* [gentoo-commits] proj/sci:master commit in: sci-chemistry/namd/files/, sci-chemistry/namd/
@ 2013-09-14 12:43 Nicolas Bock
0 siblings, 0 replies; 2+ messages in thread
From: Nicolas Bock @ 2013-09-14 12:43 UTC (permalink / raw
To: gentoo-commits
commit: 76e2047ad3f935a4b8a13a05a2e4ec623fc9fd4f
Author: Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Sat Sep 14 12:40:19 2013 +0000
Commit: Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Sat Sep 14 12:40:19 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=76e2047a
sci-chemistry/namd-2.9: Version bump; ported patches from namd-2.7_beta2-r1 and bumped EAPI to 5.
Package-Manager: portage-2.2.1
---
sci-chemistry/namd/ChangeLog | 11 ++
sci-chemistry/namd/files/namd-2.7-iml-dec.patch | 24 ++++
sci-chemistry/namd/files/namd-2.9-gentoo.patch | 151 ++++++++++++++++++++++++
sci-chemistry/namd/metadata.xml | 5 +
sci-chemistry/namd/namd-2.9.ebuild | 105 ++++++++++++++++
5 files changed, 296 insertions(+)
diff --git a/sci-chemistry/namd/ChangeLog b/sci-chemistry/namd/ChangeLog
new file mode 100644
index 0000000..4954682
--- /dev/null
+++ b/sci-chemistry/namd/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-chemistry/namd
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*namd-2.9 (14 Sep 2013)
+
+ 14 Sep 2013; Nicolas Bock <nicolasbock@gmail.com>
+ +files/namd-2.7-iml-dec.patch, +files/namd-2.9-gentoo.patch, +metadata.xml,
+ +namd-2.9.ebuild:
+ sci-chemistry/namd-2.9: Version bump; ported patches from namd-2.7_beta2-r1
+ and bumped EAPI to 5.
diff --git a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch
new file mode 100644
index 0000000..e5ee3bd
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch
@@ -0,0 +1,24 @@
+diff --git a/src/flipbinpdb.c b/src/flipbinpdb.c
+index 94b71ba..01a2529 100644
+--- a/src/flipbinpdb.c
++++ b/src/flipbinpdb.c
+@@ -9,6 +9,7 @@
+ #include <sys/mman.h>
+ #include <fcntl.h>
+ #include <stdio.h>
++#include <stdlib.h>
+
+ #ifndef MAP_FILE
+ #define MAP_FILE 0
+diff --git a/src/flipdcd.c b/src/flipdcd.c
+index 8ec85b7..1c23433 100644
+--- a/src/flipdcd.c
++++ b/src/flipdcd.c
+@@ -13,6 +13,7 @@
+ #include <sys/mman.h>
+ #include <fcntl.h>
+ #include <stdio.h>
++#include <stdlib.h>
+
+ #ifndef MAP_FILE
+ #define MAP_FILE 0
diff --git a/sci-chemistry/namd/files/namd-2.9-gentoo.patch b/sci-chemistry/namd/files/namd-2.9-gentoo.patch
new file mode 100644
index 0000000..583cc52
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.9-gentoo.patch
@@ -0,0 +1,151 @@
+diff -Naur NAMD_2.9_Source.original/Make.charm NAMD_2.9_Source/Make.charm
+--- NAMD_2.9_Source.original/Make.charm 2012-02-29 19:12:11.000000000 -0700
++++ NAMD_2.9_Source/Make.charm 2013-09-13 21:23:26.000000000 -0600
+@@ -2,5 +2,5 @@
+ # The config script will override this setting if there is a directory
+ # called charm-6.4.0 or charm in the NAMD base directory.
+
+-CHARMBASE = /Projects/namd2/charm-6.4.0
++CHARMBASE = /usr/include/charm-6.4.0
+
+diff -Naur NAMD_2.9_Source.original/Makefile NAMD_2.9_Source/Makefile
+--- NAMD_2.9_Source.original/Makefile 2012-04-27 09:53:24.000000000 -0600
++++ NAMD_2.9_Source/Makefile 2013-09-13 21:30:15.000000000 -0600
+@@ -344,10 +344,10 @@
+ $(DSTDIR)/stringhash.o
+
+ # definitions for Charm routines
+-CHARMC = $(CHARM)/bin/charmc
+-CHARMXI = $(CHARM)/bin/charmc
+-CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1
+-CHARMLIB = $(CHARM)/lib
++CHARMC = /usr/bin/charmc
++CHARMXI = /usr/bin/charmc
++CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1
++CHARMLIB = /usr/gentoo-libdir
+ CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
+ #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
+ #MSA = -DCHARM_HAS_MSA
+@@ -370,7 +370,7 @@
+
+ # Add new executables here.
+
+-BINARIES = namd2 psfgen sortreplicas charmrun flipdcd flipbinpdb
++BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb
+
+ # This should be rebuilt at every compile, but not on Win32.
+ BUILDINFO = $(DSTDIR)/buildinfo
+@@ -386,7 +386,7 @@
+
+ namd2: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS)
+ $(MAKEBUILDINFO)
+- $(CHARMC) -verbose -ld++-option \
++ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \
+ "$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
+ "$(CHARM_MODULES)" -language charm++ \
+ $(BUILDINFO).o \
+@@ -402,16 +402,9 @@
+ $(EXTRALINKLIBS) \
+ -lm -o namd2
+
+-charmrun: $(CHARM)/bin/charmrun # XXX
+- $(COPY) $(CHARM)/bin/charmrun $@
+-
+ $(LIBCUDARTSO):
+ $(COPY) $(CUDASODIR)/$(LIBCUDARTSO) $@;
+
+-WINDOWSBINARIES = namd2.exe psfgen.exe sortreplicas.exe
+-# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
+-windowsbinaries: $(WINDOWSBINARIES)
+-
+ namd2.exe: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) $(TCLDLL)
+ $(MAKEBUILDINFO)
+ $(CHARMC) -verbose \
+@@ -434,11 +427,8 @@
+ charmd_faceless.exe:
+ $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
+
+-charmrun.exe:
+- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
+-
+ psfgen: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS)
+- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
++ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
+
+ psfgen.exe: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL)
+ $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
+@@ -456,7 +446,7 @@
+ $(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -lm
+
+ flipdcd: $(SRCDIR)/flipdcd.c
+- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
+ echo "#!/bin/sh\necho unavailable on this platform" > $@; \
+ chmod +x $@
+
+@@ -466,7 +456,7 @@
+ chmod +x $@
+
+ fixdcd: $(SRCDIR)/fixdcd.c
+- $(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
++ $(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
+
+ dumpdcd: $(SRCDIR)/dumpdcd.c
+ $(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c
+@@ -665,9 +655,7 @@
+
+ DOC_FILES = README.txt announce.txt license.txt notes.txt
+
+-RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2
+-
+-WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL)
++RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen namd2
+
+ release: all
+ $(ECHO) Creating release $(RELEASE_DIR_NAME)
+@@ -678,17 +666,9 @@
+ for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \
+ /bin/rm -rf $$f; \
+ done
+- if [ -r $(CHARM)/bin/charmd ]; then \
+- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
+- fi
+- if [ -r $(CHARM)/bin/charmd_faceless ]; then \
+- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
+- fi
+ chmod -R a+rX $(RELEASE_DIR_NAME)
+ tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
+ gzip $(RELEASE_DIR_NAME).tar
+- echo $(CHARM)
+- ls -l $(CHARM)/lib
+ -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done
+
+ winrelease: winall
+diff -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.fftw NAMD_2.9_Source/arch/Linux-x86_64.fftw
+--- NAMD_2.9_Source.original/arch/Linux-x86_64.fftw 2009-02-21 21:16:04.000000000 -0700
++++ NAMD_2.9_Source/arch/Linux-x86_64.fftw 2013-09-13 20:55:02.000000000 -0600
+@@ -1,7 +1,7 @@
+
+-FFTDIR=/Projects/namd2/fftw/linux-x86_64
++FFTDIR=/usr
+ FFTINCL=-I$(FFTDIR)/include
+-FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw
++FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw
+ FFTFLAGS=-DNAMD_FFTW
+ FFT=$(FFTINCL) $(FFTFLAGS)
+
+diff -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.tcl NAMD_2.9_Source/arch/Linux-x86_64.tcl
+--- NAMD_2.9_Source.original/arch/Linux-x86_64.tcl 2011-06-17 14:38:43.000000000 -0600
++++ NAMD_2.9_Source/arch/Linux-x86_64.tcl 2013-09-13 20:56:30.000000000 -0600
+@@ -1,9 +1,9 @@
+
+ #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64
+-TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded
++TCLDIR=/usr
+ TCLINCL=-I$(TCLDIR)/include
+ #TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl
+-TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread
++TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl -lpthread
+ TCLFLAGS=-DNAMD_TCL
+ TCL=$(TCLINCL) $(TCLFLAGS)
+
diff --git a/sci-chemistry/namd/metadata.xml b/sci-chemistry/namd/metadata.xml
new file mode 100644
index 0000000..e42d0af
--- /dev/null
+++ b/sci-chemistry/namd/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-chemistry</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/namd/namd-2.9.ebuild b/sci-chemistry/namd/namd-2.9.ebuild
new file mode 100644
index 0000000..85114c2
--- /dev/null
+++ b/sci-chemistry/namd/namd-2.9.ebuild
@@ -0,0 +1,105 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils multilib toolchain-funcs flag-o-matic
+
+DESCRIPTION="A powerful and highly parallelized molecular dynamics code"
+LICENSE="namd"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/"
+
+MY_PN="NAMD"
+MY_PV="2.9"
+
+SRC_URI="${MY_PN}_${MY_PV}_Source.tar.gz"
+
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+RESTRICT="fetch"
+
+DEPEND="
+ app-shells/tcsh
+ sys-cluster/charm
+ sci-libs/fftw:2.1
+ dev-lang/tcl"
+
+RDEPEND=${DEPEND}
+
+NAMD_ARCH="Linux-x86_64-g++"
+
+NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD"
+
+S="${WORKDIR}/${MY_PN}_${MY_PV}_Source"
+
+pkg_nofetch() {
+ echo
+ einfo "Please download ${MY_PN}_${MY_PV}_Source.tar.gz from"
+ einfo "${NAMD_DOWNLOAD}"
+ einfo "after agreeing to the license and then move it to"
+ einfo "${DISTDIR}"
+ einfo "Be sure to select the ${MY_PV} version!"
+ echo
+}
+
+src_prepare() {
+ CHARM_VERSION=$(best_version sys-cluster/charm | cut -d- -f3)
+
+ # apply a few small fixes to make NAMD compile and
+ # link to the proper libraries
+ epatch "${FILESDIR}"/namd-2.9-gentoo.patch
+ epatch "${FILESDIR}"/namd-2.7-iml-dec.patch
+ sed \
+ -e "s:charm-.\+:charm-${CHARM_VERSION}:" \
+ -i Make.charm || die
+
+ rm -f charm-6.4.0.tar || die
+
+ # proper compiler and cflags
+ sed \
+ -e "s/g++/$(tc-getCXX)/" \
+ -e "s/gcc/$(tc-getCC)/" \
+ -e "s/CXXOPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/CXXOPTS = ${CXXFLAGS}/" \
+ -e "s/COPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/COPTS = ${CFLAGS}/" \
+ -i arch/${NAMD_ARCH}.arch || die
+
+ sed \
+ -e "s/gentoo-libdir/$(get_libdir)/g" \
+ -e "s/gentoo-charm/charm-${CHARM_VERSION}/g" \
+ -i Makefile || die "Failed gentooizing Makefile."
+ sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.fftw || die
+ sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || die
+}
+
+src_configure() {
+ # configure
+ ./config ${NAMD_ARCH} || die
+}
+
+src_compile() {
+ # build namd
+ cd "${S}/${NAMD_ARCH}"
+ emake
+}
+
+src_install() {
+ dodoc announce.txt license.txt notes.txt
+ cd "${S}/${NAMD_ARCH}"
+
+ # the binaries
+ dobin ${PN}2 psfgen flipbinpdb flipdcd
+}
+
+pkg_postinst() {
+ echo
+ einfo "For detailed instructions on how to run and configure"
+ einfo "NAMD please consults the extensive documentation at"
+ einfo "http://www.ks.uiuc.edu/Research/namd/"
+ einfo "and the NAMD tutorials available at"
+ einfo "http://www.ks.uiuc.edu/Training/Tutorials/"
+ einfo "Have fun :)"
+ echo
+}
^ permalink raw reply related [flat|nested] 2+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-chemistry/namd/files/, sci-chemistry/namd/
@ 2013-10-18 20:33 Christoph Junghans
0 siblings, 0 replies; 2+ messages in thread
From: Christoph Junghans @ 2013-10-18 20:33 UTC (permalink / raw
To: gentoo-commits
commit: 21640ea41422f21eb9d030d7a9f08ac1af0e65f5
Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Oct 18 20:32:10 2013 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Oct 18 20:32:10 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=21640ea4
moved to gx86
---
sci-chemistry/namd/ChangeLog | 20 ----
sci-chemistry/namd/files/namd-2.7-iml-dec.patch | 24 ----
sci-chemistry/namd/files/namd-2.9-gentoo.patch | 151 ------------------------
sci-chemistry/namd/metadata.xml | 5 -
sci-chemistry/namd/namd-2.9.ebuild | 105 ----------------
5 files changed, 305 deletions(-)
diff --git a/sci-chemistry/namd/ChangeLog b/sci-chemistry/namd/ChangeLog
deleted file mode 100644
index 09bd2cd..0000000
--- a/sci-chemistry/namd/ChangeLog
+++ /dev/null
@@ -1,20 +0,0 @@
-# ChangeLog for sci-chemistry/namd
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
- 18 Oct 2013; Christoph Junghans <ottxor@gentoo.org> namd-2.9.ebuild:
- fixed deps
-
- 14 Oct 2013; Nicolas Bock <nicolasbock@gmail.com> namd-2.9.ebuild:
- sci-chemistry/namd-2.9: Some cleanup in ebuild.
-
- 02 Oct 2013; Nicolas Bock <nicolasbock@gmail.com> namd-2.9.ebuild:
- sci-chemistry/namd-2.9: Fixed ebuild The build needs charm using static-libs.
-
-*namd-2.9 (14 Sep 2013)
-
- 14 Sep 2013; Nicolas Bock <nicolasbock@gmail.com>
- +files/namd-2.7-iml-dec.patch, +files/namd-2.9-gentoo.patch, +metadata.xml,
- +namd-2.9.ebuild:
- sci-chemistry/namd-2.9: Version bump; ported patches from namd-2.7_beta2-r1
- and bumped EAPI to 5.
diff --git a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch
deleted file mode 100644
index e5ee3bd..0000000
--- a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff --git a/src/flipbinpdb.c b/src/flipbinpdb.c
-index 94b71ba..01a2529 100644
---- a/src/flipbinpdb.c
-+++ b/src/flipbinpdb.c
-@@ -9,6 +9,7 @@
- #include <sys/mman.h>
- #include <fcntl.h>
- #include <stdio.h>
-+#include <stdlib.h>
-
- #ifndef MAP_FILE
- #define MAP_FILE 0
-diff --git a/src/flipdcd.c b/src/flipdcd.c
-index 8ec85b7..1c23433 100644
---- a/src/flipdcd.c
-+++ b/src/flipdcd.c
-@@ -13,6 +13,7 @@
- #include <sys/mman.h>
- #include <fcntl.h>
- #include <stdio.h>
-+#include <stdlib.h>
-
- #ifndef MAP_FILE
- #define MAP_FILE 0
diff --git a/sci-chemistry/namd/files/namd-2.9-gentoo.patch b/sci-chemistry/namd/files/namd-2.9-gentoo.patch
deleted file mode 100644
index 583cc52..0000000
--- a/sci-chemistry/namd/files/namd-2.9-gentoo.patch
+++ /dev/null
@@ -1,151 +0,0 @@
-diff -Naur NAMD_2.9_Source.original/Make.charm NAMD_2.9_Source/Make.charm
---- NAMD_2.9_Source.original/Make.charm 2012-02-29 19:12:11.000000000 -0700
-+++ NAMD_2.9_Source/Make.charm 2013-09-13 21:23:26.000000000 -0600
-@@ -2,5 +2,5 @@
- # The config script will override this setting if there is a directory
- # called charm-6.4.0 or charm in the NAMD base directory.
-
--CHARMBASE = /Projects/namd2/charm-6.4.0
-+CHARMBASE = /usr/include/charm-6.4.0
-
-diff -Naur NAMD_2.9_Source.original/Makefile NAMD_2.9_Source/Makefile
---- NAMD_2.9_Source.original/Makefile 2012-04-27 09:53:24.000000000 -0600
-+++ NAMD_2.9_Source/Makefile 2013-09-13 21:30:15.000000000 -0600
-@@ -344,10 +344,10 @@
- $(DSTDIR)/stringhash.o
-
- # definitions for Charm routines
--CHARMC = $(CHARM)/bin/charmc
--CHARMXI = $(CHARM)/bin/charmc
--CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1
--CHARMLIB = $(CHARM)/lib
-+CHARMC = /usr/bin/charmc
-+CHARMXI = /usr/bin/charmc
-+CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1
-+CHARMLIB = /usr/gentoo-libdir
- CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
- #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB
- #MSA = -DCHARM_HAS_MSA
-@@ -370,7 +370,7 @@
-
- # Add new executables here.
-
--BINARIES = namd2 psfgen sortreplicas charmrun flipdcd flipbinpdb
-+BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb
-
- # This should be rebuilt at every compile, but not on Win32.
- BUILDINFO = $(DSTDIR)/buildinfo
-@@ -386,7 +386,7 @@
-
- namd2: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS)
- $(MAKEBUILDINFO)
-- $(CHARMC) -verbose -ld++-option \
-+ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \
- "$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
- "$(CHARM_MODULES)" -language charm++ \
- $(BUILDINFO).o \
-@@ -402,16 +402,9 @@
- $(EXTRALINKLIBS) \
- -lm -o namd2
-
--charmrun: $(CHARM)/bin/charmrun # XXX
-- $(COPY) $(CHARM)/bin/charmrun $@
--
- $(LIBCUDARTSO):
- $(COPY) $(CUDASODIR)/$(LIBCUDARTSO) $@;
-
--WINDOWSBINARIES = namd2.exe psfgen.exe sortreplicas.exe
--# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
--windowsbinaries: $(WINDOWSBINARIES)
--
- namd2.exe: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) $(TCLDLL)
- $(MAKEBUILDINFO)
- $(CHARMC) -verbose \
-@@ -434,11 +427,8 @@
- charmd_faceless.exe:
- $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
-
--charmrun.exe:
-- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
--
- psfgen: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS)
-- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
-+ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
-
- psfgen.exe: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL)
- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
-@@ -456,7 +446,7 @@
- $(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -lm
-
- flipdcd: $(SRCDIR)/flipdcd.c
-- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
- echo "#!/bin/sh\necho unavailable on this platform" > $@; \
- chmod +x $@
-
-@@ -466,7 +456,7 @@
- chmod +x $@
-
- fixdcd: $(SRCDIR)/fixdcd.c
-- $(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
-
- dumpdcd: $(SRCDIR)/dumpdcd.c
- $(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c
-@@ -665,9 +655,7 @@
-
- DOC_FILES = README.txt announce.txt license.txt notes.txt
-
--RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2
--
--WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL)
-+RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen namd2
-
- release: all
- $(ECHO) Creating release $(RELEASE_DIR_NAME)
-@@ -678,17 +666,9 @@
- for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \
- /bin/rm -rf $$f; \
- done
-- if [ -r $(CHARM)/bin/charmd ]; then \
-- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
-- fi
-- if [ -r $(CHARM)/bin/charmd_faceless ]; then \
-- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
-- fi
- chmod -R a+rX $(RELEASE_DIR_NAME)
- tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
- gzip $(RELEASE_DIR_NAME).tar
-- echo $(CHARM)
-- ls -l $(CHARM)/lib
- -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done
-
- winrelease: winall
-diff -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.fftw NAMD_2.9_Source/arch/Linux-x86_64.fftw
---- NAMD_2.9_Source.original/arch/Linux-x86_64.fftw 2009-02-21 21:16:04.000000000 -0700
-+++ NAMD_2.9_Source/arch/Linux-x86_64.fftw 2013-09-13 20:55:02.000000000 -0600
-@@ -1,7 +1,7 @@
-
--FFTDIR=/Projects/namd2/fftw/linux-x86_64
-+FFTDIR=/usr
- FFTINCL=-I$(FFTDIR)/include
--FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw
-+FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw
- FFTFLAGS=-DNAMD_FFTW
- FFT=$(FFTINCL) $(FFTFLAGS)
-
-diff -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.tcl NAMD_2.9_Source/arch/Linux-x86_64.tcl
---- NAMD_2.9_Source.original/arch/Linux-x86_64.tcl 2011-06-17 14:38:43.000000000 -0600
-+++ NAMD_2.9_Source/arch/Linux-x86_64.tcl 2013-09-13 20:56:30.000000000 -0600
-@@ -1,9 +1,9 @@
-
- #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64
--TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded
-+TCLDIR=/usr
- TCLINCL=-I$(TCLDIR)/include
- #TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl
--TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread
-+TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl -lpthread
- TCLFLAGS=-DNAMD_TCL
- TCL=$(TCLINCL) $(TCLFLAGS)
-
diff --git a/sci-chemistry/namd/metadata.xml b/sci-chemistry/namd/metadata.xml
deleted file mode 100644
index e42d0af..0000000
--- a/sci-chemistry/namd/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-chemistry</herd>
-</pkgmetadata>
diff --git a/sci-chemistry/namd/namd-2.9.ebuild b/sci-chemistry/namd/namd-2.9.ebuild
deleted file mode 100644
index 1be231a..0000000
--- a/sci-chemistry/namd/namd-2.9.ebuild
+++ /dev/null
@@ -1,105 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-inherit eutils multilib toolchain-funcs flag-o-matic
-
-DESCRIPTION="A powerful and highly parallelized molecular dynamics code"
-LICENSE="namd"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/"
-
-MY_PN="NAMD"
-
-SRC_URI="${MY_PN}_${PV}_Source.tar.gz"
-
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-RESTRICT="fetch"
-
-DEPEND="
- app-shells/tcsh
- || ( >=sys-cluster/charm-6.5.1-r2 <=sys-cluster/charm-6.5.1-r1[static-libs] )
- sci-libs/fftw:2.1
- dev-lang/tcl"
-
-RDEPEND=${DEPEND}
-
-NAMD_ARCH="Linux-x86_64-g++"
-
-NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD"
-
-S="${WORKDIR}/${MY_PN}_${PV}_Source"
-
-pkg_nofetch() {
- echo
- einfo "Please download ${MY_PN}_${PV}_Source.tar.gz from"
- einfo "${NAMD_DOWNLOAD}"
- einfo "after agreeing to the license and then move it to"
- einfo "${DISTDIR}"
- einfo "Be sure to select the ${PV} version!"
- echo
-}
-
-src_prepare() {
- CHARM_VERSION=$(best_version sys-cluster/charm | cut -d- -f3)
-
- # apply a few small fixes to make NAMD compile and
- # link to the proper libraries
- epatch "${FILESDIR}"/namd-2.9-gentoo.patch
- epatch "${FILESDIR}"/namd-2.7-iml-dec.patch
- sed \
- -e "s:charm-.\+:charm-${CHARM_VERSION}:" \
- -i Make.charm || die
-
- # Remove charm distribution. We don't need it.
- rm -f charm-6.4.0.tar || die
-
- # proper compiler and cflags
- sed \
- -e "s/g++/$(tc-getCXX)/" \
- -e "s/gcc/$(tc-getCC)/" \
- -e "s/CXXOPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/CXXOPTS = ${CXXFLAGS}/" \
- -e "s/COPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/COPTS = ${CFLAGS}/" \
- -i arch/${NAMD_ARCH}.arch || die
-
- sed \
- -e "s/gentoo-libdir/$(get_libdir)/g" \
- -e "s/gentoo-charm/charm-${CHARM_VERSION}/g" \
- -i Makefile || die "Failed gentooizing Makefile."
- sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.fftw || die
- sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || die
-}
-
-src_configure() {
- # configure
- ./config ${NAMD_ARCH} --charm-arch . || die
-}
-
-src_compile() {
- # build namd
- cd "${S}/${NAMD_ARCH}"
- emake
-}
-
-src_install() {
- dodoc announce.txt license.txt notes.txt
- cd "${S}/${NAMD_ARCH}"
-
- # the binaries
- dobin ${PN}2 psfgen flipbinpdb flipdcd
-}
-
-pkg_postinst() {
- echo
- einfo "For detailed instructions on how to run and configure"
- einfo "NAMD please consults the extensive documentation at"
- einfo "http://www.ks.uiuc.edu/Research/namd/"
- einfo "and the NAMD tutorials available at"
- einfo "http://www.ks.uiuc.edu/Training/Tutorials/"
- einfo "Have fun :)"
- echo
-}
^ permalink raw reply related [flat|nested] 2+ messages in thread
end of thread, other threads:[~2013-10-18 20:33 UTC | newest]
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2013-09-14 12:43 [gentoo-commits] proj/sci:master commit in: sci-chemistry/namd/files/, sci-chemistry/namd/ Nicolas Bock
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2013-10-18 20:33 Christoph Junghans
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