diff options
author | Jeffrey Gardner <je_fro@gentoo.org> | 2009-06-14 04:39:28 +0000 |
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committer | Jeffrey Gardner <je_fro@gentoo.org> | 2009-06-14 04:39:28 +0000 |
commit | 5bb4d804d8263312dcb8c27a6f720574edab0768 (patch) | |
tree | 93916c82a118b3e1a839802b0c574158269f143d /sci-chemistry/namd | |
parent | 2.6.30 now in portage (diff) | |
download | je_fro-5bb4d804d8263312dcb8c27a6f720574edab0768.tar.gz je_fro-5bb4d804d8263312dcb8c27a6f720574edab0768.tar.bz2 je_fro-5bb4d804d8263312dcb8c27a6f720574edab0768.zip |
Adding for the purpose of testing Christian Becke's fix from bug #237634
svn path=/; revision=290
Diffstat (limited to 'sci-chemistry/namd')
-rw-r--r-- | sci-chemistry/namd/Manifest | 4 | ||||
-rw-r--r-- | sci-chemistry/namd/files/digest-namd-2.6 | 3 | ||||
-rw-r--r-- | sci-chemistry/namd/files/namd-2.6-gentoo-amd64.patch | 105 | ||||
-rw-r--r-- | sci-chemistry/namd/files/namd-2.7-gentoo.patch | 117 | ||||
-rw-r--r-- | sci-chemistry/namd/namd-2.7.ebuild | 103 |
5 files changed, 0 insertions, 332 deletions
diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest deleted file mode 100644 index 1ce1af3..0000000 --- a/sci-chemistry/namd/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -AUX namd-2.6-gentoo-amd64.patch 3603 RMD160 c73b9a273716c430004d87d36551a5474e6d3288 SHA1 a815851f7ebc8bb2533f38bb24b529765f2e6c54 SHA256 17f60d6add2b777726507c5badaf4dc5e0eb947d2c49c2562eda242aa8384435 -AUX namd-2.7-gentoo.patch 4046 RMD160 a7d087c47088d9a8df8f804e023d1a882e281e74 SHA1 333fe98dcfb54736f192f3baa82280dcab1fbd21 SHA256 9416859fa9f065f3f269441cbbb44d4f627b71c8cba29ba9e6765c08dae3611f -DIST NAMD_2.7b1_Source.tar.gz 26302404 RMD160 ccb73606d3f0724c55ce022aa130656444825f5e SHA1 955e096a6c70e1e7786d10334bec3cae1eb4fff6 SHA256 cf48b659667fe9e03af27c8d434567525e924ebd08c801321c71361a8f166b2e -EBUILD namd-2.7.ebuild 2599 RMD160 f14dbc6b2e5653ed74e1a3963d1d34696d40664c SHA1 fd9462dd45cb8b4bff14be944a24faf6dbb9ccb2 SHA256 9d23d15d80a6ee61874669c0f79f6ddfb3778264598c3d377b5601dc967d36ee diff --git a/sci-chemistry/namd/files/digest-namd-2.6 b/sci-chemistry/namd/files/digest-namd-2.6 deleted file mode 100644 index 9726cd1..0000000 --- a/sci-chemistry/namd/files/digest-namd-2.6 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 c7d3b5101d1de0eca045e0d2f0ffffe3 NAMD_2.6_Source.tar.gz 8963319 -RMD160 186f79322226a20398031618011104a666237298 NAMD_2.6_Source.tar.gz 8963319 -SHA256 bf353ff13eae18b5a8dc33d79d295e9fe73fb87482858309b7695ce3e24f0d0b NAMD_2.6_Source.tar.gz 8963319 diff --git a/sci-chemistry/namd/files/namd-2.6-gentoo-amd64.patch b/sci-chemistry/namd/files/namd-2.6-gentoo-amd64.patch deleted file mode 100644 index 9d65e51..0000000 --- a/sci-chemistry/namd/files/namd-2.6-gentoo-amd64.patch +++ /dev/null @@ -1,105 +0,0 @@ -diff -aurN NAMD_2.6_Source-orig/Makefile NAMD_2.6_Source/Makefile ---- NAMD_2.6_Source-orig/Makefile 2007-08-24 13:35:35.659265380 -0500 -+++ NAMD_2.6_Source/Makefile 2007-08-24 13:42:09.933733803 -0500 -@@ -232,10 +232,10 @@ - $(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/charm-9999 $(COPTD)CMK_OPTIMIZE=1 -+CHARMLIB = /usr/lib64 - - # Libraries we may have changed - LIBS = $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL) -@@ -255,7 +255,7 @@ - - # Add new executables here. - --BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb -+BINARIES = namd2 psfgen flipdcd flipbinpdb - - # This should be rebuilt at every compile, but not on Win32. - BUILDINFO = $(DSTDIR)/buildinfo -@@ -284,11 +284,6 @@ - $(CHARMOPTS) \ - -lm -o namd2 - --charmrun: $(CHARM)/bin/charmrun # XXX -- $(COPY) $(CHARM)/bin/charmrun $@ -- --windowsbinaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe -- - namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) - $(MAKEBUILDINFO) - $(CHARMC) -verbose \ -@@ -309,9 +304,6 @@ - charmd_faceless.exe: - $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe - --charmrun.exe: -- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe -- - psfgen: $(DSTDIR) $(SBOBJS) - $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(TCLLIB) $(TCLAPPLIB) -lm - -@@ -571,9 +563,7 @@ - - DOC_FILES = README.txt announce.txt license.txt notes.txt - --RELEASE_FILES = flipdcd flipbinpdb psfgen charmrun namd2 -- --WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmrun.exe charmd.exe charmd_faceless.exe $(TCLDLL) -+RELEASE_FILES = flipdcd flipbinpdb psfgen namd2 - - release: all - $(ECHO) Creating release $(RELEASE_DIR_NAME) -@@ -582,17 +572,9 @@ - for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done - cp -r .rootdir/lib $(RELEASE_DIR_NAME) - /bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS -- if [ -r $(CHARM)/bin/charmd ]; then \ -- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ -- fi -- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ -- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ -- fi - chmod -R a+rX $(RELEASE_DIR_NAME) - tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) - gzip $(RELEASE_DIR_NAME).tar -- echo $(CHARM) -- ls -l $(CHARM)/lib - -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done - - winrelease: winall -diff -aurN NAMD_2.6_Source-orig/arch/Linux-amd64.fftw NAMD_2.6_Source/arch/Linux-amd64.fftw ---- NAMD_2.6_Source-orig/arch/Linux-amd64.fftw 2007-08-24 13:35:35.663265610 -0500 -+++ NAMD_2.6_Source/arch/Linux-amd64.fftw 2007-08-24 13:43:45.623186828 -0500 -@@ -1,7 +1,6 @@ - --FFTDIR=/Projects/namd2/fftw/linux-amd64 --FFTINCL=-I$(FFTDIR)/include -I$(HOME)/fftw/include --FFTLIB=-L$(FFTDIR)/lib -L$(HOME)/fftw/lib -lsrfftw -lsfftw -+FFTINCL=-I/usr/include -+FFTLIB=-L/usr/lib64 -lsrfftw -lsfftw - FFTFLAGS=-DNAMD_FFTW - FFT=$(FFTINCL) $(FFTFLAGS) - -diff -aurN NAMD_2.6_Source-orig/arch/Linux-amd64.tcl NAMD_2.6_Source/arch/Linux-amd64.tcl ---- NAMD_2.6_Source-orig/arch/Linux-amd64.tcl 2007-08-24 13:35:35.663265610 -0500 -+++ NAMD_2.6_Source/arch/Linux-amd64.tcl 2007-08-24 13:46:44.921404457 -0500 -@@ -1,7 +1,6 @@ - --TCLDIR=/Projects/namd2/tcl/linux-amd64 --TCLINCL=-I$(TCLDIR)/include -I$(HOME)/tcl/include --TCLLIB=-L$(TCLDIR)/lib -L$(HOME)/tcl/lib -ltcl8.3 -ldl --TCLFLAGS=-DNAMD_TCL -+TCLINCL=-I/usr/include -+TCLLIB=-L/usr/lib64 -L$(HOME)/tcl/lib -ltcl -ldl -+TCLFLAGS=-DNAMD_TCL -DUSE_NON_CONST - TCL=$(TCLINCL) $(TCLFLAGS) - diff --git a/sci-chemistry/namd/files/namd-2.7-gentoo.patch b/sci-chemistry/namd/files/namd-2.7-gentoo.patch deleted file mode 100644 index 733ee8e..0000000 --- a/sci-chemistry/namd/files/namd-2.7-gentoo.patch +++ /dev/null @@ -1,117 +0,0 @@ -diff -aurN NAMD_2.7b1_Source.orig/Make.charm NAMD_2.7b1_Source/Make.charm ---- NAMD_2.7b1_Source.orig/Make.charm 2009-06-07 15:15:11.000000000 -0500 -+++ NAMD_2.7b1_Source/Make.charm 2009-06-07 15:15:11.000000000 -0500 -@@ -2,5 +2,5 @@ - # The config script will override this setting if there is a directory - # called charm-6.1 or charm in the NAMD base directory. - --CHARMBASE = /Projects/namd2/charm-6.1 -+CHARMBASE = /usr/include/charm-6.1.2 - -diff -aurN NAMD_2.7b1_Source.orig/Makefile NAMD_2.7b1_Source/Makefile ---- NAMD_2.7b1_Source.orig/Makefile 2009-06-07 15:15:11.000000000 -0500 -+++ NAMD_2.7b1_Source/Makefile 2009-06-07 15:15:11.000000000 -0500 -@@ -297,10 +297,10 @@ - $(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 - - # Libraries we may have changed - LIBS = $(CUDAOBJS) $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL) -@@ -320,7 +320,7 @@ - - # Add new executables here. - --BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb -+BINARIES = namd2 psfgen flipdcd flipbinpdb - - # This should be rebuilt at every compile, but not on Win32. - BUILDINFO = $(DSTDIR)/buildinfo -@@ -351,14 +351,6 @@ - $(CHARMOPTS) \ - -lm -o namd2 - --charmrun: $(CHARM)/bin/charmrun # XXX -- $(COPY) $(CHARM)/bin/charmrun $@ -- --WINDOWSBINARIES = namd2.exe psfgen.exe --# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe -- --windowsbinaries: $(WINDOWSBINARIES) -- - namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) $(TCLDLL) - $(MAKEBUILDINFO) - $(CHARMC) -verbose \ -@@ -381,9 +373,6 @@ - charmd_faceless.exe: - $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe - --charmrun.exe: -- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe -- - psfgen: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS) - $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm - -@@ -700,9 +689,7 @@ - - DOC_FILES = README.txt announce.txt license.txt notes.txt - --RELEASE_FILES = flipdcd flipbinpdb psfgen charmrun namd2 -- --WINDOWS_RELEASE_FILES = $(WINDOWSBINARIES) $(TCLDLL) -+RELEASE_FILES = flipdcd flipbinpdb psfgen namd2 - - release: all - $(ECHO) Creating release $(RELEASE_DIR_NAME) -@@ -711,17 +698,9 @@ - for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done - cp -r .rootdir/lib $(RELEASE_DIR_NAME) - /bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS -- 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 $$f; $(LDD) $$f; done - - winrelease: winall -diff -aurN NAMD_2.7b1_Source.orig/arch/Linux-x86_64.fftw NAMD_2.7b1_Source/arch/Linux-x86_64.fftw ---- NAMD_2.7b1_Source.orig/arch/Linux-x86_64.fftw 2009-06-07 15:15:11.000000000 -0500 -+++ NAMD_2.7b1_Source/arch/Linux-x86_64.fftw 2009-06-07 15:15:11.000000000 -0500 -@@ -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) $(FFTFLAGS) - -diff -aurN NAMD_2.7b1_Source.orig/arch/Linux-x86_64.tcl NAMD_2.7b1_Source/arch/Linux-x86_64.tcl ---- NAMD_2.7b1_Source.orig/arch/Linux-x86_64.tcl 2009-06-07 15:15:11.000000000 -0500 -+++ NAMD_2.7b1_Source/arch/Linux-x86_64.tcl 2009-06-07 18:25:07.000000000 -0500 -@@ -1,7 +1,7 @@ - --TCLDIR=/Projects/namd2/tcl/linux-x86_64 -+TCLDIR=/usr - TCLINCL=-I$(TCLDIR)/include --TCLLIB=-L$(TCLDIR)/lib -ltcl8.3 -ldl -+TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl - TCLFLAGS=-DNAMD_TCL - TCL=$(TCLINCL) $(TCLFLAGS) - diff --git a/sci-chemistry/namd/namd-2.7.ebuild b/sci-chemistry/namd/namd-2.7.ebuild deleted file mode 100644 index baa6b7c..0000000 --- a/sci-chemistry/namd/namd-2.7.ebuild +++ /dev/null @@ -1,103 +0,0 @@ -# Copyright 1999-2006 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit eutils 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="2.7b1" - -SRC_URI="${MY_PN}_${MY_PV}_Source.tar.gz" - -SLOT="0" -KEYWORDS="~amd64" -IUSE="" - -RESTRICT="fetch" - -DEPEND="|| ( app-shells/csh - app-shells/tcsh ) - virtual/libc - sys-cluster/charm - =sci-libs/fftw-2* - dev-lang/tcl" - -# CHARM="charm-9999" -# NAMD_ARCH="Linux-amd64-g++" -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_unpack() { - unpack ${A} - cd "${WORKDIR}" -# apply a few small fixes to make NAMD compile and - # link to the proper libraries - epatch "${FILESDIR}"/namd-2.7-gentoo.patch - cd "${S}" - # proper compiler and cflags - sed -e "s/g++/$(tc-getCXX)/" \ - -e "s/CXXOPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/CXXOPTS = ${CXXFLAGS}/" \ - -e "s/gcc/$(tc-getCC)/" \ - -e "s/COPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/COPTS = ${CFLAGS}/" \ - -i arch/${NAMD_ARCH}.arch || \ - die "Failed to setup ${NAMD_ARCH}.arch" - - sed -e "s/gentoo-libdir/$(get_libdir)/g" \ - -e "s/gentoo-charm/charm-6.1.2/g" \ - -i Makefile || die "Failed gentooizing Makefile." - sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.fftw || \ - die "Failed gentooizing Linux-x86_64.fftw." - sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || \ - die "Failed gentooizing Linux-x86_64.tcl." - - # configure - ./config ${NAMD_ARCH} -} - -src_compile() { - # build namd - cd "${S}/${NAMD_ARCH}" - emake || die "Failed to build namd" -} - -src_install() { - cd "${S}/${NAMD_ARCH}" - - # the binaries - dobin ${PN}2 psfgen flipbinpdb flipdcd || \ - die "Failed to install binaries" - - cd "${S}" - - # some docs - dodoc announce.txt license.txt notes.txt || \ - die "Failed to install docs" -} - -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 -} |