From: Christoph Junghans Date: Sat, 7 Mar 2015 01:18:28 +0000 (+0000) Subject: version bump X-Git-Url: http://git.tremily.us/gitweb.cgi?a=commitdiff_plain;h=847cd9df94f096fbebc28a3127706ac33d2bbfa0;p=gentoo.git version bump Package-Manager: portage-2.2.14/cvs/Linux x86_64 Manifest-Sign-Key: 0xC2000586 --- diff --git a/sci-chemistry/namd/ChangeLog b/sci-chemistry/namd/ChangeLog index 901dce286e4a..5e92658dfcff 100644 --- a/sci-chemistry/namd/ChangeLog +++ b/sci-chemistry/namd/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-chemistry/namd -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/ChangeLog,v 1.20 2013/12/13 19:39:42 nicolasbock Exp $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/ChangeLog,v 1.21 2015/03/07 01:18:22 ottxor Exp $ + +*namd-2.10 (07 Mar 2015) + + 07 Mar 2015; Christoph Junghans + +files/namd-2.10-gentoo.patch, +namd-2.10.ebuild: + version bump 13 Dec 2013; Nicolas Bock metadata.xml: sci-chemistry/namd: Updated maintainer email to gentoo.org diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest index 8e1230d973ec..cab1555dff06 100644 --- a/sci-chemistry/namd/Manifest +++ b/sci-chemistry/namd/Manifest @@ -1,6 +1,7 @@ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 +AUX namd-2.10-gentoo.patch 4636 SHA256 2bee11bb1bfa086c12acf84abf94e35c7bcba8dc269d80ce6aa20490b9ef6a0c SHA512 28ffbedb05d24a74e05a4f65424a25a4598e2172b7b4ab07fe84570e3162373e4e018f66077636bb097c6e0687666ac81dbb8b925a195f23c269829ebb9234c8 WHIRLPOOL 3616c28a38b92fe1d376fa413c6f565bd5727edfa821c98682c1cbc3834e95d1c1093c43ba99cb26904637d661c31a893c3f6e7a838b07c696c2bd3689795ab9 AUX namd-2.6-gentoo.patch 3650 SHA256 55fad22d757d83d786b279a50a724499fb915767ade827895d686df16fa829d9 SHA512 7a5e9274307784445808f84378f875a68821ef8db7c8ede76439ae4d74d00c618144dd520bc82c433b5c7e9a08d586363b028646a140db19036bfab060133abf 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b/sci-chemistry/namd/files/namd-2.10-gentoo.patch new file mode 100644 index 000000000000..e578c131c36d --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.10-gentoo.patch @@ -0,0 +1,124 @@ +diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw NAMD_2.10_Source/arch/Linux-x86_64.fftw +--- NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw 2015-03-06 17:53:44.170416075 -0700 ++++ NAMD_2.10_Source/arch/Linux-x86_64.fftw 2015-03-06 17:54:46.641162629 -0700 +@@ -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) $(FFTFLAGS) + +diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl NAMD_2.10_Source/arch/Linux-x86_64.tcl +--- NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl 2015-03-06 17:53:44.170416075 -0700 ++++ NAMD_2.10_Source/arch/Linux-x86_64.tcl 2015-03-06 17:54:46.641162629 -0700 +@@ -1,9 +1,9 @@ + + #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64 +-TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded ++TCLDIR=/usr + TCLINCL=-I$(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 -Naur NAMD_2.10_Source.orig/Makefile NAMD_2.10_Source/Makefile +--- NAMD_2.10_Source.orig/Makefile 2015-03-06 17:53:44.170416075 -0700 ++++ NAMD_2.10_Source/Makefile 2015-03-06 18:01:32.645966590 -0700 +@@ -389,10 +389,10 @@ + $(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 -module CkMulticast + #CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB + #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB +@@ -418,7 +418,7 @@ + + # Add new executables here. + +-BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb charmrun ++BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb + + # This should be rebuilt at every compile, but not on Win32. + BUILDINFO = $(DSTDIR)/buildinfo +@@ -434,7 +434,7 @@ + + namd2: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) + $(MAKEBUILDINFO) +- $(CHARMC) -verbose -ld++-option \ ++ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \ + '$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS) $(CXXMICOPTS)' \ + "$(CHARM_MODULES)" -language charm++ \ + $(BUILDINFO).o \ +@@ -484,11 +484,8 @@ + 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 +@@ -506,7 +503,7 @@ + $(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 $@ + +@@ -516,7 +513,7 @@ + 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 +@@ -711,9 +708,7 @@ + + 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) +@@ -724,17 +719,9 @@ + 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 --git a/sci-chemistry/namd/namd-2.10.ebuild b/sci-chemistry/namd/namd-2.10.ebuild new file mode 100644 index 000000000000..e85b7f3b1ede --- /dev/null +++ b/sci-chemistry/namd/namd-2.10.ebuild @@ -0,0 +1,105 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/namd-2.10.ebuild,v 1.1 2015/03/07 01:18:22 ottxor Exp $ + +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" + +RDEPEND=" + >=sys-cluster/charm-6.5.1-r2 + sci-libs/fftw:3.0 + dev-lang/tcl" + +DEPEND="${RDEPEND} + app-shells/tcsh" + +NAMD_ARCH="Linux-x86_64-g++" + +NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD" + +S="${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 "${FILESDIR}"/namd-2.10-gentoo.patch + epatch "${FILESDIR}"/namd-2.7-iml-dec.patch + sed \ + -e "/CHARMBASE =/s:= .*:= /usr/bin/charm-${CHARM_VERSION}:" \ + -i Make.charm || die + + # Remove charm distribution. We don't need it. + rm -f charm-*.tar + + # proper compiler and cflags + sed \ + -e "s/g++.*/$(tc-getCXX)/" \ + -e "s/gcc.*/$(tc-getCC)/" \ + -e "s/CXXOPTS = .*/CXXOPTS = ${CXXFLAGS} ${LDFLAGS}/" \ + -e "s/COPTS = .*/COPTS = ${CFLAGS} ${LDFLAGS}/" \ + -i arch/${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@/lib@/$(get_libdir)@g" -e '/FFTDIR=/s@=.*@=/usr@' -i arch/Linux-x86_64.fftw3 || die + sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || die +} + +src_configure() { + # configure + ./config ${NAMD_ARCH} --with-fftw3 --charm-arch . || die +} + +src_compile() { + # build namd + cd "${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 +}