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authorJeffrey Gardner <je_fro@gentoo.org>2009-06-14 04:39:28 +0000
committerJeffrey Gardner <je_fro@gentoo.org>2009-06-14 04:39:28 +0000
commit5bb4d804d8263312dcb8c27a6f720574edab0768 (patch)
tree93916c82a118b3e1a839802b0c574158269f143d /sci-chemistry
parent2.6.30 now in portage (diff)
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Adding for the purpose of testing Christian Becke's fix from bug #237634
svn path=/; revision=290
Diffstat (limited to 'sci-chemistry')
-rw-r--r--sci-chemistry/namd/Manifest4
-rw-r--r--sci-chemistry/namd/files/digest-namd-2.63
-rw-r--r--sci-chemistry/namd/files/namd-2.6-gentoo-amd64.patch105
-rw-r--r--sci-chemistry/namd/files/namd-2.7-gentoo.patch117
-rw-r--r--sci-chemistry/namd/namd-2.7.ebuild103
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
-}