From fd7319e4dc3bb89cbb39e8b346d627bc3985cfde Mon Sep 17 00:00:00 2001 From: Alexey Shvetsov Date: Sun, 4 Jul 2010 16:48:12 +0000 Subject: [PATCH] [sci-chemistry/gromacs] Fix bug #326331. thanks to Christoph Junghans Package-Manager: portage-2.2_rc67_p177/cvs/Linux x86_64 --- sci-chemistry/gromacs/ChangeLog | 7 +- sci-chemistry/gromacs/Manifest | 9 +- sci-chemistry/gromacs/gromacs-4.0.7-r4.ebuild | 307 ++++++++++++++++++ 3 files changed, 318 insertions(+), 5 deletions(-) create mode 100644 sci-chemistry/gromacs/gromacs-4.0.7-r4.ebuild diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index f24ceea63123..a53093593f04 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-chemistry/gromacs # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.51 2010/06/27 19:06:33 alexxy Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.52 2010/07/04 16:48:12 alexxy Exp $ + +*gromacs-4.0.7-r4 (04 Jul 2010) + + 04 Jul 2010; Alexey Shvetsov +gromacs-4.0.7-r4.ebuild: + Fix bug #326331. thanks to Christoph Junghans *gromacs-4.0.7-r3 (27 Jun 2010) diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 55b42079266f..e9bd2073a8ba 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -20,12 +20,13 @@ EBUILD gromacs-3.3.3.ebuild 6363 RMD160 02cc3ab83e9897408f971355a453b731006edce3 EBUILD gromacs-4.0.4.ebuild 6918 RMD160 d31ffadfe240147555b227c36456d81c35f5f5dc SHA1 52b59952c4fb4861ed6bbe2f48ba4c3443b07cd4 SHA256 078f3942a1b5bf671326be97dacb22f37783c082c154bf193e28e18c4e314d3e EBUILD gromacs-4.0.5.ebuild 6762 RMD160 c9945b966f14d1aa3fab96928a8c1269f2d0b4fb SHA1 535119ceb458903fd294f21959df4338eafd475d SHA256 dc76914d616ac4f750e9073601f1fc9cd30ab6f7b15a01152b95ef625a755c3b EBUILD gromacs-4.0.7-r3.ebuild 9489 RMD160 7f125dc953d744dab91e8b8c34b5d1406fea91b1 SHA1 b14ce5def015cda74fbf7dadd9642a9599f7caeb SHA256 38f44e6c07fdf539a4253d63ec2ccdd604f679016545f6b7ade5d7e7a80ee068 -MISC ChangeLog 10308 RMD160 c3a45df5addfd418cb67a8ad1e4af733a1addcf0 SHA1 f001fb5d7d315a62bfeb5d5fbbbf01e57c162f9b SHA256 d7d5ea4106c29cadfb0980034e3e03e5dc2578de98dad95dd90b3b8b9184e767 +EBUILD gromacs-4.0.7-r4.ebuild 9958 RMD160 669cce5d221ade95b881e573c5753b8b9e36bc7c SHA1 9356ac31bfc1e5317a68f0529dbd8b15fc0c9092 SHA256 6d947ea2171b648e3435d00768d7a6d503e08c03b09cb6fca38f0674c2897972 +MISC ChangeLog 10467 RMD160 34044c78c4da83657f6395d3c6b8268a2db8b7f9 SHA1 a79d24e14f3dc28c477842c47e8d7bdc7b2beebc SHA256 0a8fb5fb978b9a0745092e47a524a4b12c01b1148f659f88611a4f8074280e79 MISC metadata.xml 643 RMD160 e9ffc42d792f15f3d4438a0de225277ec4814041 SHA1 c83fd4a32d896b7a2586667bc684d46f9daf8693 SHA256 177885ec674e8630a9c9451a0e0a35fc83615b39b387a67002e27f1b0d6b19b2 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.15 (GNU/Linux) -iEYEARECAAYFAkwnoWAACgkQ5BmOA85PVLgeCgCePGMiZ24oHjj/S19MwuMZYHqS -KEcAn37L+8sifFj2eKET4Cl/2R9GT2T4 -=CM19 +iEYEARECAAYFAkwwu4UACgkQ5BmOA85PVLiJKQCfXuk8BBRUIW5JYjiT0fI+yBke +ykUAnj+FExDAVZpZ44RcyZ7qz5bakfPe +=P/dt -----END PGP SIGNATURE----- diff --git a/sci-chemistry/gromacs/gromacs-4.0.7-r4.ebuild b/sci-chemistry/gromacs/gromacs-4.0.7-r4.ebuild new file mode 100644 index 000000000000..f7fd10fb7df2 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-4.0.7-r4.ebuild @@ -0,0 +1,307 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.7-r4.ebuild,v 1.1 2010/07/04 16:48:12 alexxy Exp $ + +EAPI="3" + +LIBTOOLIZE="true" +TEST_PV="4.0.4" + +inherit autotools bash-completion eutils fortran multilib toolchain-funcs + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" +SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz + test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz ) + doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf ) + ffamber? ( http://ffamber.cnsm.csulb.edu/ffamber_v4.0-doc.tar.gz )" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux" +IUSE="X blas dmalloc doc -double-precision ffamber +fftw fkernels +gsl lapack +mpi +single-precision static static-libs test +xml zsh-completion" + +DEPEND="app-shells/tcsh + X? ( x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE ) + dmalloc? ( dev-libs/dmalloc ) + blas? ( virtual/blas ) + fftw? ( sci-libs/fftw:3.0 ) + gsl? ( sci-libs/gsl ) + lapack? ( virtual/lapack ) + mpi? ( virtual/mpi ) + xml? ( dev-libs/libxml2 )" + +RDEPEND="${DEPEND}" + +RESTRICT="test" + +QA_EXECSTACK="usr/lib/libgmx.so.* + usr/lib/libgmx_d.so.*" + +use static && QA_EXECSTACK="$QA_EXECSTACK usr/bin/*" + +src_prepare() { + + ( use single-precision || use double-precision ) || \ + die "Nothing to compile, enable single-precision and/or double-precision" + + if use static; then + use X && die "You cannot compile a static version with X support, disable X or static" + use xml && die "You cannot compile a static version with xml support + (see bug #306479), disable xml or static" + fi + + epatch "${FILESDIR}/${P}_upstream2010-06-08.patch.gz" + sed -e '/AC_INIT/s/4\.0\.7/&-2010-06-08/' -i configure.ac \ + || die "Failed to change version in configure.ac" + epatch "${FILESDIR}/${PN}-4.0.9999-docdir.patch" + # Fix typos in a couple of files. + sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \ + || die "Failed to fixup demo script." + + # Fix a sandbox violation that occurs when re-emerging with mpi. + sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${ED}usr/$( get_libdir )\" ; \\\\" \ + -i src/tools/Makefile.am \ + || die "sed tools/Makefile.am failed" + + sed -e "s:\$\$libdir:\$temp_libdir:" \ + -i src/tools/Makefile.am \ + || die "sed tools/Makefile.am failed" + + sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${ED}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" + + 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} $(use_with lapack external-lapack)" + fi + + # by default its better to have dynamicaly linked binaries + if use static; then + #gmx build static libs by default + myconf="${myconf} --disable-shared $(use_enable static all-static)" + else + myconf="${myconf} --disable-all-static --enable-shared $(use_enable static-libs static)" + fi + + myconf="--datadir="${EPREFIX}"/usr/share \ + --bindir="${EPREFIX}"/usr/bin \ + --libdir="${EPREFIX}"/usr/$(get_libdir) \ + --docdir="${EPREFIX}"/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 ${!p} --disable-mpi CC="$(tc-getCC)" F77="${FORTRANC}" + use mpi || continue + cd "${S}-${x}_mpi" + ECONF_SOURCE="${S}" econf ${!p} --enable-mpi CC="$(tc-getCC)" F77="${FORTRANC}" + 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}-${x}" + emake DESTDIR="${ED}" install || die "emake install for ${x} failed" + use mpi || continue + cd "${S}-${x}_mpi" + emake DESTDIR="${ED}" install-mdrun || die "emake install-mdrun for ${x} failed" + done + + sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs" + doenvd "${T}/80gromacs" + rm -f "${ED}"/usr/bin/GMXRC* + + dobashcompletion "${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.* + + cd "${S}" + dodoc AUTHORS INSTALL README + use doc && dodoc "${DISTDIR}/manual-4.0.pdf" + if use ffamber; then + use doc && dodoc "${WORKDIR}/ffamber_v4.0/README/pdfs/*.pdf" + # prepare vdwradii.dat + cat >>"${ED}"/usr/share/gromacs/top/vdwradii.dat <<-EOF + SOL MW 0 + SOL LP 0 + EOF + # regenerate aminoacids.dat + cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \ + "${ED}"/usr/share/gromacs/top/aminoacids.dat \ + | awk '{print $1}' | sort -u | tail -n+4 | wc -l \ + >> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new + cat "${WORKDIR}"/ffamber_v4.0/aminoacids*.dat \ + "${ED}"/usr/share/gromacs/top/aminoacids.dat \ + | awk '{print $1}' | sort -u | tail -n+4 \ + >> "${ED}"/usr/share/gromacs/top/aminoacids.dat.new + mv -f "${ED}"/usr/share/gromacs/top/aminoacids.dat.new \ + "${ED}"/usr/share/gromacs/top/aminoacids.dat + # copy ff files + for x in ffamber94 ffamber96 ffamber99 ffamber99p ffamber99sb \ + ffamberGS ffamberGSs ffamber03 ; do + einfo "Adding ${x} to gromacs" + cp "${WORKDIR}"/ffamber_v4.0/${x}/* "${ED}"/usr/share/gromacs/top + done + # copy suplementary files + cp "${WORKDIR}"/ffamber_v4.0/*.gro "${ED}"/usr/share/gromacs/top + cp "${WORKDIR}"/ffamber_v4.0/*.itp "${ED}"/usr/share/gromacs/top + # actualy add records to FF.dat + cat >>"${ED}"/usr/share/gromacs/top/FF.dat.new <<-EOF + ffamber94 AMBER94 Cornell protein/nucleic forcefield + ffamber96 AMBER96 Kollman protein/nucleic forcefield + ffamberGS AMBER-GS Garcia & Sanbonmatsu forcefield + ffamberGSs AMBER-GSs Nymeyer & Garcia forcefield + ffamber99 AMBER99 Wang protein/nucleic acid forcefield + ffamber99p AMBER99p protein/nucleic forcefield + ffamber99sb AMBER99sb Hornak protein/nucleic forcefield + ffamber03 AMBER03 Duan protein/nucleic forcefield + EOF + cat "${ED}"/usr/share/gromacs/top/FF.dat \ + "${ED}"/usr/share/gromacs/top/FF.dat.new \ + | tail -n+2 > "${ED}"/usr/share/gromacs/top/FF.dat.new2 + cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 | wc -l > \ + "${ED}"/usr/share/gromacs/top/FF.dat + cat "${ED}"/usr/share/gromacs/top/FF.dat.new2 >> \ + "${ED}"/usr/share/gromacs/top/FF.dat + rm -f "${ED}"/usr/share/gromacs/top/FF.dat.new* + fi +} + +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 +} -- 2.26.2