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author | 2007-08-22 22:25:27 +0000 | |
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committer | 2007-08-22 22:25:27 +0000 | |
commit | d65e5e517cd2e34bcb76feccbcffb3ba067b6fbe (patch) | |
tree | 00f0d451cbf062ff21261554d803d8260234236e /sci-chemistry/namd | |
parent | needs >=xorg-server-1.3.0 (diff) | |
download | je_fro-d65e5e517cd2e34bcb76feccbcffb3ba067b6fbe.tar.gz je_fro-d65e5e517cd2e34bcb76feccbcffb3ba067b6fbe.tar.bz2 je_fro-d65e5e517cd2e34bcb76feccbcffb3ba067b6fbe.zip |
Testing namd on amd64.
svn path=/; revision=54
Diffstat (limited to 'sci-chemistry/namd')
-rw-r--r-- | sci-chemistry/namd/Manifest | 12 | ||||
-rw-r--r-- | sci-chemistry/namd/files/digest-namd-2.6 | 3 | ||||
-rw-r--r-- | sci-chemistry/namd/files/namd-2.6-gentoo.patch | 107 | ||||
-rw-r--r-- | sci-chemistry/namd/namd-2.6.ebuild | 96 |
4 files changed, 218 insertions, 0 deletions
diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest new file mode 100644 index 0000000..69e5f28 --- /dev/null +++ b/sci-chemistry/namd/Manifest @@ -0,0 +1,12 @@ +AUX namd-2.6-gentoo.patch 3650 RMD160 e7cc7fa0e20b01295d6f7c83211f961720e8beaa SHA1 f5525811cc092c5125be93cdce0e8c4e22fbee38 SHA256 55fad22d757d83d786b279a50a724499fb915767ade827895d686df16fa829d9 +MD5 5d1edba2a5c3fbaa8df6a84cbffe2d8a files/namd-2.6-gentoo.patch 3650 +RMD160 e7cc7fa0e20b01295d6f7c83211f961720e8beaa files/namd-2.6-gentoo.patch 3650 +SHA256 55fad22d757d83d786b279a50a724499fb915767ade827895d686df16fa829d9 files/namd-2.6-gentoo.patch 3650 +DIST NAMD_2.6_Source.tar.gz 8963319 RMD160 186f79322226a20398031618011104a666237298 SHA1 3b3d83fdc54a520cb6c59b34cde03c9f74d2f443 SHA256 bf353ff13eae18b5a8dc33d79d295e9fe73fb87482858309b7695ce3e24f0d0b +EBUILD namd-2.6.ebuild 2193 RMD160 2e245c094dad8110e06b99d900a109b57f67ea6b SHA1 27122a0c038a86e02b837a170e55e0ac3bd131e3 SHA256 93691566724665f6b46c9a9dda7bb33571e40739f8ad4791725b1ab931f37763 +MD5 eeb976493bdaea80232aebfba4aeb79c namd-2.6.ebuild 2193 +RMD160 2e245c094dad8110e06b99d900a109b57f67ea6b namd-2.6.ebuild 2193 +SHA256 93691566724665f6b46c9a9dda7bb33571e40739f8ad4791725b1ab931f37763 namd-2.6.ebuild 2193 +MD5 f125c37a6c730dd4213cc69fb280de0f files/digest-namd-2.6 250 +RMD160 b71b7ad56f3f23d002ecca0ec623636690c7c895 files/digest-namd-2.6 250 +SHA256 2a4f6569fcce7447d6c81a24a115b4b410ccc4247fb4c4e5a11c63c6708aa4a1 files/digest-namd-2.6 250 diff --git a/sci-chemistry/namd/files/digest-namd-2.6 b/sci-chemistry/namd/files/digest-namd-2.6 new file mode 100644 index 0000000..9726cd1 --- /dev/null +++ b/sci-chemistry/namd/files/digest-namd-2.6 @@ -0,0 +1,3 @@ +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.patch b/sci-chemistry/namd/files/namd-2.6-gentoo.patch new file mode 100644 index 0000000..9a71de8 --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.6-gentoo.patch @@ -0,0 +1,107 @@ +diff -Naur NAMD_2.6_Source/Makefile NAMD_2.6_Source.new/Makefile +--- NAMD_2.6_Source/Makefile 2006-08-30 00:19:25.000000000 -0400 ++++ NAMD_2.6_Source.new/Makefile 2006-09-19 15:56:17.000000000 -0400 +@@ -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-5.9 $(COPTD)CMK_OPTIMIZE=1 ++CHARMLIB = /usr/lib + + # 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 -Naur NAMD_2.6_Source/arch/Linux-i686.fftw NAMD_2.6_Source.new/arch/Linux-i686.fftw +--- NAMD_2.6_Source/arch/Linux-i686.fftw 2004-02-20 17:38:36.000000000 -0500 ++++ NAMD_2.6_Source.new/arch/Linux-i686.fftw 2006-09-19 15:52:32.000000000 -0400 +@@ -1,7 +1,7 @@ + +-FFTDIR=/Projects/namd2/fftw/linux +-FFTINCL=-I$(FFTDIR)/include -I$(HOME)/fftw/include +-FFTLIB=-L$(FFTDIR)/lib -L$(HOME)/fftw/lib -lsrfftw -lsfftw ++#FFTDIR=/Projects/namd2/fftw/linux ++FFTINCL=-I/usr/include ++FFTLIB=-L/usr/lib -lsrfftw -lsfftw + FFTFLAGS=-DNAMD_FFTW + FFT=$(FFTINCL) $(FFTFLAGS) + +diff -Naur NAMD_2.6_Source/arch/Linux-i686.tcl NAMD_2.6_Source.new/arch/Linux-i686.tcl +--- NAMD_2.6_Source/arch/Linux-i686.tcl 2004-10-27 17:40:55.000000000 -0400 ++++ NAMD_2.6_Source.new/arch/Linux-i686.tcl 2006-09-19 15:56:45.000000000 -0400 +@@ -1,8 +1,8 @@ + +-TCLDIR=/Projects/namd2/tcl/linux ++#TCLDIR=/Projects/namd2/tcl/linux + #TCLDIR=$(HOME)/tcl/cray-xt3 +-TCLINCL=-I$(TCLDIR)/include -I$(HOME)/tcl/include +-TCLLIB=-L$(TCLDIR)/lib -L$(HOME)/tcl/lib -ltcl8.3 -ldl ++TCLINCL=-I/usr/include ++TCLLIB=-L/usr/lib -L$(HOME)/tcl/lib -ltcl -ldl + TCLFLAGS=-DNAMD_TCL -DUSE_NON_CONST + TCL=$(TCLINCL) $(TCLFLAGS) + diff --git a/sci-chemistry/namd/namd-2.6.ebuild b/sci-chemistry/namd/namd-2.6.ebuild new file mode 100644 index 0000000..c55c829 --- /dev/null +++ b/sci-chemistry/namd/namd-2.6.ebuild @@ -0,0 +1,96 @@ +# 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="2.6" + +SRC_URI="${MY_PN}_${MY_PV}_Source.tar.gz" + +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="" + +RESTRICT="fetch" + +DEPEND="|| ( app-shells/csh + app-shells/tcsh ) + virtual/libc + =sys-cluster/charm-5.9 + =sci-libs/fftw-2* + =dev-lang/tcl-8.4*" + +CHARM="charm-5.9" +NAMD_ARCH="Linux-i686-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 ${A} + + # apply a few small fixes to make NAMD compile and + # link to the proper libraries + epatch "${FILESDIR}"/namd-2.6-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}.arch || \ + die "Failed to setup ${NAMD_ARCH}.arch" + + # configure + ./config tcl fftw ${NAMD_ARCH} +} + +src_compile() { + # build namd + cd "${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 +} |