diff options
| -rw-r--r-- | sci-chemistry/gromacs/ChangeLog | 9 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/Manifest | 26 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/files/gromacs-4.0.4-configure-gfortran.patch | 17 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-3.3.9999.ebuild | 234 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-4.0.9999.ebuild | 234 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-9999.ebuild | 233 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/metadata.xml | 7 |
7 files changed, 743 insertions, 17 deletions
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index baa781fc9..3d9feb298 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -2,6 +2,15 @@ # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*gromacs-9999 (21 Jun 2009) +*gromacs-4.0.9999 (21 Jun 2009) +*gromacs-3.3.9999 (21 Jun 2009) + + 21 Jun 2009; Christoph Junghans <kleiner_otti@gmx.de> + +gromacs-3.3.9999.ebuild, +files/gromacs-4.0.4-configure-gfortran.patch, + +gromacs-4.0.9999.ebuild, +gromacs-9999.ebuild, metadata.xml: + added live ebuilds for old, stable, experimental branch + 21 Jun 2009; Christoph Junghans <kleiner_otti@gmx.de> gromacs-4.0.4.ebuild: Fixed some repoman errors diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 5d3bcbf9f..d7527769a 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,24 +1,20 @@ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 -- -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - +AUX gromacs-4.0.4-configure-gfortran.patch 731 RMD160 1ccea4fafd6837461114fc36bc31db4f9390fc08 SHA1 0ec79e9ab691cbae5f116adaa3245ef0b123a598 SHA256 5b902eac127bc84e188224fbfe0182ab3fa3b03c200325ada9cd628bb913b479 +DIST gmxtest-4.0.4.tgz 14845017 RMD160 c7c583415438bdef4c9996da9064254e9460cf16 SHA1 998179aa2bfbc4f80514f10ed774762f85c854c3 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361 DIST gromacs-4.0.4.tar.gz 8443779 RMD160 f90327814170c26a43d99fe7587357a46989fdec SHA1 9466f3ab95d60c0aba8916b1fcc70129cb4e4d72 SHA256 8aefd03cd3269e85c84427f05ceea6d3e16874cd4a90bf3f6fec2b2be24c426f +DIST manual-4.0.pdf 2135100 RMD160 b963642f8e1433f11328c3d0c4b1645c9de506da SHA1 8ae951ee15b2a7dc626331fce36511bc8766144c SHA256 646f810477eee2d710de6019c52056550413d0ba77baf9680195c835ddafe80a +EBUILD gromacs-3.3.9999.ebuild 6640 RMD160 e0a39da394ae160584d394bcac9cae89d001d229 SHA1 4be6d054002faf7c4a853f1ee7aad09b2da86b1d SHA256 be6ff76414e9569fc0b160e2e591d749c2e46ae975535ec34332e2d6072b2a46 EBUILD gromacs-4.0.4.ebuild 6899 RMD160 ea01958dddb6e8874410e01df9171c5e081d1856 SHA1 7e1f7e37a88ecea0840e58d3687d6b00d70b0e0f SHA256 ff452e5d24885bc5ec40fc3ca29fe1f5f6997c499667bf62ebfb6b6a23532a07 -MISC ChangeLog 945 RMD160 9a4333ed2c72bfc56045a59f8ee00b836eeeb8d0 SHA1 404d663411bb93df647c190cf4e374bd8aa50f53 SHA256 3757b6370a226899b2192b5ee5a5d55ba1c1d11018d2bb2254e70ab4c41374db -MISC metadata.xml 409 RMD160 484a62d0e282b28dcfb9992c6162deb368d90e26 SHA1 55b541c7d9581092982d1abe2da4a15f84c0fda9 SHA256 08e3609f4b9bb3002843f042cb6156c7e769c4796946a129e5886dab79e61358 -- -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.11 (GNU/Linux) - -iEYEARECAAYFAko+g0kACgkQy0OE/ans1/mOoACferIO9tF56CjAI4WOAHZDBUUY -8QAAn0OI7MFUUZDZIpo/cTQHaH59qwGy -=ChDg -- -----END PGP SIGNATURE----- +EBUILD gromacs-4.0.9999.ebuild 6640 RMD160 c48a23acd60c4943b466cbfe36cc1a10ca5d2327 SHA1 137f0801ffb4fe3a87e3881fa95d432eb3e1041b SHA256 a1a81ae8997d31d956b7aaacc00b8988d6d95c8267c82a5110656856d982441b +EBUILD gromacs-9999.ebuild 6606 RMD160 c25d3da0f931cee5cd29b7b698025b024b8c33f5 SHA1 3ede827e2fcc2b73ce709af9ff9e5af496c754d8 SHA256 07b3051e743d20b94c2f0df4360d00abad900a1baaad9a76c2924c0a373878fa +MISC ChangeLog 1292 RMD160 559051475c2bfaf9dce39fbcbab489b72aec7eaf SHA1 cac028136a6ff6c4a4597105e89913d87e368a8b SHA256 8eefd2a64bdc8ed19dfff3088deb89f5cb3fc29faae162e2c6d8fdfe09de02d5 +MISC metadata.xml 642 RMD160 885e11bdae2d4e79b5fd7b48113f44d987c62b19 SHA1 ab77d33e2f7a8e8d6aa8a997e9247fd61bd17a74 SHA256 6e3242563fd78de425260bf28a07a017afb294898a80e02bacef59ec4a83064c -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.11 (GNU/Linux) -iEYEARECAAYFAko+hDcACgkQy0OE/ans1/mfBgCfR3z5GcTCjKJ5njkyaw0l2Xxr -ccoAn1dsoTM0XGC84LzBWYJu7xrPKRjL -=iT7b +iEYEARECAAYFAko+jIoACgkQy0OE/ans1/mAMACfShjgYsM9DvJdOLPIza3xNwSB +shoAniWNBdT27i90sOnhyX/4vrCK39Wr +=co6k -----END PGP SIGNATURE----- diff --git a/sci-chemistry/gromacs/files/gromacs-4.0.4-configure-gfortran.patch b/sci-chemistry/gromacs/files/gromacs-4.0.4-configure-gfortran.patch new file mode 100644 index 000000000..c330fcaf0 --- /dev/null +++ b/sci-chemistry/gromacs/files/gromacs-4.0.4-configure-gfortran.patch @@ -0,0 +1,17 @@ +diff -Naur gromacs-4.0.4-orig/configure.ac gromacs-4.0.4/configure.ac +--- gromacs-4.0.4-orig/configure.ac 2009-04-09 21:12:31.000000000 +0200 ++++ gromacs-4.0.4/configure.ac 2009-04-09 21:13:38.000000000 +0200 +@@ -320,11 +320,11 @@ + case "${host_cpu}-${host_os}" in + alpha*-linux*) + cc_names="ccc cc gcc" +- f77_names="fort f77 g77" ++ f77_names="fort f77 g77 gfortran" + ;; + *) + cc_names="cc icc xlc gcc" +- f77_names="f77 ifort xlf xlf77 cf77 fl32 g77 fort77 f90 xlf90 pgf77 cf77 fort fort77 pgf90" ++ f77_names="f77 ifort xlf xlf77 cf77 fl32 g77 fort77 f90 xlf90 pgf77 cf77 fort fort77 pgf90 gfortran" + ;; + esac + # the (non-mpi) c compiler, which is also used for programs executed during build stage diff --git a/sci-chemistry/gromacs/gromacs-3.3.9999.ebuild b/sci-chemistry/gromacs/gromacs-3.3.9999.ebuild new file mode 100644 index 000000000..8d354932d --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-3.3.9999.ebuild @@ -0,0 +1,234 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="2" + +LIBTOOLIZE="true" +TEST_PV="4.0.4" + +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-${TEST_PV}.tgz ) + doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86" +IUSE="X blas dmalloc doc -double-precision +fftw fkernels gsl lapack mpi +single-precision static test +xml zsh-completion" + +DEPEND="app-shells/tcsh + X? ( x11-libs/libX11 ) + dmalloc? ( dev-libs/dmalloc ) + blas? ( virtual/blas ) + fftw? ( sci-libs/fftw:3.0 ) + gsl? ( sci-libs/gsl ) + lapack? ( virtual/lapack ) + mpi? ( virtual/mpi ) + xml? ( dev-libs/libxml2 )" + +RDEPEND="${DEPEND}" + +RESTRICT="test" + +EGIT_REPO_URI="git://git.gromacs.org/gromacs" +EGIT_BRANCH="release-3-3-patches" + +src_prepare() { + # 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 "${FILESDIR}/${PN}-4.0.4-configure-gfortran.patch" + + eautoreconf + + cd "${WORKDIR}" + + use test && mv gmxtest "${P}" + mv "${P}" "${P}-single" + if ( use double-precision ) ; then + einfo "Moving sources for Multiprecision Build" + cp -prP "${P}-single" "${P}-double" + fi +} + +src_configure() { + local myconf ; + local myconf_s ; + local myconf_d ; + local suffix_d ; + + #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 [[ $(gcc-version) == "4.1" ]]; then + ewarn "gcc 4.1 is not supported by gromacs" + ewarn "please run test suite" + fi + + #fortran will gone in gromacs 4.1 anyway + #note for gentoo-PREFIX on aix, fortran (xlf) is still much faster + if use fkernels; then + ewarn "Fortran kernels are usually not faster than C kernels and assembly" + ewarn "I hope, you know what are you doing..." + FORTRAN="g77 gfortran ifc" + myconf="${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} $(use_with lapack external-lapack)" + fi + + myconf="--datadir=/usr/share \ + --bindir=/usr/bin \ + --libdir=/usr/$(get_libdir) \ + --docdir=/usr/share/doc/"${PF}" \ + $(use_with dmalloc) \ + $(use_with fftw fft fftw3) \ + $(use_with gsl) \ + $(use_enable mpi) \ + $(use_with X x) \ + $(use_with xml) \ + $(use_enable static all-static) \ + ${myconf}" + + #if we build both double is suffixed + if ( use double-precision && use single-precision ); then + suffix_d="_d" + else + suffix_d="" + fi + + if use double-precision ; then + #from gromacs manual + elog + elog "For most simulations single precision is accurate enough. In some" + elog "cases double precision is required to get reasonable results:" + elog + elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization" + elog " and the calculation and diagonalization of the Hessian " + elog "-calculation of the constraint force between two large groups of atoms" + elog "-energy conservation: this can only be done without temperature coupling and" + elog " without cutoffs" + elog + einfo "Configuring Double Precison Gromacs" + cd "${WORKDIR}"/"${P}"-double + myconf_d="${myconf} --enable-double --program-suffix='${suffix_d}'" + econf ${myconf_d} || die "Double Precision econf failed" + fi + + if use single-precision ; then + einfo "Configuring Single Precison Gromacs" + cd "${WORKDIR}"/"${P}"-single + myconf_s="${myconf} --enable-float --program-suffix=''" + econf ${myconf_s} || die "configure failed" + fi +} + +src_compile() { + if use double-precision ; then + einfo "Building Double Precison Gromacs" + cd "${WORKDIR}"/"${P}"-double + emake || die "Double Precision emake failed" + fi + + if use single-precision ; then + einfo "Building Single Precison Gromacs" + cd "${WORKDIR}"/"${P}"-single + emake || die "Single Precision emake failed" + fi +} + +src_test() { + if use single-precision ; then + export PATH="${WORKDIR}/${P}-single/src/kernel:${WORKDIR}/${P}-single/src/tools:$PATH" + cd "${WORKDIR}"/"${P}"-single + emake -j1 tests || die "Single Precision test failed" + fi + + if use double-precision ; then + export PATH="${WORKDIR}/${P}-double/src/kernel:${WORKDIR}/${P}-double/src/tools:$PATH" + cd "${WORKDIR}"/"${P}"-double + emake -j1 tests || die "Double Precision test failed" + fi +} + +src_install() { + if use single-precision ; then + einfo "Installing Single Precision" + cd "${WORKDIR}"/"${P}"-single + emake DESTDIR="${D}" install || die "Installing Single Precision failed" + fi + + if use double-precision ; then + einfo "Installing Double Precision" + cd "${WORKDIR}"/"${P}"-double + emake DESTDIR="${D}" install || die "Installing Double Precision failed" + fi + + sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${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.* + + 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 +} diff --git a/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild new file mode 100644 index 000000000..63fd0da23 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-4.0.9999.ebuild @@ -0,0 +1,234 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="2" + +LIBTOOLIZE="true" +TEST_PV="4.0.4" + +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-${TEST_PV}.tgz ) + doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86" +IUSE="X blas dmalloc doc -double-precision +fftw fkernels gsl lapack mpi +single-precision static test +xml zsh-completion" + +DEPEND="app-shells/tcsh + X? ( x11-libs/libX11 ) + dmalloc? ( dev-libs/dmalloc ) + blas? ( virtual/blas ) + fftw? ( sci-libs/fftw:3.0 ) + gsl? ( sci-libs/gsl ) + lapack? ( virtual/lapack ) + mpi? ( virtual/mpi ) + xml? ( dev-libs/libxml2 )" + +RDEPEND="${DEPEND}" + +RESTRICT="test" + +EGIT_REPO_URI="git://git.gromacs.org/gromacs" +EGIT_BRANCH="release-4-0-patches" + +src_prepare() { + # 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 "${FILESDIR}/${PN}-4.0.4-configure-gfortran.patch" + + eautoreconf + + cd "${WORKDIR}" + + use test && mv gmxtest "${P}" + mv "${P}" "${P}-single" + if ( use double-precision ) ; then + einfo "Moving sources for Multiprecision Build" + cp -prP "${P}-single" "${P}-double" + fi +} + +src_configure() { + local myconf ; + local myconf_s ; + local myconf_d ; + local suffix_d ; + + #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 [[ $(gcc-version) == "4.1" ]]; then + ewarn "gcc 4.1 is not supported by gromacs" + ewarn "please run test suite" + fi + + #fortran will gone in gromacs 4.1 anyway + #note for gentoo-PREFIX on aix, fortran (xlf) is still much faster + if use fkernels; then + ewarn "Fortran kernels are usually not faster than C kernels and assembly" + ewarn "I hope, you know what are you doing..." + FORTRAN="g77 gfortran ifc" + myconf="${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} $(use_with lapack external-lapack)" + fi + + myconf="--datadir=/usr/share \ + --bindir=/usr/bin \ + --libdir=/usr/$(get_libdir) \ + --docdir=/usr/share/doc/"${PF}" \ + $(use_with dmalloc) \ + $(use_with fftw fft fftw3) \ + $(use_with gsl) \ + $(use_enable mpi) \ + $(use_with X x) \ + $(use_with xml) \ + $(use_enable static all-static) \ + ${myconf}" + + #if we build both double is suffixed + if ( use double-precision && use single-precision ); then + suffix_d="_d" + else + suffix_d="" + fi + + if use double-precision ; then + #from gromacs manual + elog + elog "For most simulations single precision is accurate enough. In some" + elog "cases double precision is required to get reasonable results:" + elog + elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization" + elog " and the calculation and diagonalization of the Hessian " + elog "-calculation of the constraint force between two large groups of atoms" + elog "-energy conservation: this can only be done without temperature coupling and" + elog " without cutoffs" + elog + einfo "Configuring Double Precison Gromacs" + cd "${WORKDIR}"/"${P}"-double + myconf_d="${myconf} --enable-double --program-suffix='${suffix_d}'" + econf ${myconf_d} || die "Double Precision econf failed" + fi + + if use single-precision ; then + einfo "Configuring Single Precison Gromacs" + cd "${WORKDIR}"/"${P}"-single + myconf_s="${myconf} --enable-float --program-suffix=''" + econf ${myconf_s} || die "configure failed" + fi +} + +src_compile() { + if use double-precision ; then + einfo "Building Double Precison Gromacs" + cd "${WORKDIR}"/"${P}"-double + emake || die "Double Precision emake failed" + fi + + if use single-precision ; then + einfo "Building Single Precison Gromacs" + cd "${WORKDIR}"/"${P}"-single + emake || die "Single Precision emake failed" + fi +} + +src_test() { + if use single-precision ; then + export PATH="${WORKDIR}/${P}-single/src/kernel:${WORKDIR}/${P}-single/src/tools:$PATH" + cd "${WORKDIR}"/"${P}"-single + emake -j1 tests || die "Single Precision test failed" + fi + + if use double-precision ; then + export PATH="${WORKDIR}/${P}-double/src/kernel:${WORKDIR}/${P}-double/src/tools:$PATH" + cd "${WORKDIR}"/"${P}"-double + emake -j1 tests || die "Double Precision test failed" + fi +} + +src_install() { + if use single-precision ; then + einfo "Installing Single Precision" + cd "${WORKDIR}"/"${P}"-single + emake DESTDIR="${D}" install || die "Installing Single Precision failed" + fi + + if use double-precision ; then + einfo "Installing Double Precision" + cd "${WORKDIR}"/"${P}"-double + emake DESTDIR="${D}" install || die "Installing Double Precision failed" + fi + + sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${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.* + + 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 +} diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild new file mode 100644 index 000000000..e8384fb66 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -0,0 +1,233 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="2" + +LIBTOOLIZE="true" +TEST_PV="4.0.4" + +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-${TEST_PV}.tgz ) + doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86" +IUSE="X blas dmalloc doc -double-precision +fftw fkernels gsl lapack mpi +single-precision static test +xml zsh-completion" + +DEPEND="app-shells/tcsh + X? ( x11-libs/libX11 ) + dmalloc? ( dev-libs/dmalloc ) + blas? ( virtual/blas ) + fftw? ( sci-libs/fftw:3.0 ) + gsl? ( sci-libs/gsl ) + lapack? ( virtual/lapack ) + mpi? ( virtual/mpi ) + xml? ( dev-libs/libxml2 )" + +RDEPEND="${DEPEND}" + +RESTRICT="test" + +EGIT_REPO_URI="git://git.gromacs.org/gromacs" + +src_prepare() { + # 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 "${FILESDIR}/${PN}-4.0.4-configure-gfortran.patch" + + eautoreconf + + cd "${WORKDIR}" + + use test && mv gmxtest "${P}" + mv "${P}" "${P}-single" + if ( use double-precision ) ; then + einfo "Moving sources for Multiprecision Build" + cp -prP "${P}-single" "${P}-double" + fi +} + +src_configure() { + local myconf ; + local myconf_s ; + local myconf_d ; + local suffix_d ; + + #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 [[ $(gcc-version) == "4.1" ]]; then + ewarn "gcc 4.1 is not supported by gromacs" + ewarn "please run test suite" + fi + + #fortran will gone in gromacs 4.1 anyway + #note for gentoo-PREFIX on aix, fortran (xlf) is still much faster + if use fkernels; then + ewarn "Fortran kernels are usually not faster than C kernels and assembly" + ewarn "I hope, you know what are you doing..." + FORTRAN="g77 gfortran ifc" + myconf="${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} $(use_with lapack external-lapack)" + fi + + myconf="--datadir=/usr/share \ + --bindir=/usr/bin \ + --libdir=/usr/$(get_libdir) \ + --docdir=/usr/share/doc/"${PF}" \ + $(use_with dmalloc) \ + $(use_with fftw fft fftw3) \ + $(use_with gsl) \ + $(use_enable mpi) \ + $(use_with X x) \ + $(use_with xml) \ + $(use_enable static all-static) \ + ${myconf}" + + #if we build both double is suffixed + if ( use double-precision && use single-precision ); then + suffix_d="_d" + else + suffix_d="" + fi + + if use double-precision ; then + #from gromacs manual + elog + elog "For most simulations single precision is accurate enough. In some" + elog "cases double precision is required to get reasonable results:" + elog + elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization" + elog " and the calculation and diagonalization of the Hessian " + elog "-calculation of the constraint force between two large groups of atoms" + elog "-energy conservation: this can only be done without temperature coupling and" + elog " without cutoffs" + elog + einfo "Configuring Double Precison Gromacs" + cd "${WORKDIR}"/"${P}"-double + myconf_d="${myconf} --enable-double --program-suffix='${suffix_d}'" + econf ${myconf_d} || die "Double Precision econf failed" + fi + + if use single-precision ; then + einfo "Configuring Single Precison Gromacs" + cd "${WORKDIR}"/"${P}"-single + myconf_s="${myconf} --enable-float --program-suffix=''" + econf ${myconf_s} || die "configure failed" + fi +} + +src_compile() { + if use double-precision ; then + einfo "Building Double Precison Gromacs" + cd "${WORKDIR}"/"${P}"-double + emake || die "Double Precision emake failed" + fi + + if use single-precision ; then + einfo "Building Single Precison Gromacs" + cd "${WORKDIR}"/"${P}"-single + emake || die "Single Precision emake failed" + fi +} + +src_test() { + if use single-precision ; then + export PATH="${WORKDIR}/${P}-single/src/kernel:${WORKDIR}/${P}-single/src/tools:$PATH" + cd "${WORKDIR}"/"${P}"-single + emake -j1 tests || die "Single Precision test failed" + fi + + if use double-precision ; then + export PATH="${WORKDIR}/${P}-double/src/kernel:${WORKDIR}/${P}-double/src/tools:$PATH" + cd "${WORKDIR}"/"${P}"-double + emake -j1 tests || die "Double Precision test failed" + fi +} + +src_install() { + if use single-precision ; then + einfo "Installing Single Precision" + cd "${WORKDIR}"/"${P}"-single + emake DESTDIR="${D}" install || die "Installing Single Precision failed" + fi + + if use double-precision ; then + einfo "Installing Double Precision" + cd "${WORKDIR}"/"${P}"-double + emake DESTDIR="${D}" install || die "Installing Double Precision failed" + fi + + sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${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.* + + 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 +} diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml index ab7d70798..8f140cfbf 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -3,9 +3,12 @@ <pkgmetadata> <herd>sci-chemistry</herd> <use> - <flag name='double-precision'>More precise calculations at the expense of - speed</flag> + <flag name='dmalloc'>Enable use of Debug Malloc</flag> + <flag name='double-precision'>More precise calculations at the expense of speed</flag> + <flag name='fkernels'>Enable building of Fortran Kernels for platforms + that dont have assembly loops</flag> <flag name='single-precision'>Single precision version of gromacs</flag> <flag name='gmxmopac7'>Support for QM/MM with mopac7</flag> + <flag name='zsh-completion'>Enable zsh completion support</flag> </use> </pkgmetadata> |