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

6 files changed, 297 insertions, 0 deletions

diff --git a/sci-chemistry/namd/ChangeLog b/sci-chemistry/namd/ChangeLog
new file mode 100644
index 000000000..495468268
--- /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/Manifest b/sci-chemistry/namd/Manifest
new file mode 100644
index 000000000..738c167a3
--- /dev/null
+++ b/sci-chemistry/namd/Manifest
@@ -0,0 +1 @@
+DIST NAMD_2.9_Source.tar.gz 8814042 SHA256 9ba6a1f87d4600a62847728d7c223295be214f9a72b5bb62552f74d644108424 SHA512 0644814a2799b560d9dcf807ba0047325bc9f0a26e3831b0465d95180784f038d69595e036daac85d59cd919c92d11a0343031975d99deb1fa3052c8a649bdd6 WHIRLPOOL 5494ccb2ee2f2792fe52ad7dcfe6da9d11453f0a9b0859d30698dea56b00d92fae73465967f82bd708abee5cd4ff50b0a6ffde86451e859e2f515af203e09286
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 000000000..e5ee3bd6c
--- /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 000000000..583cc5264
--- /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 000000000..e42d0af60
--- /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 000000000..85114c26c
--- /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
+}