diff options
author | Donnie Berkholz <dberkholz@gentoo.org> | 2010-08-04 13:59:56 -0500 |
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committer | Donnie Berkholz <dberkholz@gentoo.org> | 2010-08-04 13:59:56 -0500 |
commit | c6b1a3c018eb8ad26f589582212d121fa6b6722e (patch) | |
tree | 36cc9aba50cc79f741c73dff6db1bb87c46d68db /sci-chemistry | |
parent | pyglet: drop, newer version in science overlay. (diff) | |
download | dberkholz-c6b1a3c018eb8ad26f589582212d121fa6b6722e.tar.gz dberkholz-c6b1a3c018eb8ad26f589582212d121fa6b6722e.tar.bz2 dberkholz-c6b1a3c018eb8ad26f589582212d121fa6b6722e.zip |
namd: bump to 2.7 beta 3 for testing.
Diffstat (limited to 'sci-chemistry')
-rw-r--r-- | sci-chemistry/namd/ChangeLog | 72 | ||||
-rw-r--r-- | sci-chemistry/namd/Manifest | 13 | ||||
-rw-r--r-- | sci-chemistry/namd/files/namd-2.6-gentoo.patch | 107 | ||||
-rw-r--r-- | sci-chemistry/namd/files/namd-2.7-gentoo.patch | 117 | ||||
-rw-r--r-- | sci-chemistry/namd/files/namd-2.7-iml-dec.patch | 24 | ||||
-rw-r--r-- | sci-chemistry/namd/files/namd-2.7-ldflags.patch | 41 | ||||
-rw-r--r-- | sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch | 126 | ||||
-rw-r--r-- | sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch | 61 | ||||
-rw-r--r-- | sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch | 15 | ||||
-rw-r--r-- | sci-chemistry/namd/files/namd-makefile-gentoo.patch | 88 | ||||
-rw-r--r-- | sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch | 16 | ||||
-rw-r--r-- | sci-chemistry/namd/metadata.xml | 9 | ||||
-rw-r--r-- | sci-chemistry/namd/namd-2.7_beta3.ebuild | 116 |
13 files changed, 805 insertions, 0 deletions
diff --git a/sci-chemistry/namd/ChangeLog b/sci-chemistry/namd/ChangeLog new file mode 100644 index 0000000..4c3f229 --- /dev/null +++ b/sci-chemistry/namd/ChangeLog @@ -0,0 +1,72 @@ +# ChangeLog for sci-chemistry/namd +# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/ChangeLog,v 1.13 2010/06/24 20:37:03 jlec Exp $ + +*namd-2.7_beta2-r1 (24 Jun 2010) + + 24 Jun 2010; Justin Lecher <jlec@gentoo.org> namd-2.7_beta2.ebuild, + +namd-2.7_beta2-r1.ebuild, +files/namd-2.7-iml-dec.patch, + +files/namd-2.7-ldflags.patch: + respect LDFLAGS and declarations + + 24 Jun 2010; Justin Lecher <jlec@gentoo.org> -namd-2.7_beta1.ebuild: + Removed unneeded + +*namd-2.7_beta2 (24 Apr 2010) +*namd-2.7_beta1 (24 Apr 2010) + + 24 Apr 2010; Donnie Berkholz <dberkholz@gentoo.org>; + +namd-2.7_beta1.ebuild, +namd-2.7_beta2.ebuild, -namd-2.7.ebuild, + +files/namd-2.7_beta2-gentoo.patch: + Bump to 2.7_beta2. The previous 2.7 ebuild was actually 2.7 beta 1 but was + not named as such, so rename it to allow people to upgrade to beta 2. + + 23 Apr 2010; Donnie Berkholz <dberkholz@gentoo.org>; namd-2.7.ebuild: + All tc-get* sed replacements must happen before C*FLAGS-related ones, + otherwise we can replace things like -frecord-gcc-switches with + -frecord-x86_64-pc-linux-gnu-gcc-switches. + + 23 Sep 2009; Patrick Lauer <patrick@gentoo.org> namd-2.6.ebuild, + namd-2.7.ebuild: + Remove virtual/libc + +*namd-2.7 (08 Jun 2009) + + 08 Jun 2009; Jeff Gardner <je_fro@gentoo.org> namd-2.6.ebuild, + +namd-2.7.ebuild, +files/namd-2.7-gentoo.patch: + Latest version for testing. If anyone wants to modify and test on x86 + please feel free :) + + 03 Jun 2008; Michael Sterrett <mr_bones_@gentoo.org> namd-2.6.ebuild: + remove reference to app-shells/csh which has been removed + + 07 Jan 2007; Danny van Dyk <kugelfang@gentoo.org> -namd-2.6_beta1.ebuild: + QA: Removed unused versions. + + 20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml: + (#148281) Change herd to sci-chemistry from sci. + +*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 + alternative to app-shells/csh in DEPEND. + + 10 Nov 2005; Markus Dittrich <markusle@gentoo.org> metadata.xml, + namd-2.6_beta1.ebuild: + Changed charm dependency to sys-cluster/charm since charm + has moved from sci-libs/charm to sys-cluster/charm + +*namd-2.6_beta1 (05 Oct 2005) + + 05 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + +files/namd-barrier-fix-gentoo.patch, +files/namd-fftw-lib-gentoo.patch, + +files/namd-makefile-gentoo.patch, +files/namd-tcl-lib-gentoo.patch, + +metadata.xml, +namd-2.6_beta1.ebuild: + Initial import. Ebuild contributed by Markus Dittrich <markusle@gmail.com> + (bug #108033). + diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest new file mode 100644 index 0000000..4c39c87 --- /dev/null +++ b/sci-chemistry/namd/Manifest @@ -0,0 +1,13 @@ +AUX namd-2.6-gentoo.patch 3650 RMD160 e7cc7fa0e20b01295d6f7c83211f961720e8beaa SHA1 f5525811cc092c5125be93cdce0e8c4e22fbee38 SHA256 55fad22d757d83d786b279a50a724499fb915767ade827895d686df16fa829d9 +AUX namd-2.7-gentoo.patch 4046 RMD160 a7d087c47088d9a8df8f804e023d1a882e281e74 SHA1 333fe98dcfb54736f192f3baa82280dcab1fbd21 SHA256 9416859fa9f065f3f269441cbbb44d4f627b71c8cba29ba9e6765c08dae3611f +AUX namd-2.7-iml-dec.patch 520 RMD160 f8f33d8e10a7c6933369c3a6b857d44243bb1c74 SHA1 2edd740e3b6cb5514bde0c4742d0ca4bf6b98126 SHA256 6be7d0a3b4dff7fa39246e7ce49afb82ff508456ebbe3983e2def1202ebb3024 +AUX namd-2.7-ldflags.patch 1547 RMD160 bfaf2ca893168e1a652e75a186817d8149af94d8 SHA1 a0ce28bcc65e1cb7ff5c61723e602c26f5eef16b SHA256 ce2fd68cf2bf0c459c65caef4e71010b2ae5bf3c2c16770d44ca461291b9b924 +AUX namd-2.7_beta2-gentoo.patch 4409 RMD160 301bc17156f10a552eae4c2b3ed91ed2ea9fae6a SHA1 3cb0deb35e690156cf1a41e35482fab42480e3af SHA256 c56728dbf426540f9558db31f7e45cacc654112022f42917e715dbaa6c05373d +AUX namd-barrier-fix-gentoo.patch 2362 RMD160 c6b045a0f2ec9f29bf7f98db7a71c1533f2a20d3 SHA1 5d42ef58f08914ecdf4afe735345ff1264389544 SHA256 f0186fada88b387c0681095174be336d61b2968197d223c15c840c1ca96e4992 +AUX namd-fftw-lib-gentoo.patch 528 RMD160 bb776e58497f0ec672bf5fc9ef22d0717d8c27ad SHA1 b8ca7a0521900bd9dbf725d9ce7ed809ff2d1aa0 SHA256 04528fd52f70cccbba1ccf844b97b256a35f9b1b85ca3ef8a56b4c9308b22696 +AUX namd-makefile-gentoo.patch 2804 RMD160 e52934e5a1aa7ed34e270dc11e780b1bdef3011d SHA1 22d5bd779a280c1287c936dd855f8359fa7b1b4e SHA256 f3945ae8fff113286847d61a00d5a749b1c3a00b65394085e56ff47a0a209250 +AUX namd-tcl-lib-gentoo.patch 576 RMD160 0992dd4103b97baed85e66a8d4fc04c3991bedd1 SHA1 f1cc944b14f7f77785f1a914d3d50f44d9929aec SHA256 7a57497410f5791b1b9fa0535e66137bd1b4c5008e0253c7467bc40af7b6ac01 +DIST NAMD_2.7b2_Source.tar.gz 9094631 RMD160 ec2c46f6cdb582dca73ebdbd894a9827f2e276d9 SHA1 0acab2a3bb6fca67b767f02bf7d2d2045ce6c3b9 SHA256 5675eb08534a6e4ea7a59e52e949991b3ba42abd78b45a46976ac3d7ed3b8d67 +EBUILD namd-2.7_beta3.ebuild 3019 RMD160 7c6b2d55862b1801a11e76f01a948a877c32f723 SHA1 da5e52329540afb11086ed6622647a5fc61b13bc SHA256 d143385761f8bbee43be726bdfea6c0652757bc446feabe5142f0f4314750474 +MISC ChangeLog 2797 RMD160 050da7ba2120061612df6321b0ffd2e49c1ae9e6 SHA1 06d5dc422168a91e935ebd7d5596f4a474ce0c53 SHA256 05c0e8e730d8ba7cebcd8bb0435aa8980e686b908713cc340c222d0455ad8421 +MISC metadata.xml 282 RMD160 539a53475b01291eadb86c8c53a0fbc02b4a34d4 SHA1 7f42dcea44641b8a77ab9644791344ec6ed6c327 SHA256 3c1785eb4ab63774ed3a6b1bddd602ef24cd6795f690bb3289d5a980bca06349 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/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/files/namd-2.7-iml-dec.patch b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch new file mode 100644 index 0000000..e5ee3bd --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch @@ -0,0 +1,24 @@ +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 <sys/mman.h> + #include <fcntl.h> + #include <stdio.h> ++#include <stdlib.h> + + #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 <sys/mman.h> + #include <fcntl.h> + #include <stdio.h> ++#include <stdlib.h> + + #ifndef MAP_FILE + #define MAP_FILE 0 diff --git a/sci-chemistry/namd/files/namd-2.7-ldflags.patch b/sci-chemistry/namd/files/namd-2.7-ldflags.patch new file mode 100644 index 0000000..686eba8 --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.7-ldflags.patch @@ -0,0 +1,41 @@ +diff --git a/Makefile b/Makefile +index fd20f12..0821bed 100644 +--- a/Makefile ++++ b/Makefile +@@ -339,7 +339,7 @@ all: $(BINARIES) $(LIBCUDARTSO) + + namd2: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) + $(MAKEBUILDINFO) +- $(CHARMC) -verbose -ld++-option \ ++ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \ + "$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \ + -module NeighborLB -module commlib -language charm++ \ + $(BUILDINFO).o \ +@@ -394,23 +394,23 @@ charmrun.exe: + $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe + + psfgen: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS) +- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm ++ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm + + psfgen.exe: $(DSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL) + $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -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 $@ + + flipbinpdb: $(SRCDIR)/flipbinpdb.c +- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipbinpdb.c || \ ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipbinpdb.c || \ + echo "#!/bin/sh\necho unavailable on this platform" > $@; \ + 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 $(SRCDIR)/dumpdcd.c diff --git a/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch b/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch new file mode 100644 index 0000000..898d6b5 --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch @@ -0,0 +1,126 @@ +diff -ur NAMD_2.7b2_Source.orig//arch/Linux-x86_64.fftw NAMD_2.7b2_Source//arch/Linux-x86_64.fftw +--- NAMD_2.7b2_Source.orig//arch/Linux-x86_64.fftw 2010-04-23 14:40:54.566510874 -0500 ++++ NAMD_2.7b2_Source//arch/Linux-x86_64.fftw 2010-04-23 14:41:08.106528893 -0500 +@@ -1,7 +1,7 @@ + +-FFTDIR=/Projects/namd2/fftw/linux-x86_64 ++FFTDIR=/usr + FFTINCL=-I$(FFTDIR)/include +-FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw ++FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw + FFTFLAGS=-DNAMD_FFTW + FFT=$(FFTINCL) $(FFTFLAGS) + +diff -ur NAMD_2.7b2_Source.orig//arch/Linux-x86_64.tcl NAMD_2.7b2_Source//arch/Linux-x86_64.tcl +--- NAMD_2.7b2_Source.orig//arch/Linux-x86_64.tcl 2010-04-23 14:40:54.566510874 -0500 ++++ NAMD_2.7b2_Source//arch/Linux-x86_64.tcl 2010-04-23 14:41:08.106528893 -0500 +@@ -1,7 +1,7 @@ + +-TCLDIR=/Projects/namd2/tcl/linux-x86_64 ++TCLDIR=/usr + TCLINCL=-I$(TCLDIR)/include +-TCLLIB=-L$(TCLDIR)/lib -ltcl8.3 -ldl ++TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl + TCLFLAGS=-DNAMD_TCL + TCL=$(TCLINCL) $(TCLFLAGS) + +diff -ur NAMD_2.7b2_Source.orig//Make.charm NAMD_2.7b2_Source//Make.charm +--- NAMD_2.7b2_Source.orig//Make.charm 2010-04-23 14:40:54.556517020 -0500 ++++ NAMD_2.7b2_Source//Make.charm 2010-04-23 14:42:16.026530011 -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-6.1.3 ++CHARMBASE = /usr/include/charm-6.1.3 + +Only in NAMD_2.7b2_Source/: Make.charm.~1~ +Only in NAMD_2.7b2_Source/: Make.charm.porig +diff -ur NAMD_2.7b2_Source.orig//Makefile NAMD_2.7b2_Source//Makefile +--- NAMD_2.7b2_Source.orig//Makefile 2010-04-23 14:40:54.556517020 -0500 ++++ NAMD_2.7b2_Source//Makefile 2010-04-23 14:42:59.446523306 -0500 +@@ -300,10 +300,10 @@ + $(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) +@@ -323,7 +323,7 @@ + + # 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 +@@ -354,9 +354,6 @@ + $(CHARMOPTS) \ + -lm -o namd2 + +-charmrun: $(CHARM)/bin/charmrun # XXX +- $(COPY) $(CHARM)/bin/charmrun $@ +- + $(LIBCUDARTSO): + if [ -r $(CUDADIR)/lib64/$(LIBCUDARTSO) ]; then \ + $(COPY) $(CUDADIR)/lib64/$(LIBCUDARTSO) $@; \ +@@ -364,10 +361,6 @@ + $(COPY) $(CUDADIR)/lib/$(LIBCUDARTSO) $@; \ + fi + +-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 \ +@@ -390,9 +383,6 @@ + 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 + +@@ -716,9 +706,7 @@ + + DOC_FILES = README.txt announce.txt license.txt notes.txt + +-RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen charmrun namd2 +- +-WINDOWS_RELEASE_FILES = $(WINDOWSBINARIES) $(TCLDLL) ++RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen namd2 + + release: all + $(ECHO) Creating release $(RELEASE_DIR_NAME) +@@ -727,17 +715,9 @@ + 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 +Only in NAMD_2.7b2_Source/: Makefile.porig diff --git a/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch b/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch new file mode 100644 index 0000000..40e8e68 --- /dev/null +++ b/sci-chemistry/namd/files/namd-barrier-fix-gentoo.patch @@ -0,0 +1,61 @@ +# patch to fix compile error on gcc-3.x + +diff -Naur NAMD_2.6b1_Source/src/BackEnd.C NAMD_2.6b1_Source_patched/src/BackEnd.C +--- NAMD_2.6b1_Source/src/BackEnd.C 2003-12-31 06:37:15.000000000 +0000 ++++ NAMD_2.6b1_Source_patched/src/BackEnd.C 2005-08-22 18:59:59.000000000 +0000 +@@ -162,7 +162,7 @@ + } + + // start QD and scheduler +-void BackEnd::barrier(void) { ++void BackEnd::namd_barrier(void) { + awaken(); + suspend(); + } +diff -Naur NAMD_2.6b1_Source/src/BackEnd.h NAMD_2.6b1_Source_patched/src/BackEnd.h +--- NAMD_2.6b1_Source/src/BackEnd.h 2000-01-29 00:20:05.000000000 +0000 ++++ NAMD_2.6b1_Source_patched/src/BackEnd.h 2005-08-22 18:59:47.000000000 +0000 +@@ -17,7 +17,7 @@ + + static void suspend(void); // Let message code run... + static void awaken(void); // ...then return +- static void barrier(void); // Let message code run, then return ++ static void namd_barrier(void); // Let message code run, then return + static void ExitSchedOn(int pe); // Tell a remote processor to stop + // his scheduler + +diff -Naur NAMD_2.6b1_Source/src/ScriptTcl.C NAMD_2.6b1_Source_patched/src/ScriptTcl.C +--- NAMD_2.6b1_Source/src/ScriptTcl.C 2005-06-23 18:47:00.000000000 +0000 ++++ NAMD_2.6b1_Source_patched/src/ScriptTcl.C 2005-08-22 19:00:21.000000000 +0000 +@@ -56,7 +56,7 @@ + } + + void ScriptTcl::barrier() { +- BackEnd::barrier(); ++ BackEnd::namd_barrier(); + } + + void ScriptTcl::initcheck() { +diff -Naur NAMD_2.6b1_Source/src/main.C NAMD_2.6b1_Source_patched/src/main.C +--- NAMD_2.6b1_Source/src/main.C 2005-05-27 22:56:49.000000000 +0000 ++++ NAMD_2.6b1_Source_patched/src/main.C 2005-08-22 19:17:34.000000000 +0000 +@@ -67,7 +67,9 @@ + + #ifndef NOHOSTNAME + iout << iINFO << +- "Sending usage information to NAMD developers via UDP. Sent data is:\n" ++ "Markus says: I don't want to send usage information \n" ++ << endi; ++ iout << iINFO << "to NAMD developers :) Data not sent is:\n" + << endi; + + char sendbuf[TBSOFT_TRACK_MAXLEN]; +@@ -88,7 +90,7 @@ + sprintf(sendbuf, "1 %s %s %s %s %s %s %s", + program, versionnum, platform, numcpus, miscinfo, host, user); + iout << iINFO << sendbuf << "\n" << endi; +- send_dgram(TBSOFT_TRACK_HOST, TBSOFT_TRACK_PORT, sendbuf, strlen(sendbuf)); ++ //send_dgram(TBSOFT_TRACK_HOST, TBSOFT_TRACK_PORT, sendbuf, strlen(sendbuf)); + + #endif + return 0; diff --git a/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch b/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch new file mode 100644 index 0000000..731ea23 --- /dev/null +++ b/sci-chemistry/namd/files/namd-fftw-lib-gentoo.patch @@ -0,0 +1,15 @@ +# adjust paths for proper linking to fftw libs + +--- NAMD_2.6b1_Source/arch/Linux-i686.fftw 2004-02-20 22:38:36.000000000 +0000 ++++ NAMD_2.6b1_Source_patched/arch/Linux-i686.fftw 2005-08-22 18:50:38.000000000 +0000 +@@ -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 --git a/sci-chemistry/namd/files/namd-makefile-gentoo.patch b/sci-chemistry/namd/files/namd-makefile-gentoo.patch new file mode 100644 index 0000000..4ee5822 --- /dev/null +++ b/sci-chemistry/namd/files/namd-makefile-gentoo.patch @@ -0,0 +1,88 @@ +# provide paths for charm++ provided includes/libraries/binaries + +--- NAMD_2.6b1_Source-patched/Makefile 2005-07-22 18:50:58.000000000 +0000 ++++ NAMD_2.6b1_Source/Makefile 2005-09-30 02:28:35.000000000 +0000 +@@ -227,10 +227,10 @@ + $(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) +@@ -250,7 +250,7 @@ + + # 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 +@@ -279,10 +279,7 @@ + $(CHARMOPTS) \ + -lm -o namd2 + +-charmrun: $(CHARM)/bin/charmrun # XXX +- $(COPY) $(CHARM)/bin/charmrun $@ +- +-win32binaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe ++win32binaries: namd2.exe psfgen.exe charmd.exe charmd_faceless.exe + + namd2.exe: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) + $(MAKEBUILDINFO) +@@ -304,9 +301,6 @@ + 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 + +@@ -565,9 +559,9 @@ + + DOC_FILES = README.txt announce.txt license.txt notes.txt + +-RELEASE_FILES = namd2 psfgen charmrun flipdcd flipbinpdb ++RELEASE_FILES = namd2 psfgen flipdcd flipbinpdb + +-WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmrun.exe charmd.exe charmd_faceless.exe $(TCLDLL) ++WIN32_RELEASE_FILES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe $(TCLDLL) + + release: all + $(ECHO) Creating release $(RELEASE_DIR_NAME) +@@ -575,18 +569,18 @@ + cp $(RELEASE_FILES) $(RELEASE_DIR_NAME) + for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done + cp -r .rootdir/lib $(RELEASE_DIR_NAME) +- if [ -r $(CHARM)/bin/charmd ]; then \ +- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ ++ if [ -r /usr/bin/charmd ]; then \ ++ $(COPY) /usr/bin/charmd $(RELEASE_DIR_NAME); \ + fi +- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ +- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ ++ if [ -r /usr/bin/charmd_faceless ]; then \ ++ $(COPY) /usr/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 +- echo $(CHARM) ++ echo /usr ++ ls -l /usr/lib ++ echo /usr + file $(RELEASE_FILES) + + winrelease: winall diff --git a/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch b/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch new file mode 100644 index 0000000..0e6f0dd --- /dev/null +++ b/sci-chemistry/namd/files/namd-tcl-lib-gentoo.patch @@ -0,0 +1,16 @@ +# adjust paths for proper linking to tcl libs + +--- NAMD_2.6b1_Source/arch/Linux-i686.tcl 2004-10-27 21:40:55.000000000 +0000 ++++ NAMD_2.6b1_Source_patched/arch/Linux-i686.tcl 2005-09-14 20:50:14.000000000 +0000 +@@ -1,8 +1,8 @@ + +-TCLDIR=/Projects/namd2/tcl/linux ++#TCLDIR=/Projects/namd2/tcl/linux + #TCLDIR=$(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/metadata.xml b/sci-chemistry/namd/metadata.xml new file mode 100644 index 0000000..dafc7c9 --- /dev/null +++ b/sci-chemistry/namd/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>markusle@gentoo.org</email> + <name>Markus Dittrich</name> + </maintainer> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/namd/namd-2.7_beta3.ebuild b/sci-chemistry/namd/namd-2.7_beta3.ebuild new file mode 100644 index 0000000..f629826 --- /dev/null +++ b/sci-chemistry/namd/namd-2.7_beta3.ebuild @@ -0,0 +1,116 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/namd-2.7_beta2-r1.ebuild,v 1.1 2010/06/24 20:37:03 jlec Exp $ + +inherit eutils toolchain-funcs flag-o-matic multilib + +DESCRIPTION="A powerful and highly parallelized molecular dynamics code" +LICENSE="namd" +HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/" + +MY_PN="NAMD" +MY_PV="2.7b2" + +SRC_URI="${MY_PN}_${MY_PV}_Source.tar.gz" + +SLOT="0" +KEYWORDS="~amd64" +IUSE="cuda" + +RESTRICT="fetch" + +DEPEND=" + app-shells/tcsh + sys-cluster/charm + =sci-libs/fftw-2* + 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}/${MY_PN}_${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 ${A} + cd "${S}" + + 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-2.7_beta2-gentoo.patch + epatch "${FILESDIR}"/namd-2.7-ldflags.patch + epatch "${FILESDIR}"/namd-2.7-iml-dec.patch + sed -e "s:charm-6.1.3:charm-${CHARM_VERSION}:" \ + Make.charm || \ + die + + rm -f charm-6.1.3.tar || die + + # proper compiler and cflags + sed -e "s/g++/$(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 "Failed to setup ${NAMD_ARCH}.arch" + + sed -e "s/gentoo-libdir/$(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 "Failed gentooizing Linux-x86_64.fftw." + sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || \ + die "Failed gentooizing Linux-x86_64.tcl." + + if use cuda; then + CONFIG_OPTIONS="--with-cuda --cuda-prefix=/opt/cuda/$(get_libdir)" + fi + + # configure + ./config ${NAMD_ARCH} ${CONFIG_OPTIONS} +} + +src_compile() { + # build namd + cd "${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 +} |