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Fri, 18 Oct 2013 20:33:15 +0000 (UTC) From: "Christoph Junghans" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Christoph Junghans" Message-ID: <1382128330.21640ea41422f21eb9d030d7a9f08ac1af0e65f5.ottxor@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/namd/files/, sci-chemistry/namd/ X-VCS-Repository: proj/sci X-VCS-Files: sci-chemistry/namd/ChangeLog sci-chemistry/namd/files/namd-2.7-iml-dec.patch sci-chemistry/namd/files/namd-2.9-gentoo.patch sci-chemistry/namd/metadata.xml sci-chemistry/namd/namd-2.9.ebuild X-VCS-Directories: sci-chemistry/namd/files/ sci-chemistry/namd/ X-VCS-Committer: ottxor X-VCS-Committer-Name: Christoph Junghans X-VCS-Revision: 21640ea41422f21eb9d030d7a9f08ac1af0e65f5 X-VCS-Branch: master Date: Fri, 18 Oct 2013 20:33:15 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 1b3355e1-e7bc-420a-89bb-6321ef56b19f X-Archives-Hash: 611c932e89e7718097545c1577e4817a commit: 21640ea41422f21eb9d030d7a9f08ac1af0e65f5 Author: Christoph Junghans gentoo org> AuthorDate: Fri Oct 18 20:32:10 2013 +0000 Commit: Christoph Junghans gentoo 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 namd-2.9.ebuild: - fixed deps - - 14 Oct 2013; Nicolas Bock namd-2.9.ebuild: - sci-chemistry/namd-2.9: Some cleanup in ebuild. - - 02 Oct 2013; Nicolas Bock 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 - +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 - #include - #include -+#include - - #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 - #include - #include -+#include - - #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 @@ - - - - sci-chemistry - 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 -}