* [gentoo-commits] proj/sci:master commit in: sci-chemistry/nwchem/files/, sci-chemistry/nwchem/
@ 2012-12-02 1:34 Alexey Shvetsov
0 siblings, 0 replies; 5+ messages in thread
From: Alexey Shvetsov @ 2012-12-02 1:34 UTC (permalink / raw
To: gentoo-commits
commit: e0d920e4f7bfd13255db486199e459d5243ba38e
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 2 01:32:22 2012 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Sun Dec 2 01:32:22 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e0d920e4
[sci-chemistry/nwchem] Initial import from bug #393139. Mpi still doesnt work
Package-Manager: portage-2.2.0_alpha143
RepoMan-Options: --force
---
sci-chemistry/nwchem/ChangeLog | 12 ++
.../files/nwchem-6.1.1-adjust-dir-length.patch | 22 +++
.../nwchem/files/nwchem-6.1.1-makefile.patch | 14 ++
.../nwchem/files/nwchem-6.1.1-nwchemrc.patch | 13 ++
.../files/nwchem-6.1.1-python_makefile.patch | 12 ++
sci-chemistry/nwchem/metadata.xml | 12 ++
sci-chemistry/nwchem/nwchem-6.1.1.ebuild | 137 ++++++++++++++++++++
7 files changed, 222 insertions(+), 0 deletions(-)
diff --git a/sci-chemistry/nwchem/ChangeLog b/sci-chemistry/nwchem/ChangeLog
new file mode 100644
index 0000000..89671d8
--- /dev/null
+++ b/sci-chemistry/nwchem/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-chemistry/nwchem
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*nwchem-6.1.1 (02 Dec 2012)
+
+ 02 Dec 2012; Alexey Shvetsov <alexxy@gentoo.org>
+ +files/nwchem-6.1.1-adjust-dir-length.patch,
+ +files/nwchem-6.1.1-makefile.patch, +files/nwchem-6.1.1-nwchemrc.patch,
+ +files/nwchem-6.1.1-python_makefile.patch, +metadata.xml,
+ +nwchem-6.1.1.ebuild:
+ [sci-chemistry/nwchem] Initial import from bug #393139. Mpi still doesnt work
diff --git a/sci-chemistry/nwchem/files/nwchem-6.1.1-adjust-dir-length.patch b/sci-chemistry/nwchem/files/nwchem-6.1.1-adjust-dir-length.patch
new file mode 100644
index 0000000..859c764
--- /dev/null
+++ b/sci-chemistry/nwchem/files/nwchem-6.1.1-adjust-dir-length.patch
@@ -0,0 +1,22 @@
+--- src/nwpw/libraryps/GNUmakefile 2012-01-26 08:24:05.189490945 +0100
++++ src/nwpw/libraryps/GNUmakefile 2012-01-26 08:24:16.499490923 +0100
+@@ -10,7 +10,7 @@
+
+ USES_BLAS =
+
+- LONGNWTOP = $(shell if [ `echo $(SRCDIR) |wc -m` -gt 64 ]; then echo "Y"; fi )
++ LONGNWTOP = $(shell if [ `echo $(SRCDIR) |wc -m` -gt 80 ]; then echo "Y"; fi )
+ ifeq ($(LONGNWTOP),Y)
+ errorlongpwd:
+ @echo " "
+--- src/basis/GNUmakefile 2012-01-26 08:25:03.999490829 +0100
++++ src/basis/GNUmakefile 2012-01-26 08:25:15.549490805 +0100
+@@ -34,7 +34,7 @@
+ ########################################################
+
+ LIB_TARGETS = testbasis testbasis.o libcheck
+- LONGNWTOP = $(shell if [ `echo $(SRCDIR) |wc -m` -gt 64 ]; then echo "Y"; fi )
++ LONGNWTOP = $(shell if [ `echo $(SRCDIR) |wc -m` -gt 80 ]; then echo "Y"; fi )
+ ifeq ($(LONGNWTOP),Y)
+ errorlongpwd:
+ @echo " "
diff --git a/sci-chemistry/nwchem/files/nwchem-6.1.1-makefile.patch b/sci-chemistry/nwchem/files/nwchem-6.1.1-makefile.patch
new file mode 100644
index 0000000..a74d887
--- /dev/null
+++ b/sci-chemistry/nwchem/files/nwchem-6.1.1-makefile.patch
@@ -0,0 +1,14 @@
+--- src/tools/global/GNUmakefile 2011-12-03 14:34:01.000000000 +0100
++++ src/tools/global/GNUmakefile 2011-12-03 14:37:40.000000000 +0100
+@@ -68,7 +68,10 @@
+ $(LIBRARY):
+ (echo TARGET is $(TARGET); cd ./src; $(MAKE) || exit 1;)
+
+-$(TESTS) %.x: $(LIBRARY)
++%.x: $(LIBRARY)
++ (cd ./testing; $(MAKE) $@ || exit 1;)
++
++$(TESTS): $(LIBRARY)
+ (cd ./testing; $(MAKE) $@ || exit 1;)
+
+ all: $(TESTS)
diff --git a/sci-chemistry/nwchem/files/nwchem-6.1.1-nwchemrc.patch b/sci-chemistry/nwchem/files/nwchem-6.1.1-nwchemrc.patch
new file mode 100644
index 0000000..4e1e0af
--- /dev/null
+++ b/sci-chemistry/nwchem/files/nwchem-6.1.1-nwchemrc.patch
@@ -0,0 +1,13 @@
+--- nwchemrc 2011-12-04 11:29:37.000000000 +0100
++++ nwchemrc 2011-12-04 11:29:26.000000000 +0100
+@@ -0,0 +1,10 @@
++nwchem_basis_library /usr/share/NWChem/basis/libraries/
++nwchem_nwpw_library /usr/share/NWChem/nwpw/libraryps/
++ffield amber
++amber_1 /usr/share/NWChem/data/amber_s/
++amber_2 /usr/share/NWChem/data/amber_q/
++amber_3 /usr/share/NWChem/data/amber_x/
++amber_4 /usr/share/NWChem/data/amber_u/
++spce /usr/share/NWChem/data/solvents/spce.rst
++charmm_s /usr/share/NWChem/data/charmm_s/
++charmm_x /usr/share/NWChem/data/charmm_x/
diff --git a/sci-chemistry/nwchem/files/nwchem-6.1.1-python_makefile.patch b/sci-chemistry/nwchem/files/nwchem-6.1.1-python_makefile.patch
new file mode 100644
index 0000000..7753d8f
--- /dev/null
+++ b/sci-chemistry/nwchem/files/nwchem-6.1.1-python_makefile.patch
@@ -0,0 +1,12 @@
+--- src/config/makefile.h 2011-12-04 12:00:52.000000000 +0100
++++ src/config/makefile.h 2011-12-04 12:01:56.000000000 +0100
+@@ -2133,7 +2133,7 @@
+ #
+ ifdef USE_PYTHON64
+- CORE_LIBS += $(PYTHONHOME)/lib64/python$(PYTHONVERSION)/config/libpython$(PYTHONVERSION).a
++ CORE_LIBS += $(PYTHONHOME)/lib/libpython$(PYTHONVERSION).a
+ else
+- CORE_LIBS += $(PYTHONHOME)/lib/python$(PYTHONVERSION)/config/libpython$(PYTHONVERSION).a
++ CORE_LIBS += $(PYTHONHOME)/lib/libpython$(PYTHONVERSION).a
+ endif
+ endif
diff --git a/sci-chemistry/nwchem/metadata.xml b/sci-chemistry/nwchem/metadata.xml
new file mode 100644
index 0000000..7d880f8
--- /dev/null
+++ b/sci-chemistry/nwchem/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-chemistry</herd>
+ <maintainer>
+ <email>alexxy@gentoo.org</email>
+ <name>Alexey Shvetsov</name>
+ </maintainer>
+ <use>
+ <flag name="nwchem-tests">Install qa tests data</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-chemistry/nwchem/nwchem-6.1.1.ebuild b/sci-chemistry/nwchem/nwchem-6.1.1.ebuild
new file mode 100644
index 0000000..51a5c62
--- /dev/null
+++ b/sci-chemistry/nwchem/nwchem-6.1.1.ebuild
@@ -0,0 +1,137 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils fortran-2 multilib python toolchain-funcs
+
+DESCRIPTION="NWChem: Delivering High-Performance Computational Chemistry to Science"
+HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page"
+DATE="2012-06-27"
+SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV}-src.${DATE}.tar.gz"
+LICENSE="ECL-2.0"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="mpi examples nwchem-tests python"
+
+RDEPEND="
+ sys-fs/sysfsutils
+"
+
+DEPEND="${RDEPEND}
+ virtual/fortran
+ mpi? ( virtual/mpi[fortran] )
+"
+
+S="${WORKDIR}/${P}-src"
+
+pkg_setup() {
+ fortran-2_pkg_setup
+ python_set_active_version 2
+ python_pkg_setup
+}
+
+src_prepare() {
+ epatch "${FILESDIR}"/nwchem-${PV}-makefile.patch
+ epatch "${FILESDIR}"/nwchem-${PV}-nwchemrc.patch
+ epatch "${FILESDIR}"/nwchem-${PV}-adjust-dir-length.patch
+ if use python ; then
+ epatch "${FILESDIR}"/nwchem-${PV}-python_makefile.patch
+ fi
+ sed -e "s:DBASIS_LIBRARY=\"'\$(SRCDIR)'\":DBASIS_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
+ -i src/basis/MakeFile \
+ -i src/basis/GNUmakefile || die
+ sed -e "s:DNWPW_LIBRARY=\"'\$(SRCDIR)'\":DNWPW_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
+ -i src/nwpw/libraryps/GNUmakefile || die
+ sed -e "s:-DCOMPILATION_DIR=\"'\$(TOPDIR)'\":-DCOMPILATION_DIR=\"''\":g" \
+ -i src/GNUmakefile \
+ -i src/MakeFile
+
+ if [[ $(tc-getFC) == *-*-*-*-gfortran ]]; then
+ sed -e "s:ifneq (\$(FC),gfortran):ifneq (\$(FC),$(tc-getFC)):g" \
+ -e "s:ifeq (\$(FC),gfortran):ifeq (\$(FC),$(tc-getFC)):g" \
+ -i src/config/makefile.h || die
+ fi
+}
+
+src_compile() {
+ export USE_SUBGROUPS=yes
+ if use mpi ; then
+ export MSG_COMMS=MPI
+ export USE_MPI=yes
+ export MPI_LOC=/usr
+ export MPI_INCLUDE=$MPI_LOC/include
+ export MPI_LIB=$MPI_LOC/$(get_libdir)
+ export LIBMPI="-lfmpich -lmpich -lpthread" # fix mpi linking!
+ fi
+ if [ "$ARCH" = "amd64" ]; then
+ export NWCHEM_TARGET=LINUX64
+ elif [ "$ARCH" = "ia64" ]; then
+ export NWCHEM_TARGET=LINUX64
+ elif [ "$ARCH" = "x86" ]; then
+ export NWCHEM_TARGET=LINUX
+ elif [ "$ARCH" = "ppc" ]; then
+ export NWCHEM_TARGET=LINUX
+ else
+ die "Unknown architecture"
+ fi
+ if use python ; then
+ if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ]; then
+ export USE_PYTHON64=yes
+ fi
+ export PYTHONHOME=/usr
+ export PYTHONVERSION=$(eselect python show|awk -Fpython '{ print $2 }')
+ export PYTHONPATH="./:${S}/contrib/python/"
+ export NWCHEM_MODULES="all python"
+ else
+ export NWCHEM_MODULES="all"
+ fi
+
+ cd src
+ emake \
+ DIAG=PAR \
+ FC=$(tc-getFC) \
+ CC=$(tc-getCC) \
+ CXX=$(tc-getCXX) \
+ NWCHEM_TOP="${S}" \
+ NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem" \
+ || die "Compilation failed"
+}
+
+src_install() {
+ dobin bin/${NWCHEM_TARGET}/nwchem || die "Failed to install binary"
+
+ dodir /usr/share/NWChem/basis || die "Failed to create data directory"
+ insinto /usr/share/NWChem/basis/libraries
+ doins -r src/basis/libraries/* || die "Failed to install basis library"
+ dodir /usr/share/NWChem/data || die "Failed to create data directory"
+ insinto /usr/share/NWChem/data
+ doins -r src/data/* || die "Failed to install data"
+ dodir /usr/share/NWChem/nwpw || die "Failed to create data directory"
+ insinto /usr/share/NWChem/nwpw/libraryps
+ doins -r src/nwpw/libraryps/* || die "Failed to install data"
+
+ insinto /etc
+ doins nwchemrc
+
+ if use examples ; then
+ dodir /usr/share/NWChem/examples || die "Failed to create examples directory"
+ insinto /usr/share/NWChem/examples
+ doins -r examples/* || die "Failed to install examples"
+ fi
+
+ if use nwchem-tests ; then
+ dodir /usr/share/NWChem/tests || die "Failed to create tests directory"
+ insinto /usr/share/NWChem/tests
+ doins -r QA/tests/* || "Failed to install tests"
+ fi
+}
+
+pkg_postinst() {
+ elog
+ elog "The user will need to link \$HOME/.nwchemrc to /etc/nwchemrc"
+ elog "or copy it in order to tell NWChem the right position of the"
+ elog "basis library and other necessary data."
+ elog
+}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/nwchem/files/, sci-chemistry/nwchem/
@ 2013-07-23 10:08 Honza Macháček
0 siblings, 0 replies; 5+ messages in thread
From: Honza Macháček @ 2013-07-23 10:08 UTC (permalink / raw
To: gentoo-commits
commit: b9d88dde8cf6f0e052f600ce5b196c2a2bed6b94
Author: Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Tue Jul 23 10:07:59 2013 +0000
Commit: Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Tue Jul 23 10:07:59 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b9d88dde
sci-chemistry/nwchem updated to 6.3-r1, python makefile patch cosmetically improved, the python support linked properly to python2.
Package-Manager: portage-2.1.12.13
---
sci-chemistry/nwchem/ChangeLog | 10 +++
.../files/nwchem-6.1.1-python_makefile.patch | 10 +--
.../nwchem/files/nwchem-6.3-html_doc.patch | 82 ----------------------
.../nwchem/files/nwchem-6.3-r1-html_doc.patch | 13 ++++
.../{nwchem-6.3.ebuild => nwchem-6.3-r1.ebuild} | 10 +--
5 files changed, 33 insertions(+), 92 deletions(-)
diff --git a/sci-chemistry/nwchem/ChangeLog b/sci-chemistry/nwchem/ChangeLog
index 01bbf79..1f80267 100644
--- a/sci-chemistry/nwchem/ChangeLog
+++ b/sci-chemistry/nwchem/ChangeLog
@@ -2,6 +2,16 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*nwchem-6.3-r1 (23 Jul 2013)
+
+ 23 Jul 2013; Honza Macháček <Hloupy.Honza@centrum.cz> -nwchem-6.3.ebuild,
+ +nwchem-6.3-r1.ebuild, files/nwchem-6.1.1-adjust-dir-length.patch,
+ files/nwchem-6.1.1-makefile.patch, files/nwchem-6.1.1-nwchemrc.patch,
+ files/nwchem-6.1.1-python_makefile.patch, -files/nwchem-6.3-html_doc.patch,
+ +files/nwchem-6.3-r1-html_doc.patch:
+ Updated to 6.3-r1, python makefile patch cosmetically improved, the python
+ support linked properly to python2.
+
16 Jun 2013; Justin Lecher <jlec@gentoo.org> -nwchem-6.1.1.ebuild,
nwchem-6.3.ebuild:
Drop old; drop virtual/fortran as the eclass depends on it
diff --git a/sci-chemistry/nwchem/files/nwchem-6.1.1-python_makefile.patch b/sci-chemistry/nwchem/files/nwchem-6.1.1-python_makefile.patch
index 7753d8f..16973b6 100644
--- a/sci-chemistry/nwchem/files/nwchem-6.1.1-python_makefile.patch
+++ b/sci-chemistry/nwchem/files/nwchem-6.1.1-python_makefile.patch
@@ -1,12 +1,12 @@
--- src/config/makefile.h 2011-12-04 12:00:52.000000000 +0100
+++ src/config/makefile.h 2011-12-04 12:01:56.000000000 +0100
@@ -2133,7 +2133,7 @@
- #
+ endif
ifdef USE_PYTHON64
-- CORE_LIBS += $(PYTHONHOME)/lib64/python$(PYTHONVERSION)/config/libpython$(PYTHONVERSION).a
-+ CORE_LIBS += $(PYTHONHOME)/lib/libpython$(PYTHONVERSION).a
+- CORE_LIBS += $(PYTHONHOME)/lib64/python$(PYTHONVERSION)/config/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
++ CORE_LIBS += $(PYTHONHOME)/lib64/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
else
-- CORE_LIBS += $(PYTHONHOME)/lib/python$(PYTHONVERSION)/config/libpython$(PYTHONVERSION).a
-+ CORE_LIBS += $(PYTHONHOME)/lib/libpython$(PYTHONVERSION).a
+- CORE_LIBS += $(PYTHONHOME)/lib/python$(PYTHONVERSION)/config/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
++ CORE_LIBS += $(PYTHONHOME)/lib/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
endif
endif
diff --git a/sci-chemistry/nwchem/files/nwchem-6.3-html_doc.patch b/sci-chemistry/nwchem/files/nwchem-6.3-html_doc.patch
deleted file mode 100644
index fa0e8fa..0000000
--- a/sci-chemistry/nwchem/files/nwchem-6.3-html_doc.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-diff -Naurp old/doc/update_www new/doc/update_www
---- doc/update_www 2013-05-18 00:40:51.000000000 +0000
-+++ doc/update_www 2013-05-22 12:15:27.543414281 +0000
-@@ -16,7 +16,8 @@ set document = $argv[1]
- echo Updating WWW pages for $document.tex
- #............... public
- #foreach WWWDIR (/msrc/www/pub/docs/nwchem/doc)
--foreach WWWDIR (/msrc/emslweb/docs/nwchem/doc)
-+#foreach WWWDIR (/msrc/emslweb/docs/nwchem/doc)
-+foreach WWWDIR ("${NWCHEM_TOP}"/html)
- #
- # Now copy the revised source into the EMSL public WWW tree
- echo "update_www: Public pages .. "
-diff -Naurp old/user/geometry.tex new/user/geometry.tex
---- user/geometry.tex 2013-05-18 00:40:51.000000000 +0000
-+++ user/geometry.tex 2013-05-23 13:00:44.234316049 +0000
-@@ -472,11 +472,11 @@ and angles.
- \ifx\pdfoutput\undefined
- \includegraphics[angle=270,width=6in]{zmat1.eps}
- \else
--\includegraphics[angle=0,width=6in]{zmat1.pdf}
-+\includegraphics[angle=0,width=6in,bburx=509,bbury=201]{zmat1.pdf}
- \fi
- \end{latexonly}
- \begin{htmlonly}
--\psfig{figure=zmat1.eps,angle=270,width=6in}
-+\epsfig{figure=zmat1.eps,angle=270,width=6in}
- \end{htmlonly}
- \caption{\label{fig:zmat1} Relationships between the centers, bond angle
- and dihedral angle in Z-matrix input.}
-@@ -488,11 +488,11 @@ and dihedral angle in Z-matrix input.}
- \ifx\pdfoutput\undefined
- \includegraphics[angle=270,width=6in]{zmat2.eps}
- \else
--\includegraphics[angle=270,width=6in]{zmat2.pdf}
-+\includegraphics[angle=270,width=6in,bburx=266,bbury=485]{zmat2.pdf}
- \fi
- \end{latexonly}
- \begin{htmlonly}
--\psfig{figure=zmat2.eps,angle=270,width=6in}
-+\epsfig{figure=zmat2.eps,angle=270,width=6in}
- \end{htmlonly}
-
- \caption{\label{fig:zmat2} Relationships between the centers and two
-@@ -505,11 +505,11 @@ and dihedral angle in Z-matrix input.}
- \ifx\pdfoutput\undefined
- \includegraphics[angle=270,width=6in]{zmat3.eps}
- \else
--\includegraphics[angle=270,width=6in]{zmat3.pdf}
-+\includegraphics[angle=270,width=6in,bburx=266,bbury=482]{zmat3.pdf}
- \fi
- \end{latexonly}
- \begin{htmlonly}
--\psfig{figure=zmat3.eps,angle=270,width=6in}
-+\epsfig{figure=zmat3.eps,angle=270,width=6in}
- \end{htmlonly}
- \caption{\label{fig:zmat3} Relationships between the centers and two
- bond angles in Z-matrix input with optional parameter specified as $-1$.}
-diff -Naurp old/user/titlepage.tex new/user/titlepage.tex
---- user/titlepage.tex 2013-05-18 00:40:51.000000000 +0000
-+++ user/titlepage.tex 2013-05-23 13:01:07.304152791 +0000
-@@ -19,7 +19,7 @@
- {\bf\Large \nwchemmonth \ \nwchemyear}\\[1.0in]
-
-
--%\psfig{figure=zsm.major.ps,height=4in,width=4in}
-+%\epsfig{figure=zsm.major.ps,height=4in,width=4in}
-
-
- \end{centering}
-diff -Naurp old/user/user.tex new/user/user.tex
---- user/user.tex 2013-05-18 00:40:51.000000000 +0000
-+++ user/user.tex 2013-05-23 13:00:04.961296411 +0000
-@@ -2,7 +2,7 @@
- \input{top}
- \usepackage[dvips]{graphicx}
- \begin{htmlonly}
--\usepackage{psfig}
-+\usepackage{epsfig}
- \end{htmlonly}
-
-
diff --git a/sci-chemistry/nwchem/files/nwchem-6.3-r1-html_doc.patch b/sci-chemistry/nwchem/files/nwchem-6.3-r1-html_doc.patch
new file mode 100644
index 0000000..de7377b
--- /dev/null
+++ b/sci-chemistry/nwchem/files/nwchem-6.3-r1-html_doc.patch
@@ -0,0 +1,13 @@
+diff -Naurp old/doc/update_www new/doc/update_www
+--- doc/update_www 2013-05-18 00:40:51.000000000 +0000
++++ doc/update_www 2013-05-22 12:15:27.543414281 +0000
+@@ -16,7 +16,8 @@ set document = $argv[1]
+ echo Updating WWW pages for $document.tex
+ #............... public
+ #foreach WWWDIR (/msrc/www/pub/docs/nwchem/doc)
+-foreach WWWDIR (/msrc/emslweb/docs/nwchem/doc)
++#foreach WWWDIR (/msrc/emslweb/docs/nwchem/doc)
++foreach WWWDIR ("${NWCHEM_TOP}"/web)
+ #
+ # Now copy the revised source into the EMSL public WWW tree
+ echo "update_www: Public pages .. "
diff --git a/sci-chemistry/nwchem/nwchem-6.3.ebuild b/sci-chemistry/nwchem/nwchem-6.3-r1.ebuild
similarity index 92%
rename from sci-chemistry/nwchem/nwchem-6.3.ebuild
rename to sci-chemistry/nwchem/nwchem-6.3-r1.ebuild
index 4395d15..4ff053b 100644
--- a/sci-chemistry/nwchem/nwchem-6.3.ebuild
+++ b/sci-chemistry/nwchem/nwchem-6.3-r1.ebuild
@@ -8,11 +8,11 @@ PYTHON_COMPAT=( python{2_6,2_7} )
inherit eutils fortran-2 multilib python-single-r1 toolchain-funcs
-DATE="2013-05-17"
+DATE="2013-05-28"
DESCRIPTION="Delivering High-Performance Computational Chemistry to Science"
HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page"
-SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV}-src.${DATE}.tar.gz"
+SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV}.revision${PR#r}-src.${DATE}.tar.gz"
LICENSE="ECL-2.0"
SLOT="0"
@@ -44,7 +44,7 @@ src_prepare() {
"${FILESDIR}"/nwchem-6.1.1-nwchemrc.patch \
"${FILESDIR}"/nwchem-6.1.1-adjust-dir-length.patch
use python && epatch "${FILESDIR}"/nwchem-6.1.1-python_makefile.patch
- use doc && epatch "${FILESDIR}"/nwchem-6.3-html_doc.patch
+ use doc && epatch "${FILESDIR}"/nwchem-6.3-r1-html_doc.patch
sed \
-e "s:DBASIS_LIBRARY=\"'\$(SRCDIR)'\":DBASIS_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
@@ -90,7 +90,7 @@ src_compile() {
export USE_PYTHON64=yes
fi
export PYTHONHOME=/usr
- export PYTHONVERSION=$(eselect python show|awk -Fpython '{ print $2 }')
+ export PYTHONVERSION=$(eselect python show --python2 |awk -Fpython '{ print $2 }')
export PYTHONPATH="./:${S}/contrib/python/"
export NWCHEM_MODULES="all python"
else
@@ -137,7 +137,7 @@ src_install() {
use doc && \
insinto /usr/share/doc/"${P}" && \
doins -r doc/nwahtml && \
- doins -r html
+ doins -r web
}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/nwchem/files/, sci-chemistry/nwchem/
@ 2015-02-16 16:08 Honza Macháček
0 siblings, 0 replies; 5+ messages in thread
From: Honza Macháček @ 2015-02-16 16:08 UTC (permalink / raw
To: gentoo-commits
commit: e4668719ee18d3ef33713ab3e024bc32798a0529
Author: Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Mon Feb 16 16:09:25 2015 +0000
Commit: Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Mon Feb 16 16:09:25 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e4668719
In sci-chemistry/nwchem-6.5_p26243-r6 two new upstream patches added (Dmapp_inc and Print1e), limit for internal coordinates increased to accomodate icosahedral clusters
Package-Manager: portage-2.2.15
---
sci-chemistry/nwchem/ChangeLog | 8 ++++++++
.../nwchem/files/nwchem-6.5-icosahedron_zcoord.patch | 12 ++++++++++++
...chem-6.5_p26243-r5.ebuild => nwchem-6.5_p26243-r6.ebuild} | 7 +++++--
3 files changed, 25 insertions(+), 2 deletions(-)
diff --git a/sci-chemistry/nwchem/ChangeLog b/sci-chemistry/nwchem/ChangeLog
index 153b2dc..9b16e00 100644
--- a/sci-chemistry/nwchem/ChangeLog
+++ b/sci-chemistry/nwchem/ChangeLog
@@ -2,6 +2,14 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*nwchem-6.5_p26243-r6 (16 Feb 2015)
+
+ 16 Feb 2015; Honza Macháček <Hloupy.Honza@centrum.cz>
+ -nwchem-6.5_p26243-r5.ebuild, +nwchem-6.5_p26243-r6.ebuild,
+ +files/nwchem-6.5-icosahedron_zcoord.patch:
+ 2 new upstream patches added (Dmapp_inc and Print1e), limit for internal
+ coordinates increased to accomodate icosahedral clusters
+
*nwchem-6.5_p26243-r5 (15 Jan 2015)
15 Jan 2015; Honza Macháček <Hloupy.Honza@centrum.cz>
diff --git a/sci-chemistry/nwchem/files/nwchem-6.5-icosahedron_zcoord.patch b/sci-chemistry/nwchem/files/nwchem-6.5-icosahedron_zcoord.patch
new file mode 100644
index 0000000..acd60d3
--- /dev/null
+++ b/sci-chemistry/nwchem/files/nwchem-6.5-icosahedron_zcoord.patch
@@ -0,0 +1,12 @@
+diff -Naurp nwchem.orig/src/geom/geom_hnd.F nwchem/src/geom/geom_hnd.F
+--- nwchem.orig/src/geom/geom_hnd.F 2014-09-10 18:11:03.000000000 +0000
++++ nwchem/src/geom/geom_hnd.F 2015-01-28 16:14:38.249027101 +0000
+@@ -1644,7 +1644,7 @@ c
+ nlnba=3*mxlnba
+ if (.not. zdone) goto 55555 ! attempt to recover
+ c
+- if (nzvar .gt. 10*(max(6,3*nat-6))) then
++ if (nzvar .gt. 20*(max(6,3*nat-6))) then
+ c
+ c Made a z-matrix but it is asburdly big. Nothing yet to fix this
+ c
diff --git a/sci-chemistry/nwchem/nwchem-6.5_p26243-r5.ebuild b/sci-chemistry/nwchem/nwchem-6.5_p26243-r6.ebuild
similarity index 96%
rename from sci-chemistry/nwchem/nwchem-6.5_p26243-r5.ebuild
rename to sci-chemistry/nwchem/nwchem-6.5_p26243-r6.ebuild
index efbae8f..118d6a5 100644
--- a/sci-chemistry/nwchem/nwchem-6.5_p26243-r5.ebuild
+++ b/sci-chemistry/nwchem/nwchem-6.5_p26243-r6.ebuild
@@ -23,7 +23,9 @@ SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV%_p*}.revision${PV#*_p}-src.
http://www.nwchem-sw.org/images/Elpa_syncs.patch.gz
http://www.nwchem-sw.org/images/Xlmpoles_ifort15.patch.gz
http://www.nwchem-sw.org/images/Ifort15_fpp_offload.patch.gz
- http://www.nwchem-sw.org/images/Texas_iorb.patch.gz"
+ http://www.nwchem-sw.org/images/Texas_iorb.patch.gz
+ http://www.nwchem-sw.org/images/Dmapp_inc.patch.gz
+ http://www.nwchem-sw.org/images/Print1e.patch.gz"
LICENSE="ECL-2.0"
SLOT="0"
@@ -109,13 +111,14 @@ src_unpack() {
src_prepare() {
pushd "${S}"/src
- for p in Util_md_sockets Hbar Tcenxtask Parallelmpi Makefile_gcc4x Bcast_ccsd Elpa_syncs Xlmpoles_ifort15 Ifort15_fpp_offload Texas_iorb
+ for p in Util_md_sockets Hbar Tcenxtask Parallelmpi Makefile_gcc4x Bcast_ccsd Elpa_syncs Xlmpoles_ifort15 Ifort15_fpp_offload Texas_iorb Dmapp_inc Print1e
do epatch "${WORKDIR}"/"${p}.patch"
done
cd NWints/hondo
epatch "${WORKDIR}"/Hnd_giaxyz_noinline.patch
popd
epatch "${FILESDIR}"/nwchem-6.1.1-nwchemrc.patch
+ epatch "${FILESDIR}"/nwchem-6.5-icosahedron_zcoord.patch
use python && epatch "${FILESDIR}"/nwchem-6.5-python_makefile.patch
use doc && epatch "${FILESDIR}"/nwchem-6.3-r1-html_doc.patch
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/nwchem/files/, sci-chemistry/nwchem/
@ 2016-03-30 14:36 Honza Macháček
0 siblings, 0 replies; 5+ messages in thread
From: Honza Macháček @ 2016-03-30 14:36 UTC (permalink / raw
To: gentoo-commits
commit: 94a06710354314bfd07d9a8b124079193ddd1d4a
Author: Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Wed Mar 30 14:34:09 2016 +0000
Commit: Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Wed Mar 30 14:34:09 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=94a06710
sci-chemistry/nwchem version bumped to 6.6 with minor ebuild improvements; Infiniband support should compile, source patched to allow unique names for all atoms
Package-Manager: portage-2.2.27
.../nwchem/files/nwchem-6.6-unique_tags.patch | 12 +
sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild | 279 +++++++++++++++++++++
2 files changed, 291 insertions(+)
diff --git a/sci-chemistry/nwchem/files/nwchem-6.6-unique_tags.patch b/sci-chemistry/nwchem/files/nwchem-6.6-unique_tags.patch
new file mode 100644
index 0000000..e129406
--- /dev/null
+++ b/sci-chemistry/nwchem/files/nwchem-6.6-unique_tags.patch
@@ -0,0 +1,12 @@
+diff -Naurp nwchem-6.6.orig/src/util/nwc_const.fh nwchem-6.6/src/util/nwc_const.fh
+--- nwchem-6.6.orig/src/util/nwc_const.fh 2015-10-01 17:33:14.000000000 +0000
++++ nwchem-6.6/src/util/nwc_const.fh 2015-11-26 10:53:46.386110924 +0000
+@@ -62,7 +62,7 @@
+ * Maximum number of unique tags
+ *
+ integer nw_max_unq_tags
+- parameter (nw_max_unq_tags = 40)
++ parameter (nw_max_unq_tags = nw_max_atom)
+ *------------------------------------------------------------------------------
+ * Maximum number of general contractions in a shell
+ *
diff --git a/sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild b/sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild
new file mode 100644
index 0000000..4c10fe8
--- /dev/null
+++ b/sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild
@@ -0,0 +1,279 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs
+
+DATE="2015-10-20"
+
+DESCRIPTION="Delivering High-Performance Computational Chemistry to Science"
+HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page"
+PATCH_REPO="http://www.nwchem-sw.org/images"
+PATCH_LIST="Tddft_mxvec20 Tools_lib64 Config_libs66 Cosmo_meminit Sym_abelian
+Xccvs98 Dplot_tolrho Driver_smalleig Ga_argv Raman_displ Ga_defs Zgesvd Cosmo_dftprint"
+SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV%_p*}.revision${PV#*_p}-src.${DATE}.tar.bz2
+ $(for p in ${PATCH_LIST[@]}; do echo ${PATCH_REPO}/${p}.patch.gz; done)"
+
+LICENSE="ECL-2.0"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="blas cuda doc examples infiniband int64 lapack mrcc nwchem-tests openmp python scalapack"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )
+ scalapack? ( !int64 )
+ lapack? ( blas )
+ scalapack? ( blas )"
+
+RDEPEND="
+ sys-fs/sysfsutils
+ blas? ( virtual/blas )
+ lapack? ( virtual/lapack )
+ scalapack? ( virtual/scalapack )
+ cuda? ( dev-util/nvidia-cuda-sdk )
+ int64? (
+ blas? ( virtual/blas[int64] )
+ lapack? ( virtual/lapack[int64] )
+ )
+ python? ( ${PYTHON_DEPS} )"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig
+ app-shells/tcsh
+ virtual/mpi[fortran]
+ infiniband? ( || (
+ sys-cluster/openmpi[fortran,openmpi_fabrics_ofed]
+ sys-cluster/mvapich2[fortran]
+ ) )
+ doc? (
+ dev-texlive/texlive-latex
+ dev-tex/latex2html )"
+
+LONG_S="${WORKDIR}/Nwchem-${PV%_p*}.revision${PV#*_p}-src.${DATE}"
+S="${WORKDIR}/${PN}-${PV%_p*}"
+
+pkg_setup() {
+ # fortran-2.eclass does not handle mpi wrappers
+ export FC="mpif90"
+ export F77="mpif77"
+ export CC="mpicc"
+ export CXX="mpic++"
+
+ use openmp && FORTRAN_NEED_OPENMP=1
+
+ fortran-2_pkg_setup
+
+ if use openmp; then
+ # based on _fortran-has-openmp() of fortran-2.eclass
+ local openmp=""
+ local fcode=ebuild-openmp-flags.f
+ local _fc=$(tc-getFC)
+
+ pushd "${T}"
+ cat <<- EOF > "${fcode}"
+ 1 call omp_get_num_threads
+ 2 end
+ EOF
+
+ for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
+ "${_fc}" "${openmp}" "${fcode}" -o "${fcode}.x" && break
+ done
+
+ rm -f "${fcode}.*"
+ popd
+
+ export FC="${FC} ${openmp}"
+ export F77="${F77} ${openmp}"
+ export CC="${CC} ${openmp}"
+ export CXX="${CXX} ${openmp}"
+ fi
+
+ use python && python-single-r1_pkg_setup
+}
+
+src_unpack() {
+ unpack ${A}
+ mv "${LONG_S}" "${S}"
+}
+
+src_prepare() {
+ for p in ${PATCH_LIST[@]}
+ do epatch "${WORKDIR}"/"${p}.patch"
+ done
+ epatch "${FILESDIR}"/nwchem-6.1.1-nwchemrc.patch
+ epatch "${FILESDIR}"/nwchem-6.5-icosahedron_zcoord.patch
+ epatch "${FILESDIR}"/nwchem-6.6-unique_tags.patch
+ use python && epatch "${FILESDIR}"/nwchem-6.5-python_makefile.patch
+ use doc && epatch "${FILESDIR}"/nwchem-6.3-r1-html_doc.patch
+
+ sed \
+ -e "s:DBASIS_LIBRARY=\"'\$(SRCDIR)'\":DBASIS_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
+ -i src/basis/MakeFile src/basis/GNUmakefile || die
+ sed \
+ -e "s:DNWPW_LIBRARY=\"'\$(SRCDIR)'\":DNWPW_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
+ -i src/nwpw/libraryps/GNUmakefile || die
+ sed \
+ -e "s:-DCOMPILATION_DIR=\"'\$(TOPDIR)'\":-DCOMPILATION_DIR=\"''\":g" \
+ -i src/GNUmakefile src/MakeFile || die
+
+ if [[ $(tc-getFC) == *-*-*-*-gfortran ]]; then
+ sed \
+ -e "s:ifneq (\$(FC),gfortran):ifneq (\$(FC),$(tc-getFC)):g" \
+ -e "s:ifeq (\$(FC),gfortran):ifeq (\$(FC),$(tc-getFC)):g" \
+ -i src/config/makefile.h || die
+ fi
+}
+
+src_compile() {
+ export NWCHEM_LONG_PATHS=Y
+ use openmp && export USE_OPENMP=1
+ export USE_MPI=y
+ export USE_MPIF=y
+ export USE_MPIF4=y
+ export MPI_LOC="${EPREFIX}"/usr
+ export MPI_INCLUDE=$MPI_LOC/include
+ export MPI_LIB=$MPI_LOC/$(get_libdir)
+ export LIBMPI="$(mpif90 -showme:link)"
+ if use infiniband; then
+ export ARMCI_NETWORK=OPENIB
+ export MSG_COMMS=MPI
+ export IB_INCLUDE="-I${MPI_INCLUDE}"
+ export IB_LIB="-L${MPI_LIB}"
+ else
+ unset ARMCI_NETWORK
+ fi
+ if [ "$ARCH" = "amd64" ]; then
+ export NWCHEM_TARGET=LINUX64
+ elif [ "$ARCH" = "ia64" ]; then
+ export NWCHEM_TARGET=LINUX64
+ elif [ "$ARCH" = "x86" ]; then
+ export NWCHEM_TARGET=LINUX
+ elif [ "$ARCH" = "ppc" ]; then
+ export NWCHEM_TARGET=LINUX
+ else
+ die "Unknown architecture"
+ fi
+ if use python ; then
+ if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ]; then
+ export USE_PYTHON64=yes
+ fi
+ export PYTHONHOME=/usr
+ export PYTHONVERSION=$(eselect python show --python2 |awk -Fpython '{ print $2 }')
+ export PYTHONPATH="./:${S}/contrib/python/"
+ export NWCHEM_MODULES="all python"
+ else
+ export NWCHEM_MODULES="all"
+ fi
+ use mrcc && export MRCC_METHODS="TRUE" # Multi Reference Coupled Clusters
+ export CCSDTQ="TRUE" # Coupled Clusters Singlets + Dublets + Triplets + Quadruplets
+ export CCSDTLR="TRUE" # CCSDT (and CCSDTQ?) Linear Response
+ export EACCSD="TRUE" # Electron Affinities at the CCSD level
+ export IPCCSD="TRUE" # Ionisation Potentials at the CCSD level
+ unset BLASOPT
+ local blaspkg="blas"
+ local lapackpkg="lapack"
+ if use int64; then
+ blaspkg="blas-int64"
+ lapackpkg="lapack-int64"
+ fi
+ use blas && export BLASOPT="$($(tc-getPKG_CONFIG) --libs ${blaspkg})"
+ use lapack && export BLASOPT+=" $($(tc-getPKG_CONFIG) --libs ${lapackpkg})"
+ use scalapack && export BLASOPT+=" $($(tc-getPKG_CONFIG) --libs scalapack)"
+ if use cuda; then
+ export TCE_CUDA=Y
+ export CUDA_PATH=/opt/cuda
+ export CUDA=${CUDA_PATH}/bin/nvcc
+ export CUDA_FLAGS="-arch=compute_20 -code=sm_20,compute_20"
+ export CUDA_INCLUDE="-I${CUDA_PATH}/include"
+ export CUDA_LIBS="-L${CUDA_PATH}/$(get_libdir) -lcublas -lcufft -lcudart -lcuda -lstdc++"
+ fi
+ export LARGE_FILES="TRUE"
+
+ cd src
+ if use blas && [ "$NWCHEM_TARGET" = "LINUX64" ]; then
+ if use int64; then
+ export BLAS_SIZE=8
+ export LAPACK_SIZE=8
+ export SCALAPACK_SIZE=8
+ else
+ emake \
+ DIAG=PAR \
+ FC="$(tc-getFC)" \
+ CC="$(tc-getCC)" \
+ CXX="$(tc-getCXX)" \
+ NWCHEM_TOP="${S}" \
+ clean
+ emake \
+ DIAG=PAR \
+ FC="$(tc-getFC)" \
+ CC="$(tc-getCC)" \
+ CXX="$(tc-getCXX)" \
+ NWCHEM_TOP="${S}" \
+ 64_to_32
+ export BLAS_SIZE=4
+ export LAPACK_SIZE=4
+ export SCALAPACK_SIZE=4
+ export USE_64TO32=y
+ fi
+ fi
+ emake \
+ DIAG=PAR \
+ FC="$(tc-getFC)" \
+ CC="$(tc-getCC)" \
+ CXX="$(tc-getCXX)" \
+ NWCHEM_TOP="${S}" \
+ NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem" \
+ nwchem_config
+ emake \
+ DIAG=PAR \
+ FC="$(tc-getFC)" \
+ CC="$(tc-getCC)" \
+ CXX="$(tc-getCXX)" \
+ NWCHEM_TOP="${S}" \
+ NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem"
+
+ if use doc; then
+ cd "${S}"/doc
+ export VARTEXFONTS="${T}/fonts"
+ emake \
+ DIAG=PAR \
+ NWCHEM_TOP="${S}" \
+ pdf html
+ fi
+}
+
+src_install() {
+ dobin bin/${NWCHEM_TARGET}/nwchem
+
+ insinto /usr/share/NWChem/basis/
+ doins -r src/basis/libraries src/data
+ insinto /usr/share/NWChem/nwpw
+ doins -r src/nwpw/libraryps
+
+ insinto /etc
+ doins nwchemrc
+
+ use examples && \
+ insinto /usr/share/NWChem/ && \
+ doins -r examples
+
+ use nwchem-tests && \
+ insinto /usr/share/NWChem && \
+ doins -r QA/tests
+
+ use doc && \
+ insinto /usr/share/doc/"${P}" && \
+ doins -r doc/nwahtml && \
+ doins -r web
+
+}
+
+pkg_postinst() {
+ echo
+ elog "The user will need to link \$HOME/.nwchemrc to /etc/nwchemrc"
+ elog "or copy it in order to tell NWChem the right position of the"
+ elog "basis library and other necessary data."
+ echo
+}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/nwchem/files/, sci-chemistry/nwchem/
@ 2020-09-28 8:43 Horea Christian
0 siblings, 0 replies; 5+ messages in thread
From: Horea Christian @ 2020-09-28 8:43 UTC (permalink / raw
To: gentoo-commits
commit: 44c5807630ebbbd0b5163b90214623e3ae91479a
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Sep 28 08:41:37 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Sep 28 08:43:32 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=44c58076
sci-chemistry/nwchem: removed unmaintained package with broken distfiles
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
.../files/nwchem-6.1.1-adjust-dir-length.patch | 22 --
.../nwchem/files/nwchem-6.1.1-makefile.patch | 14 -
.../nwchem/files/nwchem-6.1.1-nwchemrc.patch | 13 -
.../files/nwchem-6.1.1-python_makefile.patch | 12 -
.../nwchem/files/nwchem-6.3-r1-html_doc.patch | 13 -
.../files/nwchem-6.5-icosahedron_zcoord.patch | 12 -
.../nwchem/files/nwchem-6.5-python_makefile.patch | 15 --
.../nwchem/files/nwchem-6.6-unique_tags.patch | 12 -
sci-chemistry/nwchem/metadata.xml | 34 ---
sci-chemistry/nwchem/nwchem-6.3_p2-r1.ebuild | 206 ---------------
sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild | 292 ---------------------
sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild | 278 --------------------
12 files changed, 923 deletions(-)
diff --git a/sci-chemistry/nwchem/files/nwchem-6.1.1-adjust-dir-length.patch b/sci-chemistry/nwchem/files/nwchem-6.1.1-adjust-dir-length.patch
deleted file mode 100644
index 859c76469..000000000
--- a/sci-chemistry/nwchem/files/nwchem-6.1.1-adjust-dir-length.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- src/nwpw/libraryps/GNUmakefile 2012-01-26 08:24:05.189490945 +0100
-+++ src/nwpw/libraryps/GNUmakefile 2012-01-26 08:24:16.499490923 +0100
-@@ -10,7 +10,7 @@
-
- USES_BLAS =
-
-- LONGNWTOP = $(shell if [ `echo $(SRCDIR) |wc -m` -gt 64 ]; then echo "Y"; fi )
-+ LONGNWTOP = $(shell if [ `echo $(SRCDIR) |wc -m` -gt 80 ]; then echo "Y"; fi )
- ifeq ($(LONGNWTOP),Y)
- errorlongpwd:
- @echo " "
---- src/basis/GNUmakefile 2012-01-26 08:25:03.999490829 +0100
-+++ src/basis/GNUmakefile 2012-01-26 08:25:15.549490805 +0100
-@@ -34,7 +34,7 @@
- ########################################################
-
- LIB_TARGETS = testbasis testbasis.o libcheck
-- LONGNWTOP = $(shell if [ `echo $(SRCDIR) |wc -m` -gt 64 ]; then echo "Y"; fi )
-+ LONGNWTOP = $(shell if [ `echo $(SRCDIR) |wc -m` -gt 80 ]; then echo "Y"; fi )
- ifeq ($(LONGNWTOP),Y)
- errorlongpwd:
- @echo " "
diff --git a/sci-chemistry/nwchem/files/nwchem-6.1.1-makefile.patch b/sci-chemistry/nwchem/files/nwchem-6.1.1-makefile.patch
deleted file mode 100644
index a74d887af..000000000
--- a/sci-chemistry/nwchem/files/nwchem-6.1.1-makefile.patch
+++ /dev/null
@@ -1,14 +0,0 @@
---- src/tools/global/GNUmakefile 2011-12-03 14:34:01.000000000 +0100
-+++ src/tools/global/GNUmakefile 2011-12-03 14:37:40.000000000 +0100
-@@ -68,7 +68,10 @@
- $(LIBRARY):
- (echo TARGET is $(TARGET); cd ./src; $(MAKE) || exit 1;)
-
--$(TESTS) %.x: $(LIBRARY)
-+%.x: $(LIBRARY)
-+ (cd ./testing; $(MAKE) $@ || exit 1;)
-+
-+$(TESTS): $(LIBRARY)
- (cd ./testing; $(MAKE) $@ || exit 1;)
-
- all: $(TESTS)
diff --git a/sci-chemistry/nwchem/files/nwchem-6.1.1-nwchemrc.patch b/sci-chemistry/nwchem/files/nwchem-6.1.1-nwchemrc.patch
deleted file mode 100644
index 4e1e0af1e..000000000
--- a/sci-chemistry/nwchem/files/nwchem-6.1.1-nwchemrc.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- nwchemrc 2011-12-04 11:29:37.000000000 +0100
-+++ nwchemrc 2011-12-04 11:29:26.000000000 +0100
-@@ -0,0 +1,10 @@
-+nwchem_basis_library /usr/share/NWChem/basis/libraries/
-+nwchem_nwpw_library /usr/share/NWChem/nwpw/libraryps/
-+ffield amber
-+amber_1 /usr/share/NWChem/data/amber_s/
-+amber_2 /usr/share/NWChem/data/amber_q/
-+amber_3 /usr/share/NWChem/data/amber_x/
-+amber_4 /usr/share/NWChem/data/amber_u/
-+spce /usr/share/NWChem/data/solvents/spce.rst
-+charmm_s /usr/share/NWChem/data/charmm_s/
-+charmm_x /usr/share/NWChem/data/charmm_x/
diff --git a/sci-chemistry/nwchem/files/nwchem-6.1.1-python_makefile.patch b/sci-chemistry/nwchem/files/nwchem-6.1.1-python_makefile.patch
deleted file mode 100644
index 16973b648..000000000
--- a/sci-chemistry/nwchem/files/nwchem-6.1.1-python_makefile.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- src/config/makefile.h 2011-12-04 12:00:52.000000000 +0100
-+++ src/config/makefile.h 2011-12-04 12:01:56.000000000 +0100
-@@ -2133,7 +2133,7 @@
- endif
- ifdef USE_PYTHON64
-- CORE_LIBS += $(PYTHONHOME)/lib64/python$(PYTHONVERSION)/config/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
-+ CORE_LIBS += $(PYTHONHOME)/lib64/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
- else
-- CORE_LIBS += $(PYTHONHOME)/lib/python$(PYTHONVERSION)/config/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
-+ CORE_LIBS += $(PYTHONHOME)/lib/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
- endif
- endif
diff --git a/sci-chemistry/nwchem/files/nwchem-6.3-r1-html_doc.patch b/sci-chemistry/nwchem/files/nwchem-6.3-r1-html_doc.patch
deleted file mode 100644
index de7377bd2..000000000
--- a/sci-chemistry/nwchem/files/nwchem-6.3-r1-html_doc.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff -Naurp old/doc/update_www new/doc/update_www
---- doc/update_www 2013-05-18 00:40:51.000000000 +0000
-+++ doc/update_www 2013-05-22 12:15:27.543414281 +0000
-@@ -16,7 +16,8 @@ set document = $argv[1]
- echo Updating WWW pages for $document.tex
- #............... public
- #foreach WWWDIR (/msrc/www/pub/docs/nwchem/doc)
--foreach WWWDIR (/msrc/emslweb/docs/nwchem/doc)
-+#foreach WWWDIR (/msrc/emslweb/docs/nwchem/doc)
-+foreach WWWDIR ("${NWCHEM_TOP}"/web)
- #
- # Now copy the revised source into the EMSL public WWW tree
- echo "update_www: Public pages .. "
diff --git a/sci-chemistry/nwchem/files/nwchem-6.5-icosahedron_zcoord.patch b/sci-chemistry/nwchem/files/nwchem-6.5-icosahedron_zcoord.patch
deleted file mode 100644
index acd60d3b3..000000000
--- a/sci-chemistry/nwchem/files/nwchem-6.5-icosahedron_zcoord.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naurp nwchem.orig/src/geom/geom_hnd.F nwchem/src/geom/geom_hnd.F
---- nwchem.orig/src/geom/geom_hnd.F 2014-09-10 18:11:03.000000000 +0000
-+++ nwchem/src/geom/geom_hnd.F 2015-01-28 16:14:38.249027101 +0000
-@@ -1644,7 +1644,7 @@ c
- nlnba=3*mxlnba
- if (.not. zdone) goto 55555 ! attempt to recover
- c
-- if (nzvar .gt. 10*(max(6,3*nat-6))) then
-+ if (nzvar .gt. 20*(max(6,3*nat-6))) then
- c
- c Made a z-matrix but it is asburdly big. Nothing yet to fix this
- c
diff --git a/sci-chemistry/nwchem/files/nwchem-6.5-python_makefile.patch b/sci-chemistry/nwchem/files/nwchem-6.5-python_makefile.patch
deleted file mode 100644
index c37310c79..000000000
--- a/sci-chemistry/nwchem/files/nwchem-6.5-python_makefile.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- src/config/makefile.h 2014-11-03 14:00:59.808794970 +0100
-+++ src/config/makefile.h 2014-11-03 14:29:13.353470102 +0100
-@@ -2521,10 +2521,10 @@
- endif
- ifdef USE_PYTHON64
-- CORE_LIBS += $(PYTHONHOME)/lib64/python$(PYTHONVERSION)/$(PYTHONCONFIGDIR)/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
-+ CORE_LIBS += $(PYTHONHOME)/lib64/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
- else
- ifeq ($(GOTMINGW32),1)
- CORE_LIBS += $(PYTHONHOME)/libs/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
- else
-- CORE_LIBS += $(PYTHONHOME)/lib/python$(PYTHONVERSION)/$(PYTHONCONFIGDIR)/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
-+ CORE_LIBS += $(PYTHONHOME)/lib/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)
- endif
- endif
diff --git a/sci-chemistry/nwchem/files/nwchem-6.6-unique_tags.patch b/sci-chemistry/nwchem/files/nwchem-6.6-unique_tags.patch
deleted file mode 100644
index e129406e1..000000000
--- a/sci-chemistry/nwchem/files/nwchem-6.6-unique_tags.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naurp nwchem-6.6.orig/src/util/nwc_const.fh nwchem-6.6/src/util/nwc_const.fh
---- nwchem-6.6.orig/src/util/nwc_const.fh 2015-10-01 17:33:14.000000000 +0000
-+++ nwchem-6.6/src/util/nwc_const.fh 2015-11-26 10:53:46.386110924 +0000
-@@ -62,7 +62,7 @@
- * Maximum number of unique tags
- *
- integer nw_max_unq_tags
-- parameter (nw_max_unq_tags = 40)
-+ parameter (nw_max_unq_tags = nw_max_atom)
- *------------------------------------------------------------------------------
- * Maximum number of general contractions in a shell
- *
diff --git a/sci-chemistry/nwchem/metadata.xml b/sci-chemistry/nwchem/metadata.xml
deleted file mode 100644
index 61993bb4b..000000000
--- a/sci-chemistry/nwchem/metadata.xml
+++ /dev/null
@@ -1,34 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <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>
- </maintainer>
- <use>
- <flag name="blas">
-Use external BLAS library instead of the internal routines
-</flag>
- <flag name="cuda">
-Enable CUDA GPU support for the Tensor Contraction Engine generated
-methods (CI, MBPT, CC)
-</flag>
- <flag name="int64">
-Use 64 bits integers
-</flag>
- <flag name="lapack">
-Use external LAPACK library instead of the internal routines
-</flag>
- <flag name="mrcc">
-Compile the routines for Multi Reference Coupled Clusters theory
-</flag>
- <flag name="nwchem-tests">Install qa tests data</flag>
- <flag name="scalapack">
-Use external SCALAPACK library
-</flag>
- </use>
-</pkgmetadata>
diff --git a/sci-chemistry/nwchem/nwchem-6.3_p2-r1.ebuild b/sci-chemistry/nwchem/nwchem-6.3_p2-r1.ebuild
deleted file mode 100644
index 980b6f392..000000000
--- a/sci-chemistry/nwchem/nwchem-6.3_p2-r1.ebuild
+++ /dev/null
@@ -1,206 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs
-
-DATE="2013-10-17"
-
-DESCRIPTION="Delivering High-Performance Computational Chemistry to Science"
-HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page"
-SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV%_p*}.revision${PV#*_p}-src.${DATE}.tar.gz"
-
-LICENSE="ECL-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="blas mpi doc examples nwchem-tests openmp mrcc python"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
- sys-fs/sysfsutils
- python? ( ${PYTHON_DEPS} )"
-DEPEND="${RDEPEND}
- app-shells/tcsh
- mpi? ( virtual/mpi[fortran] )
- doc? (
- dev-texlive/texlive-latex
- dev-tex/latex2html )"
-
-LONG_S="${WORKDIR}/${PN}-${PV%_p*}.revision${PV#*_p}-src.${DATE}"
-S="${WORKDIR}/${PN}"
-
-pkg_setup() {
- # fortran-2.eclass does not handle mpi wrappers
- if use mpi; then
- export FC="mpif90"
- export F77="mpif77"
- export CC="mpicc"
- export CXX="mpic++"
- else
- tc-export FC F77 CC CXX
- fi
-
- use openmp && FORTRAN_NEED_OPENMP=1
-
- fortran-2_pkg_setup
-
- if use openmp; then
- # based on _fortran-has-openmp() of fortran-2.eclass
- local openmp=""
- local fcode=ebuild-openmp-flags.f
- local _fc=$(tc-getFC)
-
- pushd "${T}"
- cat <<- EOF > "${fcode}"
- 1 call omp_get_num_threads
- 2 end
- EOF
-
- for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
- "${_fc}" "${openmp}" "${fcode}" -o "${fcode}.x" && break
- done
-
- rm -f "${fcode}.*"
- popd
-
- append-flags "${openmp}"
- fi
-
- use python && python-single-r1_pkg_setup
-}
-
-src_unpack() {
- unpack ${A}
- mv "${LONG_S}" "${S}"
-}
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/nwchem-6.1.1-makefile.patch \
- "${FILESDIR}"/nwchem-6.1.1-nwchemrc.patch \
- "${FILESDIR}"/nwchem-6.1.1-adjust-dir-length.patch
- use python && epatch "${FILESDIR}"/nwchem-6.1.1-python_makefile.patch
- use doc && epatch "${FILESDIR}"/nwchem-6.3-r1-html_doc.patch
-
- sed \
- -e "s:DBASIS_LIBRARY=\"'\$(SRCDIR)'\":DBASIS_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
- -i src/basis/MakeFile src/basis/GNUmakefile || die
- sed \
- -e "s:DNWPW_LIBRARY=\"'\$(SRCDIR)'\":DNWPW_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
- -i src/nwpw/libraryps/GNUmakefile || die
- sed \
- -e "s:-DCOMPILATION_DIR=\"'\$(TOPDIR)'\":-DCOMPILATION_DIR=\"''\":g" \
- -i src/GNUmakefile src/MakeFile || die
-
- if [[ $(tc-getFC) == *-*-*-*-gfortran ]]; then
- sed \
- -e "s:ifneq (\$(FC),gfortran):ifneq (\$(FC),$(tc-getFC)):g" \
- -e "s:ifeq (\$(FC),gfortran):ifeq (\$(FC),$(tc-getFC)):g" \
- -i src/config/makefile.h || die
- fi
-}
-
-src_compile() {
- export USE_SUBGROUPS=yes
- if use mpi ; then
- export MSG_COMMS=MPI
- export USE_MPI=y
- export USE_MPIF=y
- export MPI_LOC="${EPREFIX}"/usr
- export MPI_INCLUDE=$MPI_LOC/include
- export MPI_LIB=$MPI_LOC/$(get_libdir)
- export LIBMPI="$(mpif90 -showme:link)"
- else
- unset USE_MPI
- unset USE_MPIF
- export MSG_COMMS=TCGMSG
- export ARMCI_NETWORK=SOCKETS
- fi
- if [ "$ARCH" = "amd64" ]; then
- export NWCHEM_TARGET=LINUX64
- elif [ "$ARCH" = "ia64" ]; then
- export NWCHEM_TARGET=LINUX64
- elif [ "$ARCH" = "x86" ]; then
- export NWCHEM_TARGET=LINUX
- elif [ "$ARCH" = "ppc" ]; then
- export NWCHEM_TARGET=LINUX
- else
- die "Unknown architecture"
- fi
- if use python ; then
- if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ]; then
- export USE_PYTHON64=yes
- fi
- export PYTHONHOME=/usr
- export PYTHONVERSION=$(eselect python show --python2 |awk -Fpython '{ print $2 }')
- export PYTHONPATH="./:${S}/contrib/python/"
- export NWCHEM_MODULES="all python"
- else
- export NWCHEM_MODULES="all"
- fi
- use mrcc && export MRCC_THEORY="TRUE"
- if use blas; then
- export HAS_BLAS=yes
- export BLASOPT="$(pkg-config --libs blas)"
- else
- unset HAS_BLAS
- unset BLASOPT
- fi
- export LARGE_FILES="TRUE"
-
- cd src
- emake \
- DIAG=PAR \
- FC=$(tc-getFC) \
- CC=$(tc-getCC) \
- CXX=$(tc-getCXX) \
- NWCHEM_TOP="${S}" \
- NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem"
-
- if use doc; then
- cd "${S}"/doc
- export VARTEXFONTS="${T}/fonts"
- emake \
- DIAG=PAR \
- NWCHEM_TOP="${S}" \
- pdf html
- fi
-}
-
-src_install() {
- dobin bin/${NWCHEM_TARGET}/nwchem
-
- insinto /usr/share/NWChem/basis/
- doins -r src/basis/libraries src/data
- insinto /usr/share/NWChem/nwpw
- doins -r src/nwpw/libraryps
-
- insinto /etc
- doins nwchemrc
-
- use examples && \
- insinto /usr/share/NWChem/ && \
- doins -r examples
-
- use nwchem-tests && \
- insinto /usr/share/NWChem && \
- doins -r QA/tests
-
- use doc && \
- insinto /usr/share/doc/"${P}" && \
- doins -r doc/nwahtml && \
- doins -r web
-
-}
-
-pkg_postinst() {
- echo
- elog "The user will need to link \$HOME/.nwchemrc to /etc/nwchemrc"
- elog "or copy it in order to tell NWChem the right position of the"
- elog "basis library and other necessary data."
- echo
-}
diff --git a/sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild b/sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild
deleted file mode 100644
index f11a699df..000000000
--- a/sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild
+++ /dev/null
@@ -1,292 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs
-
-DATE="2014-09-10"
-
-DESCRIPTION="Delivering High-Performance Computational Chemistry to Science"
-HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page"
-SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV%_p*}.revision${PV#*_p}-src.${DATE}.tar.gz
- http://www.nwchem-sw.org/images/Util_md_sockets.patch.gz
- http://www.nwchem-sw.org/images/Hbar.patch.gz
- http://www.nwchem-sw.org/images/Tcenxtask.patch.gz
- http://www.nwchem-sw.org/images/Hnd_giaxyz_noinline.patch.gz
- http://www.nwchem-sw.org/images/Parallelmpi.patch.gz
- http://www.nwchem-sw.org/images/Makefile_gcc4x.patch.gz
- http://www.nwchem-sw.org/images/Bcast_ccsd.patch.gz
- http://www.nwchem-sw.org/images/Elpa_syncs.patch.gz
- http://www.nwchem-sw.org/images/Xlmpoles_ifort15.patch.gz
- http://www.nwchem-sw.org/images/Ifort15_fpp_offload.patch.gz
- http://www.nwchem-sw.org/images/Texas_iorb.patch.gz
- http://www.nwchem-sw.org/images/Dmapp_inc.patch.gz
- http://www.nwchem-sw.org/images/Print1e.patch.gz
- http://www.nwchem-sw.org/images/Hnd_rys.patch.gz
- http://www.nwchem-sw.org/images/Tddft_grad.patch.gz"
-
-LICENSE="ECL-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="blas cuda doc examples infiniband int64 lapack mrcc nwchem-tests openmp python scalapack"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )
- scalapack? ( !int64 )
- lapack? ( blas )
- scalapack? ( blas )"
-
-RDEPEND="
- sys-fs/sysfsutils
- blas? ( virtual/blas )
- lapack? ( virtual/lapack )
- scalapack? ( virtual/scalapack )
- cuda? ( dev-util/nvidia-cuda-sdk )
- int64? (
- blas? ( virtual/blas[int64] )
- lapack? ( virtual/lapack[int64] )
- )
- python? ( ${PYTHON_DEPS} )"
-DEPEND="${RDEPEND}
- virtual/pkgconfig
- app-shells/tcsh
- virtual/mpi[fortran]
- infiniband? ( || (
- sys-cluster/openmpi[fortran,openmpi_fabrics_ofed]
- sys-cluster/mvapich2[fortran]
- ) )
- doc? (
- dev-texlive/texlive-latex
- dev-tex/latex2html )"
-
-LONG_S="${WORKDIR}/Nwchem-${PV%_p*}.revision${PV#*_p}-src.${DATE}"
-S="${WORKDIR}/${PN}"
-
-pkg_setup() {
- # fortran-2.eclass does not handle mpi wrappers
- export FC="mpif90"
- export F77="mpif77"
- export CC="mpicc"
- export CXX="mpic++"
-
- use openmp && FORTRAN_NEED_OPENMP=1
-
- fortran-2_pkg_setup
-
- if use openmp; then
- # based on _fortran-has-openmp() of fortran-2.eclass
- local openmp=""
- local fcode=ebuild-openmp-flags.f
- local _fc=$(tc-getFC)
-
- pushd "${T}"
- cat <<- EOF > "${fcode}"
- 1 call omp_get_num_threads
- 2 end
- EOF
-
- for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
- "${_fc}" "${openmp}" "${fcode}" -o "${fcode}.x" && break
- done
-
- rm -f "${fcode}.*"
- popd
-
-# append-flags "${openmp}"
-# append-ldflags "${openmp}
- export FC="${FC} ${openmp}"
- export F77="${F77} ${openmp}"
- export CC="${CC} ${openmp}"
- export CXX="${CXX} ${openmp}"
- fi
-
- use python && python-single-r1_pkg_setup
-}
-
-src_unpack() {
- unpack ${A}
- mv "${LONG_S}" "${S}"
-}
-
-src_prepare() {
- pushd "${S}"/src
- for p in Util_md_sockets Hbar Tcenxtask Parallelmpi Makefile_gcc4x Bcast_ccsd Elpa_syncs Xlmpoles_ifort15 Ifort15_fpp_offload Texas_iorb Dmapp_inc Print1e Hnd_rys Tddft_grad
- do epatch "${WORKDIR}"/"${p}.patch"
- done
- cd NWints/hondo
- epatch "${WORKDIR}"/Hnd_giaxyz_noinline.patch
- popd
- epatch "${FILESDIR}"/nwchem-6.1.1-nwchemrc.patch
- epatch "${FILESDIR}"/nwchem-6.5-icosahedron_zcoord.patch
- use python && epatch "${FILESDIR}"/nwchem-6.5-python_makefile.patch
- use doc && epatch "${FILESDIR}"/nwchem-6.3-r1-html_doc.patch
-
- sed \
- -e "s:DBASIS_LIBRARY=\"'\$(SRCDIR)'\":DBASIS_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
- -i src/basis/MakeFile src/basis/GNUmakefile || die
- sed \
- -e "s:DNWPW_LIBRARY=\"'\$(SRCDIR)'\":DNWPW_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
- -i src/nwpw/libraryps/GNUmakefile || die
- sed \
- -e "s:-DCOMPILATION_DIR=\"'\$(TOPDIR)'\":-DCOMPILATION_DIR=\"''\":g" \
- -i src/GNUmakefile src/MakeFile || die
-
- if [[ $(tc-getFC) == *-*-*-*-gfortran ]]; then
- sed \
- -e "s:ifneq (\$(FC),gfortran):ifneq (\$(FC),$(tc-getFC)):g" \
- -e "s:ifeq (\$(FC),gfortran):ifeq (\$(FC),$(tc-getFC)):g" \
- -i src/config/makefile.h || die
- fi
-}
-
-src_compile() {
- export NWCHEM_LONG_PATHS=Y
- use openmp && export USE_OPENMP=1
- export USE_MPI=y
- export USE_MPIF=y
- export USE_MPIF4=y
- export MPI_LOC="${EPREFIX}"/usr
- export MPI_INCLUDE=$MPI_LOC/include
- export MPI_LIB=$MPI_LOC/$(get_libdir)
- export LIBMPI="$(mpif90 -showme:link)"
- if use infiniband; then
- export ARMCI_NETWORK=OPENIB
- export MSG_COMMS=MPI
- else
- unset ARMCI_NETWORK
- fi
- if [ "$ARCH" = "amd64" ]; then
- export NWCHEM_TARGET=LINUX64
- elif [ "$ARCH" = "ia64" ]; then
- export NWCHEM_TARGET=LINUX64
- elif [ "$ARCH" = "x86" ]; then
- export NWCHEM_TARGET=LINUX
- elif [ "$ARCH" = "ppc" ]; then
- export NWCHEM_TARGET=LINUX
- else
- die "Unknown architecture"
- fi
- if use python ; then
- if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ]; then
- export USE_PYTHON64=yes
- fi
- export PYTHONHOME=/usr
- export PYTHONVERSION=$(eselect python show --python2 |awk -Fpython '{ print $2 }')
- export PYTHONPATH="./:${S}/contrib/python/"
- export NWCHEM_MODULES="all python"
- else
- export NWCHEM_MODULES="all"
- fi
- use mrcc && export MRCC_METHODS="TRUE" # Multi Reference Coupled Clusters
- export CCSDTQ="TRUE" # Coupled Clusters Singlets + Dublets + Triplets + Quadruplets
- export CCSDTLR="TRUE" # CCSDT (and CCSDTQ?) Linear Response
- export EACCSD="TRUE" # Electron Affinities at the CCSD level
- export IPCCSD="TRUE" # Ionisation Potentials at the CCSD level
- unset BLASOPT
- local blaspkg="blas"
- local lapackpkg="lapack"
- if use int64; then
- blaspkg="blas-int64"
- lapackpkg="lapack-int64"
- fi
- use blas && export BLASOPT="$($(tc-getPKG_CONFIG) --libs ${blaspkg})"
- use lapack && export BLASOPT+=" $($(tc-getPKG_CONFIG) --libs ${lapackpkg})"
- use scalapack && export BLASOPT+=" $($(tc-getPKG_CONFIG) --libs scalapack)"
- if use cuda; then
- export TCE_CUDA=Y
- export CUDA_PATH=/opt/cuda
- export CUDA=${CUDA_PATH}/bin/nvcc
- export CUDA_FLAGS="-arch=compute_20 -code=sm_20,compute_20"
- export CUDA_INCLUDE="-I${CUDA_PATH}/include"
- export CUDA_LIBS="-L${CUDA_PATH}/$(get_libdir) -lcublas -lcufft -lcudart -lcuda -lstdc++"
- fi
- export LARGE_FILES="TRUE"
-
- cd src
- if use blas && [ "$NWCHEM_TARGET" = "LINUX64" ]; then
- if use int64; then
- export BLAS_SIZE=8
- export LAPACK_SIZE=8
- export SCALAPACK_SIZE=8
- else
- emake \
- DIAG=PAR \
- FC="$(tc-getFC)" \
- CC="$(tc-getCC)" \
- CXX="$(tc-getCXX)" \
- NWCHEM_TOP="${S}" \
- clean
- emake \
- DIAG=PAR \
- FC="$(tc-getFC)" \
- CC="$(tc-getCC)" \
- CXX="$(tc-getCXX)" \
- NWCHEM_TOP="${S}" \
- 64_to_32
- export BLAS_SIZE=4
- export LAPACK_SIZE=4
- export SCALAPACK_SIZE=4
- export USE_64TO32=y
- fi
- fi
- emake \
- DIAG=PAR \
- FC="$(tc-getFC)" \
- CC="$(tc-getCC)" \
- CXX="$(tc-getCXX)" \
- NWCHEM_TOP="${S}" \
- NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem" \
- nwchem_config
- emake \
- DIAG=PAR \
- FC="$(tc-getFC)" \
- CC="$(tc-getCC)" \
- CXX="$(tc-getCXX)" \
- NWCHEM_TOP="${S}" \
- NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem"
-
- if use doc; then
- cd "${S}"/doc
- export VARTEXFONTS="${T}/fonts"
- emake \
- DIAG=PAR \
- NWCHEM_TOP="${S}" \
- pdf html
- fi
-}
-
-src_install() {
- dobin bin/${NWCHEM_TARGET}/nwchem
-
- insinto /usr/share/NWChem/basis/
- doins -r src/basis/libraries src/data
- insinto /usr/share/NWChem/nwpw
- doins -r src/nwpw/libraryps
-
- insinto /etc
- doins nwchemrc
-
- use examples && \
- insinto /usr/share/NWChem/ && \
- doins -r examples
-
- use nwchem-tests && \
- insinto /usr/share/NWChem && \
- doins -r QA/tests
-
- use doc && \
- insinto /usr/share/doc/"${P}" && \
- doins -r doc/nwahtml && \
- doins -r web
-
-}
-
-pkg_postinst() {
- echo
- elog "The user will need to link \$HOME/.nwchemrc to /etc/nwchemrc"
- elog "or copy it in order to tell NWChem the right position of the"
- elog "basis library and other necessary data."
- echo
-}
diff --git a/sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild b/sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild
deleted file mode 100644
index fc2f110e9..000000000
--- a/sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild
+++ /dev/null
@@ -1,278 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs
-
-DATE="2015-10-20"
-
-DESCRIPTION="Delivering High-Performance Computational Chemistry to Science"
-HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page"
-PATCH_REPO="http://www.nwchem-sw.org/images"
-PATCH_LIST="Tddft_mxvec20 Tools_lib64 Config_libs66 Cosmo_meminit Sym_abelian
-Xccvs98 Dplot_tolrho Driver_smalleig Ga_argv Raman_displ Ga_defs Zgesvd Cosmo_dftprint"
-SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV%_p*}.revision${PV#*_p}-src.${DATE}.tar.bz2
- $(for p in ${PATCH_LIST[@]}; do echo ${PATCH_REPO}/${p}.patch.gz; done)"
-
-LICENSE="ECL-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="blas cuda doc examples infiniband int64 lapack mrcc nwchem-tests openmp python scalapack"
-
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )
- scalapack? ( !int64 )
- lapack? ( blas )
- scalapack? ( blas )"
-
-RDEPEND="
- sys-fs/sysfsutils
- blas? ( virtual/blas )
- lapack? ( virtual/lapack )
- scalapack? ( virtual/scalapack )
- cuda? ( dev-util/nvidia-cuda-sdk )
- int64? (
- blas? ( virtual/blas[int64] )
- lapack? ( virtual/lapack[int64] )
- )
- python? ( ${PYTHON_DEPS} )"
-DEPEND="${RDEPEND}
- virtual/pkgconfig
- app-shells/tcsh
- virtual/mpi[fortran]
- infiniband? ( || (
- sys-cluster/openmpi[fortran,openmpi_fabrics_ofed]
- sys-cluster/mvapich2[fortran]
- ) )
- doc? (
- dev-texlive/texlive-latex
- dev-tex/latex2html )"
-
-LONG_S="${WORKDIR}/Nwchem-${PV%_p*}.revision${PV#*_p}-src.${DATE}"
-S="${WORKDIR}/${PN}-${PV%_p*}"
-
-pkg_setup() {
- # fortran-2.eclass does not handle mpi wrappers
- export FC="mpif90"
- export F77="mpif77"
- export CC="mpicc"
- export CXX="mpic++"
-
- use openmp && FORTRAN_NEED_OPENMP=1
-
- fortran-2_pkg_setup
-
- if use openmp; then
- # based on _fortran-has-openmp() of fortran-2.eclass
- local openmp=""
- local fcode=ebuild-openmp-flags.f
- local _fc=$(tc-getFC)
-
- pushd "${T}"
- cat <<- EOF > "${fcode}"
- 1 call omp_get_num_threads
- 2 end
- EOF
-
- for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
- "${_fc}" "${openmp}" "${fcode}" -o "${fcode}.x" && break
- done
-
- rm -f "${fcode}.*"
- popd
-
- export FC="${FC} ${openmp}"
- export F77="${F77} ${openmp}"
- export CC="${CC} ${openmp}"
- export CXX="${CXX} ${openmp}"
- fi
-
- use python && python-single-r1_pkg_setup
-}
-
-src_unpack() {
- unpack ${A}
- mv "${LONG_S}" "${S}"
-}
-
-src_prepare() {
- for p in ${PATCH_LIST[@]}
- do epatch "${WORKDIR}"/"${p}.patch"
- done
- epatch "${FILESDIR}"/nwchem-6.1.1-nwchemrc.patch
- epatch "${FILESDIR}"/nwchem-6.5-icosahedron_zcoord.patch
- epatch "${FILESDIR}"/nwchem-6.6-unique_tags.patch
- use python && epatch "${FILESDIR}"/nwchem-6.5-python_makefile.patch
- use doc && epatch "${FILESDIR}"/nwchem-6.3-r1-html_doc.patch
-
- sed \
- -e "s:DBASIS_LIBRARY=\"'\$(SRCDIR)'\":DBASIS_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
- -i src/basis/MakeFile src/basis/GNUmakefile || die
- sed \
- -e "s:DNWPW_LIBRARY=\"'\$(SRCDIR)'\":DNWPW_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
- -i src/nwpw/libraryps/GNUmakefile || die
- sed \
- -e "s:-DCOMPILATION_DIR=\"'\$(TOPDIR)'\":-DCOMPILATION_DIR=\"''\":g" \
- -i src/GNUmakefile src/MakeFile || die
-
- if [[ $(tc-getFC) == *-*-*-*-gfortran ]]; then
- sed \
- -e "s:ifneq (\$(FC),gfortran):ifneq (\$(FC),$(tc-getFC)):g" \
- -e "s:ifeq (\$(FC),gfortran):ifeq (\$(FC),$(tc-getFC)):g" \
- -i src/config/makefile.h || die
- fi
-}
-
-src_compile() {
- export NWCHEM_LONG_PATHS=Y
- use openmp && export USE_OPENMP=1
- export USE_MPI=y
- export USE_MPIF=y
- export USE_MPIF4=y
- export MPI_LOC="${EPREFIX}"/usr
- export MPI_INCLUDE=$MPI_LOC/include
- export MPI_LIB=$MPI_LOC/$(get_libdir)
- export LIBMPI="$(mpif90 -showme:link)"
- if use infiniband; then
- export ARMCI_NETWORK=OPENIB
- export MSG_COMMS=MPI
- export IB_INCLUDE="-I${MPI_INCLUDE}"
- export IB_LIB="-L${MPI_LIB}"
- else
- unset ARMCI_NETWORK
- fi
- if [ "$ARCH" = "amd64" ]; then
- export NWCHEM_TARGET=LINUX64
- elif [ "$ARCH" = "ia64" ]; then
- export NWCHEM_TARGET=LINUX64
- elif [ "$ARCH" = "x86" ]; then
- export NWCHEM_TARGET=LINUX
- elif [ "$ARCH" = "ppc" ]; then
- export NWCHEM_TARGET=LINUX
- else
- die "Unknown architecture"
- fi
- if use python ; then
- if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ]; then
- export USE_PYTHON64=yes
- fi
- export PYTHONHOME=/usr
- export PYTHONVERSION=$(eselect python show --python2 |awk -Fpython '{ print $2 }')
- export PYTHONPATH="./:${S}/contrib/python/"
- export NWCHEM_MODULES="all python"
- else
- export NWCHEM_MODULES="all"
- fi
- use mrcc && export MRCC_METHODS="TRUE" # Multi Reference Coupled Clusters
- export CCSDTQ="TRUE" # Coupled Clusters Singlets + Dublets + Triplets + Quadruplets
- export CCSDTLR="TRUE" # CCSDT (and CCSDTQ?) Linear Response
- export EACCSD="TRUE" # Electron Affinities at the CCSD level
- export IPCCSD="TRUE" # Ionisation Potentials at the CCSD level
- unset BLASOPT
- local blaspkg="blas"
- local lapackpkg="lapack"
- if use int64; then
- blaspkg="blas-int64"
- lapackpkg="lapack-int64"
- fi
- use blas && export BLASOPT="$($(tc-getPKG_CONFIG) --libs ${blaspkg})"
- use lapack && export BLASOPT+=" $($(tc-getPKG_CONFIG) --libs ${lapackpkg})"
- use scalapack && export BLASOPT+=" $($(tc-getPKG_CONFIG) --libs scalapack)"
- if use cuda; then
- export TCE_CUDA=Y
- export CUDA_PATH=/opt/cuda
- export CUDA=${CUDA_PATH}/bin/nvcc
- export CUDA_FLAGS="-arch=compute_20 -code=sm_20,compute_20"
- export CUDA_INCLUDE="-I${CUDA_PATH}/include"
- export CUDA_LIBS="-L${CUDA_PATH}/$(get_libdir) -lcublas -lcufft -lcudart -lcuda -lstdc++"
- fi
- export LARGE_FILES="TRUE"
-
- cd src
- if use blas && [ "$NWCHEM_TARGET" = "LINUX64" ]; then
- if use int64; then
- export BLAS_SIZE=8
- export LAPACK_SIZE=8
- export SCALAPACK_SIZE=8
- else
- emake \
- DIAG=PAR \
- FC="$(tc-getFC)" \
- CC="$(tc-getCC)" \
- CXX="$(tc-getCXX)" \
- NWCHEM_TOP="${S}" \
- clean
- emake \
- DIAG=PAR \
- FC="$(tc-getFC)" \
- CC="$(tc-getCC)" \
- CXX="$(tc-getCXX)" \
- NWCHEM_TOP="${S}" \
- 64_to_32
- export BLAS_SIZE=4
- export LAPACK_SIZE=4
- export SCALAPACK_SIZE=4
- export USE_64TO32=y
- fi
- fi
- emake \
- DIAG=PAR \
- FC="$(tc-getFC)" \
- CC="$(tc-getCC)" \
- CXX="$(tc-getCXX)" \
- NWCHEM_TOP="${S}" \
- NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem" \
- nwchem_config
- emake \
- DIAG=PAR \
- FC="$(tc-getFC)" \
- CC="$(tc-getCC)" \
- CXX="$(tc-getCXX)" \
- NWCHEM_TOP="${S}" \
- NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem"
-
- if use doc; then
- cd "${S}"/doc
- export VARTEXFONTS="${T}/fonts"
- emake \
- DIAG=PAR \
- NWCHEM_TOP="${S}" \
- pdf html
- fi
-}
-
-src_install() {
- dobin bin/${NWCHEM_TARGET}/nwchem
-
- insinto /usr/share/NWChem/basis/
- doins -r src/basis/libraries src/data
- insinto /usr/share/NWChem/nwpw
- doins -r src/nwpw/libraryps
-
- insinto /etc
- doins nwchemrc
-
- use examples && \
- insinto /usr/share/NWChem/ && \
- doins -r examples
-
- use nwchem-tests && \
- insinto /usr/share/NWChem && \
- doins -r QA/tests
-
- use doc && \
- insinto /usr/share/doc/"${P}" && \
- doins -r doc/nwahtml && \
- doins -r web
-
-}
-
-pkg_postinst() {
- echo
- elog "The user will need to link \$HOME/.nwchemrc to /etc/nwchemrc"
- elog "or copy it in order to tell NWChem the right position of the"
- elog "basis library and other necessary data."
- echo
-}
^ permalink raw reply related [flat|nested] 5+ messages in thread
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2013-07-23 10:08 [gentoo-commits] proj/sci:master commit in: sci-chemistry/nwchem/files/, sci-chemistry/nwchem/ Honza Macháček
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2012-12-02 1:34 Alexey Shvetsov
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