From 3c78c08574c433ca90382d347e6b0c5b33c09ff8 Mon Sep 17 00:00:00 2001 From: Jeffrey Gardner Date: Wed, 20 Dec 2006 04:44:52 +0000 Subject: [PATCH] Fixup for bugs 135146 118421 and 147614. Package-Manager: portage-2.1.1-r2 --- sci-chemistry/gromacs/ChangeLog | 7 +- sci-chemistry/gromacs/Manifest | 19 +- .../gromacs/files/digest-gromacs-3.3.1-r1 | 3 + .../gromacs/files/gromacs-alpha-axp_asm.patch | 11 + sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild | 215 ++++++++++++++++++ 5 files changed, 250 insertions(+), 5 deletions(-) create mode 100644 sci-chemistry/gromacs/files/digest-gromacs-3.3.1-r1 create mode 100644 sci-chemistry/gromacs/files/gromacs-alpha-axp_asm.patch create mode 100644 sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index beedbdb8758b..a5c6cf341039 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-chemistry/gromacs # Copyright 2002-2006 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.12 2006/09/20 05:08:59 dberkholz Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.13 2006/12/20 04:44:52 je_fro Exp $ + +*gromacs-3.3.1-r1 (17 Dec 2006) + + 17 Dec 2006; Jeff Gardner +gromacs-3.3.1-r1.ebuild: + Fixup to address bugs 135146 118421 and 147614. 20 Sep 2006; Donnie Berkholz ; metadata.xml: (#148281) Change herd to sci-chemistry from sci. diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 32466b77c83a..f87d97ff5a3d 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,3 +1,7 @@ +AUX gromacs-alpha-axp_asm.patch 613 RMD160 56a617d34b9aa96f71cb84124271107d56557773 SHA1 96518a8fa20c0d597b5cb26b843f28f26d998942 SHA256 d6ae7d258e975a0c12a8b09bef11874eb0e25d4708f299b3e265c97ada69afee +MD5 aa14e5e53e2eb5409072fd53896b4578 files/gromacs-alpha-axp_asm.patch 613 +RMD160 56a617d34b9aa96f71cb84124271107d56557773 files/gromacs-alpha-axp_asm.patch 613 +SHA256 d6ae7d258e975a0c12a8b09bef11874eb0e25d4708f299b3e265c97ada69afee files/gromacs-alpha-axp_asm.patch 613 AUX gromacs-ppc64-altivec.patch 571 RMD160 e6bdccd29a29fb9ee85f0ca4a15f2ea229b6f52a SHA1 fe059c262d4fdbc9b918769dc88dd8a2ed177b6b SHA256 1e60a3a12cfd706af1860ca2ff36074291540f8ffa3616636eb612037f0611c3 MD5 46d715de402fc04d726086455ba7f074 files/gromacs-ppc64-altivec.patch 571 RMD160 e6bdccd29a29fb9ee85f0ca4a15f2ea229b6f52a files/gromacs-ppc64-altivec.patch 571 @@ -13,6 +17,10 @@ EBUILD gromacs-3.2.1.ebuild 1897 RMD160 1abe85e471969fcde5ee6a714b76d820418178f0 MD5 5af09df5d0c864672c46c64a841c0177 gromacs-3.2.1.ebuild 1897 RMD160 1abe85e471969fcde5ee6a714b76d820418178f0 gromacs-3.2.1.ebuild 1897 SHA256 7785a56bace8bbef4bdec432128c9d88d2427b667645790ea78df90929074c20 gromacs-3.2.1.ebuild 1897 +EBUILD gromacs-3.3.1-r1.ebuild 5666 RMD160 60f483c934e90edd6816eeca8040b42735051261 SHA1 e79f9ab0d9cb9698520bff0a0dbfda13781ee1a5 SHA256 0e2b506523cd3ce562d8b9f48c09e860361c766f7d6ab7e6469220d7abee9afa +MD5 7b82165b82e235365bfad859e7587f24 gromacs-3.3.1-r1.ebuild 5666 +RMD160 60f483c934e90edd6816eeca8040b42735051261 gromacs-3.3.1-r1.ebuild 5666 +SHA256 0e2b506523cd3ce562d8b9f48c09e860361c766f7d6ab7e6469220d7abee9afa gromacs-3.3.1-r1.ebuild 5666 EBUILD gromacs-3.3.1.ebuild 2163 RMD160 b7748b8989987d6acb0562e744702e38f79acd47 SHA1 fa5febc72867f35d1cc9714f558a9a2c9ed36353 SHA256 cabc59520dd654c54b45aa9175785e57d8826d15f93868efeadd9a895a940306 MD5 a4e8a17060ded547ec8d8288bbbc3594 gromacs-3.3.1.ebuild 2163 RMD160 b7748b8989987d6acb0562e744702e38f79acd47 gromacs-3.3.1.ebuild 2163 @@ -21,10 +29,10 @@ EBUILD gromacs-3.3.ebuild 1956 RMD160 3ff47faef23a3860b42d2fec7c2fa0f845ccab2a S MD5 d963556dde12c545dc60726f29fd3128 gromacs-3.3.ebuild 1956 RMD160 3ff47faef23a3860b42d2fec7c2fa0f845ccab2a gromacs-3.3.ebuild 1956 SHA256 4c51f3241c5d14d8aec8037c2f07f6a17ccbbb4189684c9f67a3a55d7fe02eeb gromacs-3.3.ebuild 1956 -MISC ChangeLog 4709 RMD160 9ccbf0f0c494e82ca29b1b2738913c68d203e75b SHA1 82f63e9e7a761a94ad71ecd275f6b1e69a831088 SHA256 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590f94df114cae1a0a53387dfead13fadd4cad00003a6b3f454f2ae1a7f3e6e9 files/di MD5 0ad487900dfecda21c7258f45d995525 files/digest-gromacs-3.3.1 244 RMD160 427f90b98362a786e7d5fca69d9069742b943ebf files/digest-gromacs-3.3.1 244 SHA256 2eaa348fdc15b37c1fb15fb5394f6a26578c22bfd21ea4e719ba6308bbab40fc files/digest-gromacs-3.3.1 244 +MD5 0ad487900dfecda21c7258f45d995525 files/digest-gromacs-3.3.1-r1 244 +RMD160 427f90b98362a786e7d5fca69d9069742b943ebf files/digest-gromacs-3.3.1-r1 244 +SHA256 2eaa348fdc15b37c1fb15fb5394f6a26578c22bfd21ea4e719ba6308bbab40fc files/digest-gromacs-3.3.1-r1 244 diff --git a/sci-chemistry/gromacs/files/digest-gromacs-3.3.1-r1 b/sci-chemistry/gromacs/files/digest-gromacs-3.3.1-r1 new file mode 100644 index 000000000000..dc4a56cb42ec --- /dev/null +++ b/sci-chemistry/gromacs/files/digest-gromacs-3.3.1-r1 @@ -0,0 +1,3 @@ +MD5 1af34a99950813ca7cf893253c447cd1 gromacs-3.3.1.tar.gz 7992897 +RMD160 48e6f9098ac4f5b834f4beb050846c60aea18fff gromacs-3.3.1.tar.gz 7992897 +SHA256 3df40151ff5364fab1c4d8692ec247d8245437e954882a803178cbe6b812d81f gromacs-3.3.1.tar.gz 7992897 diff --git a/sci-chemistry/gromacs/files/gromacs-alpha-axp_asm.patch b/sci-chemistry/gromacs/files/gromacs-alpha-axp_asm.patch new file mode 100644 index 000000000000..071b11f4b3bf --- /dev/null +++ b/sci-chemistry/gromacs/files/gromacs-alpha-axp_asm.patch @@ -0,0 +1,11 @@ +diff -Naur gromacs-3.2.1/src/gmxlib/Makefile.in gromacs-3.2.1-new/src/gmxlib/Makefile.in +--- gromacs-3.2.1/src/gmxlib/Makefile.in 2004-03-01 20:49:02.000000000 +0100 ++++ gromacs-3.2.1-new/src/gmxlib/Makefile.in 2006-05-30 17:40:33.000000000 +0200 +@@ -301,6 +301,7 @@ + LTF77COMPILE = $(LIBTOOL) --mode=compile $(F77) $(AM_FFLAGS) $(FFLAGS) + F77LD = $(F77) + CCASCOMPILE = $(CCAS) $(AM_CCASFLAGS) $(CCASFLAGS) ++LTASCOMPILE = $(LIBTOOL) --mode=compile $(AS) $(AM_ASFLAGS) $(ASFLAGS) + LTCCASCOMPILE = $(LIBTOOL) --mode=compile $(CCAS) $(AM_CCASFLAGS) \ + $(CCASFLAGS) + DIST_SOURCES = $(libgmx@LIBSUFFIX@_la_SOURCES) \ diff --git a/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild b/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild new file mode 100644 index 000000000000..1d2d9ca51872 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild @@ -0,0 +1,215 @@ +# Copyright 1999-2006 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild,v 1.1 2006/12/20 04:44:52 je_fro Exp $ + +inherit eutils fortran multilib + +IUSE="3dnow X altivec double-precision mpi sse sse2" + +# mopac7 qm/mm is broken until we can get files from +# http://md.chem.rug.nl/~groenhof/qmmm.html +# or somewhere else... + +DESCRIPTION="The ultimate molecular dynamics simulation package" +SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz" +HOMEPAGE="http://www.gromacs.org/" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86" + +DEPEND=">=sci-libs/fftw-3.0.1 + mpi? ( virtual/mpi ) + >=sys-devel/binutils-2.12* + app-shells/tcsh + X? ( x11-libs/libX11 + x11-libs/libXt + x11-libs/libXp + x11-libs/libXext + x11-proto/xproto + virtual/motif )" + +# mopac7? ( sci-chemistry/mopac7 ) + +src_unpack() { + + unpack ${A} + if use ppc64 && use altivec ; then + epatch "${FILESDIR}"/${PN}-ppc64-altivec.patch + fi + + if use alpha ; then + epatch ${FILESDIR}/${PN}-alpha-axp_asm.patch + fi + + cd "${S}" + +# Fix a typo in a couple of files. + sed -e "s:_nb_kerne010_x86_64_sse2:_nb_kernel010_x86_64_sse2:" \ + -i src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/nb_kernel010_x86_64_sse2.intel_syntax.s \ + -i src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/nb_kernel010_x86_64_sse2.s \ + || die "Failed to fix sse2 typo." + +# Fix a sandbox violation that occurs when re-emerging with mpi. + sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \ + -i src/tools/Makefile.am \ + || die "sed tools/Makefile.am failed" + + sed -e "s:\$\$libdir:\$temp_libdir:" \ + -i src/tools/Makefile.am \ + || die "sed tools/Makefile.am failed" + + cd "${WORKDIR}" && mv ${P} ${P}-single ; + + use double-precision && cp -prP ${P}-single ${P}-double ; + + if use mpi ; then + cp -prP ${P}-single ${P}-single-mpi + use double-precision && cp -prP ${P}-double ${P}-double-mpi + fi +} + +src_compile() { + # static should work but something's broken. + # gcc spec file may be screwed up. + # Static linking should try -lgcc instead of -lgcc_s. + # For more info: + # http://lists.debian.org/debian-gcc/2002/debian-gcc-200201/msg00150.html + +# We will compile single precision by default, and suffix double-precision with _d. +# Sparc is the only arch I can test on that needs to use fortran. +local myconf ; + +case "${ARCH}" in + + x86) + myconf="$myconf $(use_enable sse ia32-sse)" + myconf="$myconf $(use_enable sse2 ia32-sse)" + myconf="$myconf $(use_enable 3dnow ia32-3dnow)" + +# If you don't enable at least one of the above, you must use g77, not gfortran. + if ! use sse && ! use sse2 && ! use 3dnow ; then + + if ! has_version "=sys-devel/gcc-3*" ; then + die "If you must run gromacs without sse (not recommended) gfortran will not work." + else myconf="$myconf --enable-fortran" && fortran_pkg_setup + + fi + fi + ;; + + amd64) + myconf="$myconf --enable-x86-64-sse" + ;; + + ppc) + if use altivec ; then + myconf="$myconf --enable-ppc-altivec --disable-fortran" + else + if ! has_version "=sys-devel/gcc-3*" ; then + + die "If you must run gromacs without sse (not recommended) gfortran will not work." + fi + myconf="$myconf --enable-fortran" && fortran_pkg_setup + fi + ;; + + ppc64) + if use altivec ; then + myconf="$myconf --enable-ppc-altivec --disable-fortran" + else + if ! has_version "=sys-devel/gcc-3*" ; then + die "If you must run gromacs without sse (not recommended) gfortran will not work." + fi + myconf="$myconf --enable-fortran" && fortran_pkg_setup + fi + ;; + + sparc) + if ! has_version "=sys-devel/gcc-3*" ; then + + die "If you must run gromacs without sse (not recommended) gfortran will not work." + else + myconf="$myconf --enable-fortran" && fortran_pkg_setup + fi + ;; + + ia64) + myconf="$myconf --enable-ia64-asm" + ;; + + alpha) + myconf="$myconf --enable-axp-asm" + ;; + +esac + +myconf="--enable-shared \ + --datadir=/usr/share \ + --bindir=/usr/bin \ + --libdir=/usr/$(get_libdir) \ + --with-fft=fftw3 \ + $(use_with X x) \ + ${myconf}" + +# $(use_with mopac7 qmmm-mopac) \ + +cd "${WORKDIR}"/${P}-single + econf ${myconf} --enable-float || die "configure single-precision failed" + + emake || die "emake single failed" + + if use mpi ; then + cd "${WORKDIR}"/${P}-single-mpi + econf ${myconf} --enable-float --enable-mpi --program-suffix=_mpi \ + || die "failed to configure single-mpi mdrun" + emake mdrun || die "failed to make single-precision mpi mdrun" ; + fi + + if use double-precision ; then + cd "${WORKDIR}"/${P}-double + + econf ${myconf} --enable-double --program-suffix=_d \ + || die "configure double-precision failed" + + emake || die "emake double failed" + + if use mpi ; then + cd "${WORKDIR}"/${P}-double-mpi + econf ${myconf} --enable-double --enable-mpi --program-suffix=_mpi_d \ + || die "failed to configure double-mpi mdrun" ; + + emake mdrun \ + || die "failed to make double-precision mpi mdrun" ; + fi + fi + +} + +src_install () { + cd ${WORKDIR}/${P}-single ; + emake DESTDIR=${D} install || die "installing single failed" + + if use mpi ; then + cd "${WORKDIR}"/${P}-single-mpi + emake DESTDIR=${D} install-mdrun \ + || die "installing mdrun_mpi failed" + fi + + if use double-precision ; then + cd ${WORKDIR}/${P}-double && emake DESTDIR=${D} install \ + || die "installing double failed" + + if use mpi ; then + cd "${WORKDIR}"/${P}-double-mpi + emake DESTDIR=${D} install-mdrun \ + || die "installing mdrun_mpi_d failed" + fi + + fi + + dodoc AUTHORS INSTALL README + + # Move html and leave examples and templates under /usr/share/gromacs. + mv "${D}"/usr/share/"${PN}"/html "${D}"/usr/share/doc/"${PF}"/ +} -- 2.26.2