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-rw-r--r--sci-chemistry/gromacs/ChangeLog6
-rw-r--r--sci-chemistry/gromacs/gromacs-4.5.4-r2.ebuild245
-rw-r--r--sci-chemistry/gromacs/gromacs-4.5.5.ebuild245
3 files changed, 5 insertions, 491 deletions
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 0a50f170f547..a0716e8c8d63 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,10 @@
# ChangeLog for sci-chemistry/gromacs
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.102 2012/01/06 02:16:45 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.103 2012/01/06 02:21:02 ottxor Exp $
+
+ 06 Jan 2012; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.4-r2.ebuild,
+ -gromacs-4.5.5.ebuild:
+ remove obsolete
06 Jan 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.5-r1.ebuild:
keyword ~x86-macos
diff --git a/sci-chemistry/gromacs/gromacs-4.5.4-r2.ebuild b/sci-chemistry/gromacs/gromacs-4.5.4-r2.ebuild
deleted file mode 100644
index bbcf8ae6fd31..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.5.4-r2.ebuild
+++ /dev/null
@@ -1,245 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4-r2.ebuild,v 1.8 2011/09/10 14:47:53 ottxor Exp $
-
-EAPI="4"
-
-TEST_PV="4.0.4"
-MANUAL_PV="4.5.4"
-
-#to find external blas/lapack
-CMAKE_MIN_VERSION="2.8.5-r2"
-
-inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
-
-if [ "${PV%9999}" != "${PV}" ]; then
- EGIT_REPO_URI="git://git.gromacs.org/gromacs"
- EGIT_BRANCH="release-4-5-patches"
- inherit git-2
-else
- SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
-fi
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="${SRC_URI}
- http://dev.gentoo.org/~alexxy/gromacs/0001-Make-stack-non-executable-for-GAS-assembly.patch.gz
- http://dev.gentoo.org/~alexxy/gromacs/0002-Make-stack-non-executable-for-ATT-assembly.patch.gz
- doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )
- test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
-mpi +single-precision sse2 test +threads xml zsh-completion"
-REQUIRED_USE="fkernels? ( !threads )"
-
-CDEPEND="
- X? (
- x11-libs/libX11
- x11-libs/libSM
- x11-libs/libICE
- )
- blas? ( virtual/blas )
- fftw? ( sci-libs/fftw:3.0 )
- fkernels? ( virtual/fortran )
- gsl? ( sci-libs/gsl )
- lapack? ( virtual/lapack )
- mpi? ( virtual/mpi )
- xml? ( dev-libs/libxml2:2 )"
-DEPEND="${CDEPEND}
- dev-util/pkgconfig"
-RDEPEND="${CDEPEND}
- app-shells/tcsh"
-
-RESTRICT="test"
-
-pkg_setup() {
- use fkernels && fortran-2_pkg_setup
-}
-
-src_prepare() {
- #add user patches from /etc/portage/patches/sci-chemistry/gromacs
- epatch_user
-
- if use mpi && use threads; then
- elog "mdrun uses only threads OR mpi, and gromacs favours the"
- elog "use of mpi over threads, so a mpi-version of mdrun will"
- elog "be compiled. If you want to run mdrun on shared memory"
- elog "machines only, you can safely disable mpi"
- fi
-
- # Add patches for non-exec stack
- epatch "${WORKDIR}/0001-Make-stack-non-executable-for-GAS-assembly.patch"
- epatch "${WORKDIR}/0002-Make-stack-non-executable-for-ATT-assembly.patch"
-
- GMX_DIRS=""
- use single-precision && GMX_DIRS+=" float"
- use double-precision && GMX_DIRS+=" double"
- #if neither single-precision nor double-precision is enabled
- #build at least default (single)
- [ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
-
- for x in ${GMX_DIRS}; do
- mkdir -p "${WORKDIR}/${P}_${x}" || die
- use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
- done
-}
-
-src_configure() {
- local mycmakeargs_pre=( )
- #from gromacs configure
- if use fftw; then
- mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
- else
- mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
- ewarn "WARNING: The built-in FFTPACK routines are slow."
- ewarn "Are you sure you don\'t want to use FFTW?"
- ewarn "It is free and much faster..."
- fi
-
- if [[ $(gcc-version) == "4.1" ]]; then
- eerror "gcc 4.1 is not supported by gromacs"
- eerror "please run test suite"
- die
- fi
-
- #note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
- #note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
- if use fkernels; then
- ewarn "Fortran kernels are usually not faster than C kernels and assembly"
- ewarn "I hope, you know what are you doing..."
- fi
-
- if use double-precision ; then
- #from gromacs manual
- elog
- elog "For most simulations single precision is accurate enough. In some"
- elog "cases double precision is required to get reasonable results:"
- elog
- elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
- elog " and the calculation and diagonalization of the Hessian "
- elog "-calculation of the constraint force between two large groups of atoms"
- elog "-energy conservation: this can only be done without temperature coupling and"
- elog " without cutoffs"
- elog
- fi
-
- if use mpi ; then
- elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
- elog "we configure/compile gromacs twice (with and without mpi) and only"
- elog "install mdrun with mpi support. In addtion you will get libgmx and"
- elog "libmd with and without mpi support."
- fi
-
- #go from slowest to fasterest acceleration
- local acce="none"
- use fkernels && acce="fortran"
- use altivec && acce="altivec"
- use ia64 && acce="ia64"
- use sse2 && acce="sse"
-
- mycmakeargs_pre+=(
- $(cmake-utils_use X GMX_X11)
- $(cmake-utils_use blas GMX_EXTERNAL_BLAS)
- $(cmake-utils_use gsl GMX_GSL)
- $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
- $(cmake-utils_use threads GMX_THREADS)
- $(cmake-utils_use xml GMX_XML)
- -DGMX_DEFAULT_SUFFIX=off
- -DGMX_ACCELERATION="$acce"
- -DLIB="$(get_libdir)"
- )
-
- for x in ${GMX_DIRS}; do
- einfo "Configuring for ${x} precision"
- local suffix=""
- #if we build single and double - double is suffixed
- use double-precision && use single-precision && \
- [ "${x}" = "double" ] && suffix="_d"
- local p
- [ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
- mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
- -DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
- CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
- use mpi || continue
- einfo "Configuring for ${x} precision with mpi"
- mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
- CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
- done
-}
-
-src_compile() {
- for x in ${GMX_DIRS}; do
- einfo "Compiling for ${x} precision"
- CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile
- use mpi || continue
- einfo "Compiling for ${x} precision with mpi"
- CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
- cmake-utils_src_compile mdrun
- done
-}
-
-src_test() {
- for x in ${GMX_DIRS}; do
- local oldpath="${PATH}"
- export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
- cd "${WORKDIR}/${P}_${x}"
- emake -j1 tests || die "${x} Precision test failed"
- export PATH="${oldpath}"
- done
-}
-
-src_install() {
- for x in ${GMX_DIRS}; do
- CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake-utils_src_install
- use mpi || continue
- #cmake-utils_src_install does not support args
- #using cmake-utils_src_compile instead
- CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
- cmake-utils_src_make install-mdrun DESTDIR="${D}"
- done
-
- sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
- echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
-
- doenvd "${T}/80gromacs"
- rm -f "${ED}"/usr/bin/GMXRC*
-
- newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
- if use zsh-completion ; then
- insinto /usr/share/zsh/site-functions
- newins "${ED}"/usr/bin/completion.zsh _${PN}
- fi
- rm -f "${ED}"/usr/bin/completion.*
-
- # Fix typos in a couple of files.
- sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
- || die "Failed to fixup demo script."
-
- cd "${S}"
- dodoc AUTHORS INSTALL* README*
- if use doc; then
- newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
- dohtml -r "${ED}usr/share/gromacs/html/"
- fi
- rm -rf "${ED}usr/share/gromacs/html/"
-}
-
-pkg_postinst() {
- env-update && source /etc/profile
- einfo
- einfo "Please read and cite:"
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
- einfo "http://dx.doi.org/10.1021/ct700301q"
- einfo
- einfo $(g_luck)
- einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
- einfo
- elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
diff --git a/sci-chemistry/gromacs/gromacs-4.5.5.ebuild b/sci-chemistry/gromacs/gromacs-4.5.5.ebuild
deleted file mode 100644
index 4a70357d3bb8..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.5.5.ebuild
+++ /dev/null
@@ -1,245 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.5.ebuild,v 1.4 2011/12/14 16:45:32 ago Exp $
-
-EAPI="4"
-
-TEST_PV="4.0.4"
-MANUAL_PV="4.5.4"
-
-#to find external blas/lapack
-CMAKE_MIN_VERSION="2.8.5-r2"
-
-inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
-
-if [ "${PV%9999}" != "${PV}" ]; then
- EGIT_REPO_URI="git://git.gromacs.org/gromacs"
- EGIT_BRANCH="release-4-5-patches"
- inherit git-2
-else
- SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
-fi
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="${SRC_URI}
- http://dev.gentoo.org/~alexxy/gromacs/0001-Make-stack-non-executable-for-GAS-assembly.patch.gz
- http://dev.gentoo.org/~alexxy/gromacs/0002-Make-stack-non-executable-for-ATT-assembly.patch.gz
- doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )
- test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha amd64 ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux"
-IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
-mpi +single-precision sse2 test +threads xml zsh-completion"
-REQUIRED_USE="fkernels? ( !threads )"
-
-CDEPEND="
- X? (
- x11-libs/libX11
- x11-libs/libSM
- x11-libs/libICE
- )
- blas? ( virtual/blas )
- fftw? ( sci-libs/fftw:3.0 )
- fkernels? ( virtual/fortran )
- gsl? ( sci-libs/gsl )
- lapack? ( virtual/lapack )
- mpi? ( virtual/mpi )
- xml? ( dev-libs/libxml2:2 )"
-DEPEND="${CDEPEND}
- dev-util/pkgconfig"
-RDEPEND="${CDEPEND}
- app-shells/tcsh"
-
-RESTRICT="test"
-
-pkg_setup() {
- use fkernels && fortran-2_pkg_setup
-}
-
-src_prepare() {
- #add user patches from /etc/portage/patches/sci-chemistry/gromacs
- epatch_user
-
- if use mpi && use threads; then
- elog "mdrun uses only threads OR mpi, and gromacs favours the"
- elog "use of mpi over threads, so a mpi-version of mdrun will"
- elog "be compiled. If you want to run mdrun on shared memory"
- elog "machines only, you can safely disable mpi"
- fi
-
- # Add patches for non-exec stack
- epatch "${WORKDIR}/0001-Make-stack-non-executable-for-GAS-assembly.patch"
- epatch "${WORKDIR}/0002-Make-stack-non-executable-for-ATT-assembly.patch"
-
- GMX_DIRS=""
- use single-precision && GMX_DIRS+=" float"
- use double-precision && GMX_DIRS+=" double"
- #if neither single-precision nor double-precision is enabled
- #build at least default (single)
- [ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
-
- for x in ${GMX_DIRS}; do
- mkdir -p "${WORKDIR}/${P}_${x}" || die
- use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
- done
-}
-
-src_configure() {
- local mycmakeargs_pre=( )
- #from gromacs configure
- if use fftw; then
- mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
- else
- mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
- ewarn "WARNING: The built-in FFTPACK routines are slow."
- ewarn "Are you sure you don\'t want to use FFTW?"
- ewarn "It is free and much faster..."
- fi
-
- if [[ $(gcc-version) == "4.1" ]]; then
- eerror "gcc 4.1 is not supported by gromacs"
- eerror "please run test suite"
- die
- fi
-
- #note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
- #note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
- if use fkernels; then
- ewarn "Fortran kernels are usually not faster than C kernels and assembly"
- ewarn "I hope, you know what are you doing..."
- fi
-
- if use double-precision ; then
- #from gromacs manual
- elog
- elog "For most simulations single precision is accurate enough. In some"
- elog "cases double precision is required to get reasonable results:"
- elog
- elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
- elog " and the calculation and diagonalization of the Hessian "
- elog "-calculation of the constraint force between two large groups of atoms"
- elog "-energy conservation: this can only be done without temperature coupling and"
- elog " without cutoffs"
- elog
- fi
-
- if use mpi ; then
- elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
- elog "we configure/compile gromacs twice (with and without mpi) and only"
- elog "install mdrun with mpi support. In addtion you will get libgmx and"
- elog "libmd with and without mpi support."
- fi
-
- #go from slowest to fasterest acceleration
- local acce="none"
- use fkernels && acce="fortran"
- use altivec && acce="altivec"
- use ia64 && acce="ia64"
- use sse2 && acce="sse"
-
- mycmakeargs_pre+=(
- $(cmake-utils_use X GMX_X11)
- $(cmake-utils_use blas GMX_EXTERNAL_BLAS)
- $(cmake-utils_use gsl GMX_GSL)
- $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
- $(cmake-utils_use threads GMX_THREADS)
- $(cmake-utils_use xml GMX_XML)
- -DGMX_DEFAULT_SUFFIX=off
- -DGMX_ACCELERATION="$acce"
- -DGMXLIB="$(get_libdir)"
- )
-
- for x in ${GMX_DIRS}; do
- einfo "Configuring for ${x} precision"
- local suffix=""
- #if we build single and double - double is suffixed
- use double-precision && use single-precision && \
- [ "${x}" = "double" ] && suffix="_d"
- local p
- [ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
- mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
- -DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
- CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
- use mpi || continue
- einfo "Configuring for ${x} precision with mpi"
- mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
- CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
- done
-}
-
-src_compile() {
- for x in ${GMX_DIRS}; do
- einfo "Compiling for ${x} precision"
- CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile
- use mpi || continue
- einfo "Compiling for ${x} precision with mpi"
- CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
- cmake-utils_src_compile mdrun
- done
-}
-
-src_test() {
- for x in ${GMX_DIRS}; do
- local oldpath="${PATH}"
- export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
- cd "${WORKDIR}/${P}_${x}"
- emake -j1 tests || die "${x} Precision test failed"
- export PATH="${oldpath}"
- done
-}
-
-src_install() {
- for x in ${GMX_DIRS}; do
- CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake-utils_src_install
- use mpi || continue
- #cmake-utils_src_install does not support args
- #using cmake-utils_src_compile instead
- CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
- cmake-utils_src_make install-mdrun DESTDIR="${D}"
- done
-
- sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
- echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
-
- doenvd "${T}/80gromacs"
- rm -f "${ED}"/usr/bin/GMXRC*
-
- newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
- if use zsh-completion ; then
- insinto /usr/share/zsh/site-functions
- newins "${ED}"/usr/bin/completion.zsh _${PN}
- fi
- rm -f "${ED}"/usr/bin/completion.*
-
- # Fix typos in a couple of files.
- sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
- || die "Failed to fixup demo script."
-
- cd "${S}"
- dodoc AUTHORS INSTALL* README*
- if use doc; then
- newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
- dohtml -r "${ED}usr/share/gromacs/html/"
- fi
- rm -rf "${ED}usr/share/gromacs/html/"
-}
-
-pkg_postinst() {
- env-update && source /etc/profile
- einfo
- einfo "Please read and cite:"
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
- einfo "http://dx.doi.org/10.1021/ct700301q"
- einfo
- einfo $(g_luck)
- einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
- einfo
- elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
-}