diff options
| -rw-r--r-- | sci-chemistry/namd/Manifest | 3 | ||||
| -rw-r--r-- | sci-chemistry/namd/files/namd-2.7-gentoo.patch | 117 | ||||
| -rw-r--r-- | sci-chemistry/namd/namd-2.7.ebuild | 36 |
3 files changed, 141 insertions, 15 deletions
diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest index 440f6f0..011f671 100644 --- a/sci-chemistry/namd/Manifest +++ b/sci-chemistry/namd/Manifest @@ -1,3 +1,4 @@ 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 2244 RMD160 f02c25aae72ea2165d923f58d4e7c1da13e01a48 SHA1 782d153320df1a6634a3962a6868b5ea9c5305e8 SHA256 747a19d3373be9efcbdf47f8a287c1c629415eccf00ff923555e4d187adaefc0 +EBUILD namd-2.7.ebuild 2605 RMD160 c61db970aafe40781d793f9d082ec3f9d9918374 SHA1 5563379a8bc6a2ce9fc3fe595154492c64fac67b SHA256 3f1e26645d52bcffbca96d17668af948905833cd10d414dfafd73e90efef0be1 diff --git a/sci-chemistry/namd/files/namd-2.7-gentoo.patch b/sci-chemistry/namd/files/namd-2.7-gentoo.patch new file mode 100644 index 0000000..733ee8e --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.7-gentoo.patch @@ -0,0 +1,117 @@ +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 index d8de799..07a0ec8 100644 --- a/sci-chemistry/namd/namd-2.7.ebuild +++ b/sci-chemistry/namd/namd-2.7.ebuild @@ -2,8 +2,6 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -# This is broken and needs work. - inherit eutils toolchain-funcs flag-o-matic DESCRIPTION="A powerful and highly parallelized molecular dynamics code" @@ -28,7 +26,7 @@ DEPEND="|| ( app-shells/csh =sci-libs/fftw-2* =dev-lang/tcl-8.4*" -CHARM="charm-9999" +# CHARM="charm-9999" # NAMD_ARCH="Linux-amd64-g++" NAMD_ARCH="Linux-x86_64-g++" @@ -46,21 +44,31 @@ pkg_nofetch() { echo } -src_prepare() { - # apply a few small fixes to make NAMD compile and +src_unpack() { + unpack ${A} + cd "${WORKDIR}" +# apply a few small fixes to make NAMD compile and # link to the proper libraries -# epatch "${FILESDIR}"/namd-2.6-gentoo-amd64.patch - + epatch "${FILESDIR}"/namd-2.7-gentoo.patch + cd "${S}" # proper compiler and cflags -# sed -e "s/g++/$(tc-getCXX)/" \ -# -e "s/CXXOPTS = -O3 -march=pentiumpro -ffast-math -static/CXXOPTS = ${CXXFLAGS}/" \ -# -e "s/gcc/$(tc-getCC)/" \ -# -e "s/COPTS = -O3 -march=pentiumpro -ffast-math -static/COPTS = ${CFLAGS}/" \ -# -i arch/${NAMD_ARCH}-g++.arch || \ -# die "Failed to setup ${NAMD_ARCH}.arch" + sed -e "s/g++/$(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 tcl fftw ${NAMD_ARCH} + ./config ${NAMD_ARCH} } src_compile() { |