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# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI="2"
LIBTOOLIZE="true"
TEST_PV="4.0.4"
EGIT_REPO_URI="git://git.gromacs.org/gromacs"
EGIT_BRANCH="release-4-0-patches"
inherit autotools bash-completion eutils fortran git multilib
DESCRIPTION="The ultimate molecular dynamics simulation package"
HOMEPAGE="http://www.gromacs.org/"
SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack mpi +single-precision static test +xml zsh-completion"
DEPEND="app-shells/tcsh
X? ( x11-libs/libX11
x11-libs/libSM
x11-libs/libICE )
dmalloc? ( dev-libs/dmalloc )
blas? ( virtual/blas )
fftw? ( sci-libs/fftw:3.0 )
gsl? ( sci-libs/gsl )
lapack? ( virtual/lapack )
mpi? ( virtual/mpi )
xml? ( dev-libs/libxml2 )"
RDEPEND="${DEPEND}"
RESTRICT="test"
src_prepare() {
epatch "${FILESDIR}/${P}-docdir.patch"
epatch "${FILESDIR}/${P}-ccache.patch"
# Fix typos in a couple of files.
sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
|| die "Failed to fixup demo script."
# 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"
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"
use fkernels && epatch "${FILESDIR}/${P}-configure-gfortran.patch"
eautoreconf
GMX_DIRS=""
use single-precision && GMX_DIRS+=" single"
use double-precision && GMX_DIRS+=" double"
for x in ${GMX_DIRS}; do
mkdir "${S}-${x}" || die
use test && cp -r "${WORKDIR}"/gmxtest "${S}-${x}"
use mpi || continue
mkdir "${S}-${x}_mpi" || die
done
}
src_configure() {
local myconf
local myconfsingle
local myconfdouble
local suffixdouble
#leave all assembly options enabled mdrun is smart enough to deside itself
#there so no gentoo on bluegene!
myconf="${myconf} --disable-bluegene"
#from gromacs configure
if ! use fftw; then
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 [[ $(gcc-version) == "4.1" ]]; then
eerror "gcc 4.1 is not supported by gromacs"
eerror "please run test suite"
die
fi
#note for gentoo-PREFIX on apple: use --enable-apple-64bit
#fortran will gone in gromacs 4.1 anyway
#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
if use fkernels; then
ewarn "Fortran kernels are usually not faster than C kernels and assembly"
ewarn "I hope, you know what are you doing..."
FORTRAN="g77 gfortran ifc"
myconf="${myconf} --enable-fortran" && fortran_pkg_setup
else
myconf="${myconf} --disable-fortran"
fi
# if we need external blas
if use blas; then
export LIBS="${LIBS} -lblas"
myconf="${myconf} $(use_with blas external-blas)"
fi
# if we need external lapack
if use lapack; then
export LIBS="${LIBS} -llapack"
myconf="${myconf} $(use_with lapack external-lapack)"
fi
# by default its better to have dynamicaly linked binaries
if use static; then
myconf="${myconf} $(use_enable static all-static)"
else
myconf="${myconf} --enable-shared"
fi
myconf="--datadir=/usr/share \
--bindir=/usr/bin \
--libdir=/usr/$(get_libdir) \
--docdir=/usr/share/doc/"${PF}" \
$(use_with dmalloc) \
$(use_with fftw fft fftw3) \
$(use_with gsl) \
$(use_with X x) \
$(use_with xml) \
${myconf}"
#if we build single and double - double is suffixed
if ( use double-precision && use single-precision ); then
suffixdouble="_d"
else
suffixdouble=""
fi
if use double-precision ; then
#from gromacs manual
elog
elog "For most simulations single precision is accurate enough. In some"
elog "cases double precision is required to get reasonable results:"
elog
elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
elog " and the calculation and diagonalization of the Hessian "
elog "-calculation of the constraint force between two large groups of atoms"
elog "-energy conservation: this can only be done without temperature coupling and"
elog " without cutoffs"
elog
fi
if use mpi ; then
elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
elog "we configure/compile gromacs twice (with and without mpi) and only"
elog "install mdrun with mpi support. In addtion you will get libgmx and"
elog "libmd with and without mpi support."
fi
myconfdouble="${myconf} --enable-double --program-suffix='${suffixdouble}'"
myconfsingle="${myconf} --enable-float --program-suffix=''"
for x in ${GMX_DIRS}; do
einfo "Configuring for ${x} precision"
cd "${S}-${x}"
local p=myconf${x}
ECONF_SOURCE="${S}" econf ${!p} --disable-mpi
use mpi || continue
cd "${S}-${x}_mpi"
ECONF_SOURCE="${S}" econf ${!p} --enable-mpi
done
}
src_compile() {
for x in ${GMX_DIRS}; do
cd "${S}-${x}"
einfo "Compiling for ${x} precision"
emake || die "emake for ${x} precision failed"
use mpi || continue
cd "${S}-${x}_mpi"
emake mdrun || die "emake mdrun for ${x} precision failed"
done
}
src_test() {
for x in ${GMX_DIRS}; do
local oldpath="${PATH}"
export PATH="${S}-${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
cd "${S}-${x}"
emake -j1 tests || die "${x} Precision test failed"
export PATH="${oldpath}"
done
}
src_install() {
for x in ${GMX_DIRS}; do
cd "${S}-${x}"
emake DESTDIR="${D}" install || die "emake install for ${x} failed"
use mpi || continue
cd "${S}-${x}_mpi"
emake DESTDIR="${D}" install-mdrun || die "emake install-mdrun for ${x} failed"
done
sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${D}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
doenvd "${T}/80gromacs"
rm -f "${D}"/usr/bin/GMXRC*
dobashcompletion "${D}"/usr/bin/completion.bash ${PN}
if use zsh-completion ; then
insinto /usr/share/zsh/site-functions
newins "${D}"/usr/bin/completion.zsh _${PN}
fi
rm -r "${D}"/usr/bin/completion.*
cd "${S}"
dodoc AUTHORS INSTALL README
use doc && dodoc "${DISTDIR}"/manual-4.0.pdf
}
pkg_postinst() {
env-update && source /etc/profile
elog
elog "Please read and cite:"
elog "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
elog "http://dx.doi.org/10.1021/ct700301q"
elog
bash-completion_pkg_postinst
elog
elog $(luck)
elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
elog
}
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