diff options
author | Markus Dittrich <markusle@gentoo.org> | 2006-09-19 23:17:56 +0000 |
---|---|---|
committer | Markus Dittrich <markusle@gentoo.org> | 2006-09-19 23:17:56 +0000 |
commit | 3ff665814096c2bf243706e0430da44d55586973 (patch) | |
tree | 69b363df15fe1262ee6b92b54476bdde19b6d27d /sci-chemistry/namd | |
parent | New MythTV eclass that downloads svn revisions and patches and merges them in... (diff) | |
download | historical-3ff665814096c2bf243706e0430da44d55586973.tar.gz historical-3ff665814096c2bf243706e0430da44d55586973.tar.bz2 historical-3ff665814096c2bf243706e0430da44d55586973.zip |
Version bump. This fixes bug #148146.
Package-Manager: portage-2.1.2_pre1
Diffstat (limited to 'sci-chemistry/namd')
-rw-r--r-- | sci-chemistry/namd/ChangeLog | 10 | ||||
-rw-r--r-- | sci-chemistry/namd/Manifest | 52 | ||||
-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 |
5 files changed, 253 insertions, 15 deletions
diff --git a/sci-chemistry/namd/ChangeLog b/sci-chemistry/namd/ChangeLog index c8604e35bc79..de9948b838bf 100644 --- a/sci-chemistry/namd/ChangeLog +++ b/sci-chemistry/namd/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-chemistry/namd -# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/ChangeLog,v 1.3 2005/12/22 16:32:19 markusle Exp $ +# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/ChangeLog,v 1.4 2006/09/19 23:17:56 markusle Exp $ + +*namd-2.6 (19 Sep 2006) + + 19 Sep 2006; Markus Dittrich <markusle@gentoo.org> + +files/namd-2.6-gentoo.patch, +namd-2.6.ebuild: + Version bump. This fixes bug #148146. 22 Dec 2005; Markus Dittrich <markusle@gentoo.org> namd-2.6_beta1.ebuild: removed from package.mask and marked ~x86. Added app-shells/tcsh as diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest index 2c4b2117c2e7..02acea22cf4b 100644 --- a/sci-chemistry/namd/Manifest +++ b/sci-chemistry/namd/Manifest @@ -1,18 +1,44 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - -MD5 ac9a8b3e0a83eb2fb778e7cdc602d2bf ChangeLog 973 -MD5 657770d1760ff431fb8f8972c1c11ccc files/digest-namd-2.6_beta1 70 +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 +AUX namd-barrier-fix-gentoo.patch 2362 RMD160 c6b045a0f2ec9f29bf7f98db7a71c1533f2a20d3 SHA1 5d42ef58f08914ecdf4afe735345ff1264389544 SHA256 f0186fada88b387c0681095174be336d61b2968197d223c15c840c1ca96e4992 MD5 c1bfcdb371a5b74c577aa14d32f88d4b files/namd-barrier-fix-gentoo.patch 2362 +RMD160 c6b045a0f2ec9f29bf7f98db7a71c1533f2a20d3 files/namd-barrier-fix-gentoo.patch 2362 +SHA256 f0186fada88b387c0681095174be336d61b2968197d223c15c840c1ca96e4992 files/namd-barrier-fix-gentoo.patch 2362 +AUX namd-fftw-lib-gentoo.patch 528 RMD160 bb776e58497f0ec672bf5fc9ef22d0717d8c27ad SHA1 b8ca7a0521900bd9dbf725d9ce7ed809ff2d1aa0 SHA256 04528fd52f70cccbba1ccf844b97b256a35f9b1b85ca3ef8a56b4c9308b22696 MD5 df60c46a295673222f31348cee4dda67 files/namd-fftw-lib-gentoo.patch 528 +RMD160 bb776e58497f0ec672bf5fc9ef22d0717d8c27ad files/namd-fftw-lib-gentoo.patch 528 +SHA256 04528fd52f70cccbba1ccf844b97b256a35f9b1b85ca3ef8a56b4c9308b22696 files/namd-fftw-lib-gentoo.patch 528 +AUX namd-makefile-gentoo.patch 2804 RMD160 e52934e5a1aa7ed34e270dc11e780b1bdef3011d SHA1 22d5bd779a280c1287c936dd855f8359fa7b1b4e SHA256 f3945ae8fff113286847d61a00d5a749b1c3a00b65394085e56ff47a0a209250 MD5 099224935074d14aa720ab88f4e36b0b files/namd-makefile-gentoo.patch 2804 +RMD160 e52934e5a1aa7ed34e270dc11e780b1bdef3011d files/namd-makefile-gentoo.patch 2804 +SHA256 f3945ae8fff113286847d61a00d5a749b1c3a00b65394085e56ff47a0a209250 files/namd-makefile-gentoo.patch 2804 +AUX namd-tcl-lib-gentoo.patch 576 RMD160 0992dd4103b97baed85e66a8d4fc04c3991bedd1 SHA1 f1cc944b14f7f77785f1a914d3d50f44d9929aec SHA256 7a57497410f5791b1b9fa0535e66137bd1b4c5008e0253c7467bc40af7b6ac01 MD5 11475a5133058462e1e7a1fd33052974 files/namd-tcl-lib-gentoo.patch 576 -MD5 df166a2ae1cb64196abc394d4fa522ed metadata.xml 272 +RMD160 0992dd4103b97baed85e66a8d4fc04c3991bedd1 files/namd-tcl-lib-gentoo.patch 576 +SHA256 7a57497410f5791b1b9fa0535e66137bd1b4c5008e0253c7467bc40af7b6ac01 files/namd-tcl-lib-gentoo.patch 576 +DIST NAMD_2.6_Source.tar.gz 8963319 RMD160 186f79322226a20398031618011104a666237298 SHA1 3b3d83fdc54a520cb6c59b34cde03c9f74d2f443 SHA256 bf353ff13eae18b5a8dc33d79d295e9fe73fb87482858309b7695ce3e24f0d0b +DIST NAMD_2.6b1_Source.tar.gz 8805263 +EBUILD namd-2.6.ebuild 2284 RMD160 2360a865aa1a029b2aae83b7c906bc625b959464 SHA1 757795138abd2eb5c13abb68c29d46f535768b78 SHA256 1e3b1c80b98e342e234588e1bea9245aba8e3b0db12786e00ef753827fc91e19 +MD5 34d117d6a8a0c4fd79648772cebb6e3b namd-2.6.ebuild 2284 +RMD160 2360a865aa1a029b2aae83b7c906bc625b959464 namd-2.6.ebuild 2284 +SHA256 1e3b1c80b98e342e234588e1bea9245aba8e3b0db12786e00ef753827fc91e19 namd-2.6.ebuild 2284 +EBUILD namd-2.6_beta1.ebuild 2727 RMD160 4124cf25699df813f4da9553072350e919fddba9 SHA1 ea1859e30eb8c776d6c4053bad81880b0d4e38db SHA256 6c34a3a6e135086cbfa62c175cc31ce6a033025af31235071f93301cb19dc376 MD5 8b3e7b8076242855669122ddd67d053f namd-2.6_beta1.ebuild 2727 ------BEGIN PGP SIGNATURE----- -Version: GnuPG v1.4.2 (GNU/Linux) - -iD8DBQFDrS6KI1lqEGTUzyQRAiJPAKCj9Zc3l/+XnF0Qzp54G90D7kGHbwCfR15G -dOc+dol/EPDrYKDashmIzAE= -=3BWD ------END PGP SIGNATURE----- +RMD160 4124cf25699df813f4da9553072350e919fddba9 namd-2.6_beta1.ebuild 2727 +SHA256 6c34a3a6e135086cbfa62c175cc31ce6a033025af31235071f93301cb19dc376 namd-2.6_beta1.ebuild 2727 +MISC ChangeLog 1142 RMD160 3c548f15cc8adf0617784cb1c1e391e1e52efc26 SHA1 1ccedfa697f43d777b35aaeaf7d4d191820b5d58 SHA256 ed7d019945e03794839836e38b0f246a8cbadfcd2b0f09b6974a217db227b9e6 +MD5 30c5a2805e2da63becfc64d537ec9fc9 ChangeLog 1142 +RMD160 3c548f15cc8adf0617784cb1c1e391e1e52efc26 ChangeLog 1142 +SHA256 ed7d019945e03794839836e38b0f246a8cbadfcd2b0f09b6974a217db227b9e6 ChangeLog 1142 +MISC metadata.xml 272 RMD160 42331a21c1e7a31cfe105f705fe3073de14b6b14 SHA1 960809f50e770bf2df44dda2557cf62ab9190c13 SHA256 36ae23839abbf283daf51b7f9585af067c0504484f5ca61e2f08113912becb77 +MD5 df166a2ae1cb64196abc394d4fa522ed metadata.xml 272 +RMD160 42331a21c1e7a31cfe105f705fe3073de14b6b14 metadata.xml 272 +SHA256 36ae23839abbf283daf51b7f9585af067c0504484f5ca61e2f08113912becb77 metadata.xml 272 +MD5 f125c37a6c730dd4213cc69fb280de0f files/digest-namd-2.6 250 +RMD160 b71b7ad56f3f23d002ecca0ec623636690c7c895 files/digest-namd-2.6 250 +SHA256 2a4f6569fcce7447d6c81a24a115b4b410ccc4247fb4c4e5a11c63c6708aa4a1 files/digest-namd-2.6 250 +MD5 657770d1760ff431fb8f8972c1c11ccc files/digest-namd-2.6_beta1 70 +RMD160 5b059f5b89f50a8a96afee174f7d66fcd5377e1d files/digest-namd-2.6_beta1 70 +SHA256 e7cfa75427a67aeeac7e8e221fbd86aab09846d5216194769e1bee46f35d3497 files/digest-namd-2.6_beta1 70 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 000000000000..9726cd1e1806 --- /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 000000000000..9a71de8d3bd7 --- /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 000000000000..8a1d259d35e8 --- /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: /var/cvsroot/gentoo-x86/sci-chemistry/namd/namd-2.6.ebuild,v 1.1 2006/09/19 23:17:56 markusle Exp $ + +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" +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 +} |