
+
+src_configure() {
+	local mycmakeargs_pre=( ) extra fft_opts=( )
+
+	#go from slowest to fastest acceleration
+	local acce="None"
+	use cpu_flags_x86_sse2 && acce="SSE2"
+	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+	use cpu_flags_x86_avx && acce="AVX_256"
+	use cpu_flags_x86_avx2 && acce="AVX2_256"
+
+	#to create man pages, build tree binaries are executed (bug #398437)
+	[[ ${CHOST} = *-darwin* ]] && \
+		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
+	if use fftw; then
+		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
+	elif use mkl && has_version "=sci-libs/mkl-10*"; then
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
+			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
+		)
+	elif use mkl; then
+		local bits=$(get_libdir)
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
+			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
+		)
+	else
+		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
+	fi
+
+	mycmakeargs_pre+=(
+		"${fft_opts[@]}"
+		$(cmake-utils_use X GMX_X11)
+		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
+		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
+		$(cmake-utils_use openmp GMX_OPENMP)
+		$(cmake-utils_use offensive GMX_COOL_QUOTES)
+		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
+		$(cmake-utils_use tng GMX_USE_TNG)
+		$(cmake-utils_use doc GMX_BUILD_MANUAL)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_SIMD="$acce"
+		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
+		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
+		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
+		-DBUILD_TESTING=OFF
+		-DGMX_BUILD_UNITTESTS=OFF
+		${extra}
+	)
+
+	for x in ${GMX_DIRS}; do
+		einfo "Configuring for ${x} precision"
+		local suffix=""
+		#if we build single and double - double is suffixed
+		use double-precision && use single-precision && \
+			[[ ${x} = "double" ]] && suffix="_d"
+		local p
+		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+		local cuda=( "-DGMX_GPU=OFF" )
+		[[ ${x} = "float" ]] && use cuda && \
+			cuda=( -DGMX_GPU=ON )
+		mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_MPI=OFF
+			$(cmake-utils_use threads GMX_THREAD_MPI)
+			"${cuda[@]}"
+			-DGMX_OPENMM=OFF
+			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
+			-DGMX_BINARY_SUFFIX="${suffix}"
+			-DGMX_LIBS_SUFFIX="${suffix}"
+			)
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
+		use mpi || continue
+		einfo "Configuring for ${x} precision with mpi"
+		mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_THREAD_MPI=OFF
+			-DGMX_MPI=ON ${cuda}
+			-DGMX_OPENMM=OFF
+			-DGMX_BUILD_MDRUN_ONLY=ON
+			-DBUILD_SHARED_LIBS=OFF
+			-DGMX_BUILD_MANUAL=OFF
+			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
+			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
+			)
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		einfo "Compiling for ${x} precision"
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile
+		# not 100% necessary for rel ebuilds as available from website
+		if use doc; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}"\
+				cmake-utils_src_compile manual
+		fi
+		use mpi || continue
+		einfo "Compiling for ${x} precision with mpi"
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+			cmake-utils_src_compile
+	done
+}
+
+src_test() {
+	for x in ${GMX_DIRS}; do
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_make check
+	done
+}
+
+src_install() {
+	for x in ${GMX_DIRS}; do
+		BUILD_DIR="${WORKDIR}/${P}_${x}" \
+			cmake-utils_src_install
+		if use doc; then
+			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+		fi
+		use mpi || continue
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+			cmake-utils_src_install
+	done
+
+	if use tng; then
+		insinto /usr/include/tng
+		doins src/external/tng_io/include/tng/*h
+	fi
+	# drop unneeded stuff
+	rm "${ED}"usr/bin/GMXRC* || die
+	for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
+		local n=${x##*/gmx-completion-}
+		n="${n%.bash}"
+		cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
+		newbashcomp "${T}"/"${n}" "${n}"
+	done
+	rm "${ED}"usr/bin/gmx-completion*.bash || die
+	readme.gentoo_create_doc
+}
+
+pkg_postinst() {
+	einfo
+	einfo  "Please read and cite:"
+	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+	einfo  "http://dx.doi.org/10.1021/ct700301q"
+	einfo
+	readme.gentoo_print_elog
+}


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2015-12-15  0:24 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2015-12-15  0:24 UTC (permalink / raw
  To: gentoo-commits

commit:     98e18f884c5eb090079fa831504e2859c7023300
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Dec 15 00:24:28 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Dec 15 00:24:28 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=98e18f88

sci-chemistry/gromacs: merge change from 5.1.9999

Package-Manager: portage-2.2.25

 sci-chemistry/gromacs/ChangeLog           |  3 +++
 sci-chemistry/gromacs/gromacs-9999.ebuild | 42 ++++++++++++++++++-------------
 2 files changed, 28 insertions(+), 17 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 5248d93..2caa2a8 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  15 Dec 2015; Christoph Junghans <ottxor@gentoo.org> gromacs-9999.ebuild:
+  sci-chemistry/gromacs: merge change from 5.1.9999
+
 *gromacs-5.1.9999 (20 Aug 2015)
 
   20 Aug 2015; Christoph Junghans <ottxor@gentoo.org> +gromacs-5.1.9999.ebuild:

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 933074f..031dfca 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -4,8 +4,6 @@
 
 EAPI=5
 
-TEST_PV="5.0-rc1"
-
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
 inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
@@ -15,11 +13,13 @@ if [[ $PV = *9999* ]]; then
 		https://gerrit.gromacs.org/gromacs.git
 		git://github.com/gromacs/gromacs.git
 		http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="master"
+	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}"
 	inherit git-r3
+	KEYWORDS=""
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
+		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
+	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
@@ -32,8 +32,7 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-KEYWORDS=""
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -83,8 +82,8 @@ src_unpack() {
 		git-r3_src_unpack
 		if use test; then
 			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
-			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
+			EGIT_BRANCH="${EGIT_BRANCH}" \
+			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
 				git-r3_src_unpack
 		fi
 	fi
@@ -154,7 +153,6 @@ src_configure() {
 		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
 		$(cmake-utils_use tng GMX_USE_TNG)
 		$(cmake-utils_use doc GMX_BUILD_MANUAL)
-		$(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
 		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
@@ -188,6 +186,8 @@ src_configure() {
 			-DGMX_LIBS_SUFFIX="${suffix}"
 			)
 		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
 		mycmakeargs=(
@@ -202,6 +202,8 @@ src_configure() {
 			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
 			)
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
 	done
 }
 
@@ -210,9 +212,7 @@ src_compile() {
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
 			cmake-utils_src_compile
-		# generate bash completion
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile completion
+		# not 100% necessary for rel ebuilds as available from website
 		if use doc; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}"\
 				cmake-utils_src_compile manual
@@ -238,16 +238,24 @@ src_install() {
 		if use doc; then
 			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
 		fi
-		newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs
 		use mpi || continue
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
 			cmake-utils_src_install
 	done
-	# drop unneeded stuff
-	rm -f "${ED}"usr/bin/gmx-completion*
-	rm -f "${ED}"usr/bin/g_options*
-	rm -f "${ED}"usr/bin/GMXRC*
 
+	if use tng; then
+		insinto /usr/include/tng
+		doins src/external/tng_io/include/tng/*h
+	fi
+	# drop unneeded stuff
+	rm "${ED}"usr/bin/GMXRC* || die
+	for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
+		local n=${x##*/gmx-completion-}
+		n="${n%.bash}"
+		cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
+		newbashcomp "${T}"/"${n}" "${n}"
+	done
+	rm "${ED}"usr/bin/gmx-completion*.bash || die
 	readme.gentoo_create_doc
 }
 


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2016-02-11  9:11 Justin Lecher
  0 siblings, 0 replies; 102+ messages in thread
From: Justin Lecher @ 2016-02-11  9:11 UTC (permalink / raw
  To: gentoo-commits

commit:     8bea49d050711122ab0bc18bfa229d6ac4e0ce8a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Feb 11 09:09:00 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Feb 11 09:09:00 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8bea49d0

sci-chemistry/gromacs: Move to nextgen readme.gentoo eclass

* Bump EAPI to 6

Package-Manager: portage-2.2.27
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild | 6 +++---
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild | 6 +++---
 sci-chemistry/gromacs/gromacs-5.1.9999.ebuild | 6 +++---
 sci-chemistry/gromacs/gromacs-9999.ebuild     | 6 +++---
 sci-chemistry/gromacs/metadata.xml            | 8 ++++----
 5 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index b5b75f0..b21624d 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -1,15 +1,15 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
 TEST_PV="4.6.6"
 MANUAL_PV="4.6.6"
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs
 
 if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git

diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
index b5d7896..e7548ff 100644
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
@@ -1,12 +1,12 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs
 
 if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git

diff --git a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild
index 031dfca..4fb8aae 100644
--- a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild
@@ -1,12 +1,12 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs
 
 if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 031dfca..4fb8aae 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -1,12 +1,12 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs
 
 if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 7b53e54..613f221 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -12,10 +12,10 @@
   <use>
     <flag name="cuda">Enable cuda non-bonded kernels</flag>
     <flag name="double-precision">More precise calculations at the expense of speed</flag>
-	<flag name="single-precision">Single precision version of gromacs (default)</flag>
-	<flag name="boost">Enable external boost library</flag>
-	<flag name="tng">Enable new trajectory format - tng</flag>
-	<flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag>
+    <flag name="single-precision">Single precision version of gromacs (default)</flag>
+    <flag name="boost">Enable external boost library</flag>
+    <flag name="tng">Enable new trajectory format - tng</flag>
+    <flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag>
     <!-- acceleration optimization flags -->
     <flag name="offensive">Enable gromacs partly offensive quotes</flag>
     <flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2016-03-14  2:17 Christoph Junghans
  0 siblings, 0 replies; 102+ messages in thread
From: Christoph Junghans @ 2016-03-14  2:17 UTC (permalink / raw
  To: gentoo-commits

commit:     1d5ff96f4e9214493f79ec1c759f75aee4995ab1
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Mar 14 02:17:09 2016 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Mar 14 02:17:09 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1d5ff96f

sci-chemistry/gromacs: fied EAPI=6 build

Package-Manager: portage-2.2.26

 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild | 14 +++++++-------
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild | 20 ++++++++++----------
 sci-chemistry/gromacs/gromacs-5.1.9999.ebuild | 18 +++++++++---------
 sci-chemistry/gromacs/gromacs-9999.ebuild     | 18 +++++++++---------
 4 files changed, 35 insertions(+), 35 deletions(-)

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index b21624d..e00c4f9 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -154,12 +154,12 @@ src_configure() {
 
 	mycmakeargs_pre+=(
 		"${fft_opts[@]}"
-		$(cmake-utils_use X GMX_X11)
-		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use gsl GMX_GSL)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use openmp GMX_OPENMP)
-		$(cmake-utils_use offensive GMX_COOL_QUOTES)
+		-DGMX_X11=$(usex X)
+		-DGMX_EXTERNAL_BLAS=$(usex blas)
+		-DGMX_GSL=$(usex gsl)
+		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
+		-DGMX_OPENMP=$(usex openmp)
+		-DGMX_COOL_QUOTES=$(usex offensive)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_ACCELERATION="$acce"
 		-DGMXLIB="$(get_libdir)"
@@ -182,7 +182,7 @@ src_configure() {
 		[[ ${x} = "float" ]] && use cuda && \
 			cuda=( -DGMX_GPU=ON )
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-			$(cmake-utils_use threads GMX_THREAD_MPI) "${cuda[@]}" -DGMX_OPENMM=OFF
+			-DGMX_THREAD_MPI=$(usex threads) "${cuda[@]}" -DGMX_OPENMM=OFF
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
 			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
 		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure

diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
index e7548ff..5d1717e 100644
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
@@ -145,15 +145,15 @@ src_configure() {
 
 	mycmakeargs_pre+=(
 		"${fft_opts[@]}"
-		$(cmake-utils_use X GMX_X11)
-		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use openmp GMX_OPENMP)
-		$(cmake-utils_use offensive GMX_COOL_QUOTES)
-		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
-		$(cmake-utils_use tng GMX_USE_TNG)
-		$(cmake-utils_use doc GMX_BUILD_MANUAL)
-		$(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES)
+		-DGMX_X11=$(usex X)
+		-DGMX_EXTERNAL_BLAS=$(usex blas)
+		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
+		-DGMX_OPENMP=$(usex openmp)
+		-DGMX_COOL_QUOTES=$(usex offensive)
+		-DGMX_EXTERNAL_BOOST=$(usex boost)
+		-DGMX_USE_TNG=$(usex tng)
+		-DGMX_BUILD_MANUAL=$(usex doc)
+		-DGMX_SYMLINK_OLD_BINARY_NAMES=$(usex make-symlinks)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
 		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
@@ -179,7 +179,7 @@ src_configure() {
 		mycmakeargs=(
 			${mycmakeargs_pre[@]} ${p}
 			-DGMX_MPI=OFF
-			$(cmake-utils_use threads GMX_THREAD_MPI)
+			-DGMX_THREAD_MPI=$(usex threads)
 			"${cuda[@]}"
 			-DGMX_OPENMM=OFF
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"

diff --git a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild
index 4fb8aae..9711c22 100644
--- a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild
@@ -145,14 +145,14 @@ src_configure() {
 
 	mycmakeargs_pre+=(
 		"${fft_opts[@]}"
-		$(cmake-utils_use X GMX_X11)
-		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use openmp GMX_OPENMP)
-		$(cmake-utils_use offensive GMX_COOL_QUOTES)
-		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
-		$(cmake-utils_use tng GMX_USE_TNG)
-		$(cmake-utils_use doc GMX_BUILD_MANUAL)
+		-DGMX_X11=$(usex X)
+		-DGMX_EXTERNAL_BLAS=$(usex blas)
+		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
+		-DGMX_OPENMP=$(usex openmp)
+		-DGMX_COOL_QUOTES=$(usex offensive)
+		-DGMX_EXTERNAL_BOOST=$(usex boost)
+		-DGMX_USE_TNG=$(usex tng)
+		-DGMX_BUILD_MANUAL=$(usex doc)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
 		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
@@ -178,7 +178,7 @@ src_configure() {
 		mycmakeargs=(
 			${mycmakeargs_pre[@]} ${p}
 			-DGMX_MPI=OFF
-			$(cmake-utils_use threads GMX_THREAD_MPI)
+			-DGMX_THREAD_MPI=$(usex threads)
 			"${cuda[@]}"
 			-DGMX_OPENMM=OFF
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 4fb8aae..9711c22 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -145,14 +145,14 @@ src_configure() {
 
 	mycmakeargs_pre+=(
 		"${fft_opts[@]}"
-		$(cmake-utils_use X GMX_X11)
-		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use openmp GMX_OPENMP)
-		$(cmake-utils_use offensive GMX_COOL_QUOTES)
-		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
-		$(cmake-utils_use tng GMX_USE_TNG)
-		$(cmake-utils_use doc GMX_BUILD_MANUAL)
+		-DGMX_X11=$(usex X)
+		-DGMX_EXTERNAL_BLAS=$(usex blas)
+		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
+		-DGMX_OPENMP=$(usex openmp)
+		-DGMX_COOL_QUOTES=$(usex offensive)
+		-DGMX_EXTERNAL_BOOST=$(usex boost)
+		-DGMX_USE_TNG=$(usex tng)
+		-DGMX_BUILD_MANUAL=$(usex doc)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
 		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
@@ -178,7 +178,7 @@ src_configure() {
 		mycmakeargs=(
 			${mycmakeargs_pre[@]} ${p}
 			-DGMX_MPI=OFF
-			$(cmake-utils_use threads GMX_THREAD_MPI)
+			-DGMX_THREAD_MPI=$(usex threads)
 			"${cuda[@]}"
 			-DGMX_OPENMM=OFF
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2016-07-11 18:41 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2016-07-11 18:41 UTC (permalink / raw
  To: gentoo-commits

commit:     074a0765dd244f6e507328aafe52bbf9d2c8ad8c
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Mon Jul 11 18:40:35 2016 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Mon Jul 11 18:40:35 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=074a0765

sci-chemistry/gromacs: Add live version for 2016 release

Package-Manager: portage-2.3.0

 .../gromacs/{gromacs-9999.ebuild => gromacs-2016.9999.ebuild}          | 3 +--
 sci-chemistry/gromacs/gromacs-9999.ebuild                              | 3 +--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
similarity index 97%
copy from sci-chemistry/gromacs/gromacs-9999.ebuild
copy to sci-chemistry/gromacs/gromacs-2016.9999.ebuild
index 9711c22..b30ff55 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
@@ -32,7 +32,7 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -41,7 +41,6 @@ CDEPEND="
 		x11-libs/libICE
 		)
 	blas? ( virtual/blas )
-	boost? ( >=dev-libs/boost-1.55 )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
 	fftw? ( sci-libs/fftw:3.0 )
 	lapack? ( virtual/lapack )

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 9711c22..b30ff55 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -32,7 +32,7 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -41,7 +41,6 @@ CDEPEND="
 		x11-libs/libICE
 		)
 	blas? ( virtual/blas )
-	boost? ( >=dev-libs/boost-1.55 )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
 	fftw? ( sci-libs/fftw:3.0 )
 	lapack? ( virtual/lapack )


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2016-07-11 18:41 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2016-07-11 18:41 UTC (permalink / raw
  To: gentoo-commits

commit:     1074d459b232e4d62bb1c31ae05246d763f13073
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Mon Jul 11 18:41:09 2016 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Mon Jul 11 18:41:09 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1074d459

sci-chemistry/gromacs: Add myself as maintainer

Package-Manager: portage-2.3.0

 sci-chemistry/gromacs/metadata.xml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 613f221..0c7b107 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -5,6 +5,10 @@
     <email>ottxor@gentoo.org</email>
     <name>Christoph Junghans</name>
   </maintainer>
+  <maintainer type="person">
+	  <email>alexxy@gentoo.org</email>
+	  <name>Alexey Shvetsov</name>
+  </maintainer>
   <maintainer type="project">
     <email>sci-chemistry@gentoo.org</email>
     <name>Gentoo Chemistry Project</name>


^ permalink raw reply related	[flat|nested] 102+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/
@ 2016-07-11 19:40 Alexey Shvetsov
  0 siblings, 0 replies; 102+ messages in thread
From: Alexey Shvetsov @ 2016-07-11 19:40 UTC (permalink / raw
  To: gentoo-commits

commit:     e505c9758afd89769db26e1c46adce0215a0daea
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Mon Jul 11 19:40:06 2016 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Mon Jul 11 19:40:06 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e505c975

sci-chemistry/gromacs: Add 2016 RC1

Package-Manager: portage-2.3.0

 sci-chemistry/gromacs/gromacs-2016.9999.ebuild                 | 10 ++++------
 .../{gromacs-2016.9999.ebuild => gromacs-2016_rc1.ebuild}      | 10 ++++------
 sci-chemistry/gromacs/gromacs-9999.ebuild                      | 10 ++++------
 sci-chemistry/gromacs/metadata.xml                             |  3 ++-
 4 files changed, 14 insertions(+), 19 deletions(-)

diff --git a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
index b30ff55..1ca0343 100644
--- a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
@@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then
 	KEYWORDS=""
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
+		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
 	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
@@ -32,7 +32,7 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -43,6 +43,7 @@ CDEPEND="
 	blas? ( virtual/blas )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
 	fftw? ( sci-libs/fftw:3.0 )
+	hwloc? ( sys-apps/hwloc )
 	lapack? ( virtual/lapack )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
@@ -149,15 +150,13 @@ src_configure() {
 		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
 		-DGMX_OPENMP=$(usex openmp)
 		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_EXTERNAL_BOOST=$(usex boost)
 		-DGMX_USE_TNG=$(usex tng)
 		-DGMX_BUILD_MANUAL=$(usex doc)
+		-DGMX_HWLOC=$(usex hwloc)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
 		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
 		-DBUILD_TESTING=OFF
 		-DGMX_BUILD_UNITTESTS=OFF
 		${extra}
@@ -179,7 +178,6 @@ src_configure() {
 			-DGMX_MPI=OFF
 			-DGMX_THREAD_MPI=$(usex threads)
 			"${cuda[@]}"
-			-DGMX_OPENMM=OFF
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
 			-DGMX_BINARY_SUFFIX="${suffix}"
 			-DGMX_LIBS_SUFFIX="${suffix}"

diff --git a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild b/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild
similarity index 96%
copy from sci-chemistry/gromacs/gromacs-2016.9999.ebuild
copy to sci-chemistry/gromacs/gromacs-2016_rc1.ebuild
index b30ff55..1ca0343 100644
--- a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild
@@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then
 	KEYWORDS=""
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
+		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
 	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
@@ -32,7 +32,7 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -43,6 +43,7 @@ CDEPEND="
 	blas? ( virtual/blas )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
 	fftw? ( sci-libs/fftw:3.0 )
+	hwloc? ( sys-apps/hwloc )
 	lapack? ( virtual/lapack )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
@@ -149,15 +150,13 @@ src_configure() {
 		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
 		-DGMX_OPENMP=$(usex openmp)
 		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_EXTERNAL_BOOST=$(usex boost)
 		-DGMX_USE_TNG=$(usex tng)
 		-DGMX_BUILD_MANUAL=$(usex doc)
+		-DGMX_HWLOC=$(usex hwloc)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
 		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
 		-DBUILD_TESTING=OFF
 		-DGMX_BUILD_UNITTESTS=OFF
 		${extra}
@@ -179,7 +178,6 @@ src_configure() {
 			-DGMX_MPI=OFF
 			-DGMX_THREAD_MPI=$(usex threads)
 			"${cuda[@]}"
-			-DGMX_OPENMM=OFF
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
 			-DGMX_BINARY_SUFFIX="${suffix}"
 			-DGMX_LIBS_SUFFIX="${suffix}"

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index b30ff55..1ca0343 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then
 	KEYWORDS=""
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
+		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
 	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
@@ -32,7 +32,7 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -43,6 +43,7 @@ CDEPEND="
 	blas? ( virtual/blas )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
 	fftw? ( sci-libs/fftw:3.0 )
+	hwloc? ( sys-apps/hwloc )
 	lapack? ( virtual/lapack )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
@@ -149,15 +150,13 @@ src_configure() {
 		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
 		-DGMX_OPENMP=$(usex openmp)
 		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_EXTERNAL_BOOST=$(usex boost)
 		-DGMX_USE_TNG=$(usex tng)
 		-DGMX_BUILD_MANUAL=$(usex doc)
+		-DGMX_HWLOC=$(usex hwloc)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
 		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
 		-DBUILD_TESTING=OFF
 		-DGMX_BUILD_UNITTESTS=OFF
 		${extra}
@@ -179,7 +178,6 @@ src_configure() {
 			-DGMX_MPI=OFF
 			-DGMX_THREAD_MPI=$(usex threads)
 			"${cuda[@]}"
-			-DGMX_OPENMM=OFF
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
 			-DGMX_BINARY_SUFFIX="${suffix}"
 			-DGMX_LIBS_SUFFIX="${suffix}"

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 0c7b107..e98cd51 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -17,7 +17,8 @@
     <flag name="cuda">Enable cuda non-bonded kernels</flag>
     <flag name="double-precision">More precise calculations at the expense of speed</flag>
     <flag name="single-precision">Single precision version of gromacs (default)</flag>
-    <flag name="boost">Enable external boost library</flag>
+	<flag name="boost">Enable external boost library</flag>
+	<flag name="hwloc">Enable HWLoc lib support</flag>
     <flag name="tng">Enable new trajectory format - tng</flag>
     <flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag>
     <!-- acceleration optimization flags -->


^ permalink raw reply related	[flat|nested] 102+ messages in thread

end of thread, other threads:[~2016-07-11 19:40 UTC | newest]

Thread overview: 102+ messages (download: mbox.gz follow: Atom feed
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2012-11-27  5:43 [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/ Christoph Junghans
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2016-07-11 19:40 Alexey Shvetsov
2016-07-11 18:41 Alexey Shvetsov
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2014-04-08  8:14 Alexey Shvetsov
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2014-02-16 23:04 Christoph Junghans
2014-02-05 12:09 Alexey Shvetsov
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2014-01-28  7:55 Justin Lecher
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2013-12-07 16:22 Justin Lecher
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2013-12-03  4:47 Alexey Shvetsov
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2013-12-03  4:00 Alexey Shvetsov
2013-06-02 17:40 Christoph Junghans
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2013-03-10  1:04 Christoph Junghans
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2013-02-12  4:21 Christoph Junghans
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2013-01-28  4:48 Christoph Junghans
2013-01-21 20:30 Christoph Junghans
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2013-01-21 14:33 Alexey Shvetsov
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2013-01-18  2:58 Christoph Junghans
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2012-12-30 23:31 Christoph Junghans
2012-12-29 22:59 Christoph Junghans
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2012-12-26 22:36 Christoph Junghans
2012-12-26 18:58 Christoph Junghans
2012-12-26  3:59 Christoph Junghans
2012-12-26  1:03 Christoph Junghans
2012-12-22 19:46 Christoph Junghans
2012-12-20  5:51 Christoph Junghans
2012-12-08 22:15 Christoph Junghans
2012-11-30 21:18 Christoph Junghans
2012-11-19  0:48 Christoph Junghans
2012-10-04 14:39 Christoph Junghans
2012-10-03 14:54 Christoph Junghans
2012-08-09  5:15 Christoph Junghans
2012-07-25  1:25 Christoph Junghans
2012-06-19 14:10 Alexey Shvetsov
2012-06-11  2:15 Christoph Junghans
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2012-04-19 19:43 Alexey Shvetsov
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2012-03-04  1:23 Christoph Junghans
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2012-02-12  1:34 Christoph Junghans
2012-02-05 21:31 Christoph Junghans
2012-02-05  0:30 Christoph Junghans
2011-09-28  7:32 Christoph Junghans
2011-09-10 14:52 Christoph Junghans
2011-07-18 18:30 Christoph Junghans
2011-06-25 17:22 Justin Lecher
2011-06-25 12:58 Christoph Junghans
2011-06-21 20:26 Christoph Junghans
2011-06-21 11:54 Justin Lecher
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2011-05-01 15:13 Christoph Junghans
2011-04-10 12:28 Christoph Junghans
2011-03-17 23:18 Alexey Shvetsov
2011-03-08 20:59 Christoph Junghans
2011-03-07 12:01 Justin Lecher
2011-03-01 15:31 Alexey Shvetsov
2011-02-19 14:50 Christoph Junghans
2011-02-17 22:29 Christoph Junghans
2011-02-14 21:00 Christoph Junghans
2011-02-13 17:27 Christoph Junghans

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