diff options
| -rw-r--r-- | sci-chemistry/gamess/ChangeLog | 10 | ||||
| -rw-r--r-- | sci-chemistry/gamess/Manifest | 14 | ||||
| -rw-r--r-- | sci-chemistry/gamess/gamess-20100325.2.ebuild | 315 |
3 files changed, 336 insertions, 3 deletions
diff --git a/sci-chemistry/gamess/ChangeLog b/sci-chemistry/gamess/ChangeLog index 2b92975e1f07..1c838dcd01ae 100644 --- a/sci-chemistry/gamess/ChangeLog +++ b/sci-chemistry/gamess/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-chemistry/gamess -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/ChangeLog,v 1.39 2009/11/30 15:13:46 alexxy Exp $ +# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/ChangeLog,v 1.40 2010/05/24 12:38:11 alexxy Exp $ + +*gamess-20100325.2 (24 May 2010) + + 24 May 2010; Alexey Shvetsov <alexxy@gentoo.org> + +gamess-20100325.2.ebuild: + Version bump with improved qmmm stuff 30 Nov 2009; Alexey Shvetsov <alexxy@gentoo.org> gamess-20090112.3-r1.ebuild: diff --git a/sci-chemistry/gamess/Manifest b/sci-chemistry/gamess/Manifest index 88cb1555f29e..f0cf39953387 100644 --- a/sci-chemistry/gamess/Manifest +++ b/sci-chemistry/gamess/Manifest @@ -1,13 +1,25 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX gamess-20080411.1.gentoo.patch 12549 RMD160 531faefa0d45a8d249c089aec8138783406563e5 SHA1 c8a93487889528d74384096562398f5096a76f5c SHA256 7df4e4c70da0a9029043c86a4607bbc58f35cf4e34994df393e02dcd3ac7f2b5 AUX gamess-20090112.1.gentoo.patch 12259 RMD160 08dea4576f98233af6b36d73fccbe52b8eec4961 SHA1 f24da2cdf997b2d58a7f991111e0555407ce1f3b SHA256 fcaa3aafda7f95b45bbc45d98cb3875048e6b2b3c06730c97492f7b77d120255 DIST gamess-20080411.1.tar.gz 10301653 RMD160 9742a676cc2da693fff78594cdc0edf0f380a2de SHA1 8e0e01b255ebad8e2fd9b2012248648a11212b5c SHA256 493a99448afc6de15b6f054b702c6e67646e020cfee551aca0ef48a374fc6d05 DIST gamess-20090112.1.tar.gz 10823509 RMD160 409aafba9136a441c1524fe30eb1fccdff1f9883 SHA1 4af8dd470700649d32317d8ab57814b010a4403d SHA256 9f7763933479ba8aa730c392af25b8a271152115a0392707786b45871b52f6e0 DIST gamess-20090112.3.tar.gz 11000803 RMD160 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6456 RMD160 f26f2ccab0b5c230da6be09efd017555f6a815be SHA1 3ff4edc79c03d71f457101616b2ace00c4b0c066 SHA256 5674413ba5f411e9a5cde75677387c87fdf62d8f0eb65ddbf7b2e136807ffefa EBUILD gamess-20090112.3-r1.ebuild 8851 RMD160 3c6d7c66b0bbf2f4cc42d5ed04117bd19b063e3d SHA1 616a0eaccb9b080250524da2d3571ee255cb0d95 SHA256 5446ab8819c515b4d4d0f208985439bc1febe6811e041d1206e5c513ed35e44a EBUILD gamess-20090112.3.ebuild 8092 RMD160 3ed0193d970f44ee1ad69008f1dbd687bd80db08 SHA1 bd4939fbf4d0752926b3b4c729d6cd0e8204edde SHA256 2bb1b4d791156fc28f562a871ed035eb950e59c182f247778e736bdb79480347 -MISC ChangeLog 8524 RMD160 5e758d8357c12d0d421727fc78bd205ea35775d4 SHA1 c27ccd9be7302fcdb472ebc34128b699e46e9fae SHA256 4edb120c101db34dbf30afff48ddb6916812603f8b9299542b5d2ddbd8433169 +EBUILD gamess-20100325.2.ebuild 9874 RMD160 33b3ebd79752ff560f278984a8a39c8ee7cb7463 SHA1 aebd5956560c6a20c15955736b9fd84af88b0739 SHA256 fed84b0f780e31dbe749aee3c6358859b2c80b2a4c9c9b8b1d4b432a5422d61b +MISC ChangeLog 8679 RMD160 8dc6e8291e0518ee043430930793487ba65f39ff SHA1 af9567e947c1a0a2b462e8f85a86e729a59992e9 SHA256 b819d045f4b6570fa9dbdaf971ed16bcb0e0871e998f7e7d43d25113f6a389e1 MISC metadata.xml 432 RMD160 36785f37503fb3d7ab09a459d5c146ba9f2639c5 SHA1 3e7483cf552e4946b0791b97f40fae541c8ee1aa SHA256 bcc821dc1c54441f16d9b763e7dd172cc8a1f9b51a6e93fa9af5dc2fa56f3e8d +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.15 (GNU/Linux) + +iEYEARECAAYFAkv6cz4ACgkQ5BmOA85PVLhcaACfTA4zCUwA+ujN4Okl6AsQFX4U +/WcAnRVRug+BmVTGZraOfHtMpCWjWB9l +=LucQ +-----END PGP SIGNATURE----- diff --git a/sci-chemistry/gamess/gamess-20100325.2.ebuild b/sci-chemistry/gamess/gamess-20100325.2.ebuild new file mode 100644 index 000000000000..753db5d445ec --- /dev/null +++ b/sci-chemistry/gamess/gamess-20100325.2.ebuild @@ -0,0 +1,315 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/gamess-20100325.2.ebuild,v 1.1 2010/05/24 12:38:11 alexxy Exp $ + +EAPI="2" + +inherit eutils toolchain-funcs fortran flag-o-matic + +DESCRIPTION="A powerful quantum chemistry package" +LICENSE="gamess" +HOMEPAGE="http://www.msg.chem.iastate.edu/GAMESS/GAMESS.html" +SRC_URI=" + ${P}.tar.gz + qmmm-tinker? ( tinker.tar.Z )" + +SLOT="0" +# NOTE: PLEASE do not stabilize gamess. It does not make sense +# since the tarball has fetch restrictions and upstream only +# provides the latest version. In other words: As soon as a +# new version comes out the stable version will be useless since +# users can not get at the tarball any more. +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="hardened mpi qmmm-tinker" + +RESTRICT="fetch" + +DEPEND="app-shells/tcsh + hardened? ( sys-apps/paxctl ) + mpi? ( virtual/mpi ) + virtual/blas" + +RDEPEND="${DEPEND} + net-misc/openssh" + +S="${WORKDIR}/${PN}" + +GAMESS_DOWNLOAD="http://www.msg.ameslab.gov/GAMESS/License_Agreement.html" +GAMESS_VERSION="12 JAN 2009 (R3)" +FORTRAN="ifc g77 gfortran" + +pkg_nofetch() { + echo + elog "Please download ${PN}-current.tar.gz from" + elog "${GAMESS_DOWNLOAD}." + elog "Be sure to select the version ${GAMESS_VERSION} tarball!!" + elog "Then move the tarball to" + elog "${DISTDIR}/${P}.tar.gz" + if use qmmm-tinker ; then + elog "Also download http://www.msg.ameslab.gov/GAMESS/tinker.tar.Z" + elog "and place tinker.tar.Z to ${DISTDIR}" + fi + echo +} + +pkg_setup() { + fortran_pkg_setup + + # currently amd64 is only supported with gfortran + if [[ "${ARCH}" == "amd64" ]] && [[ "${FORTRANC}" != "gfortran" ]]; + then die "You will need gfortran to compile gamess on amd64" + fi + + # note about qmmm-tinker + if use qmmm-tinker; then + if [ "x$QMMM_GAMESS_MAXMM" == "x" || \ + "x$QMMM_GAMESS_MAXCLASS" == "x" || \ + "x$QMMM_GAMESS_MAXCTYP" == "x" || \ + "x$QMMM_GAMESS_MAXHESS" == "x" ]; then + einfo "By default MM subsistem is restricted to 1000 atoms" + einfo "if you want larger MM subsystems then you should set" + einfo "QMMM_GAMESS_MAXMM variable to needed value in your make.conf" + einfo "By default maximum number of atom classes types and size of" + einfo "hessian are restricted to 250, 500 and 1000000 respectively" + einfo "If you want larger sizes set:" + einfo "QMMM_GAMESS_MAXCLASS" + einfo "QMMM_GAMESS_MAXCTYP" + einfo "QMMM_GAMESS_MAXHESS" + einfo "in your make.conf" + ebeep 5 + fi + fi + + #note about mpi + if use mpi; then + ewarn "" + ewarn "You should adjust rungms script for your mpi implentation" + ewarn "because deafult one will not work" + ewarn "" + fi +} + +src_unpack() { + unpack ${A} + + if use qmmm-tinker; then + mv tinker gamess/ || die "failed to move tinker directory" + fi +} + +src_prepare() { + # apply LINUX-arch patches to gamess makesfiles + epatch "${FILESDIR}"/${PN}-20090112.1.gentoo.patch + # select arch + # NOTE: please leave lked alone; it should be good as is!! + cd "${S}" + local active_arch; + if [[ "${ARCH}" == "amd64" ]]; then + active_arch="linux64"; + else + active_arch="linux32"; + fi + sed -e "s:gentoo-target:${active_arch}:" \ + -i comp compall ddi/compddi \ + || die "Failed to select proper architecure" + + # for hardened-gcc let't turn off ssp, since it breakes + # a few routines + if use hardened && [[ "${FORTRANC}" = "g77" ]]; then + FFLAGS="${FFLAGS} -fno-stack-protector-all" + fi + + # Enable mpi stuff + if use mpi; then + sed -e "s:set COMM = sockets:set COMM = mpi:g" \ + -i ddi/compddi || die "Enabling mpi build failed" + sed -e "s:MPI_INCLUDE_PATH = ' ':MPI_INCLUDE_PATH = '-I/usr/include ':g" \ + -i ddi/compddi || die "Enabling mpi build failed" + sed -e "s:MSG_LIBRARIES='../ddi/libddi.a -lpthread':MSG_LIBRARIES='../ddi/libddi.a -lmpi -lpthread':g" \ + -i lked || die "Enabling mpi build failed" + fi + + # enable NEO + sed -e "s:NEO=false:NEO=true:" -i compall lked || \ + die "Failed to enable NEO code" + # enable GAMESS-qmmm + if use qmmm-tinker; then + sed -e "s:TINKER=false:TINKER=true:" -i compall lked || \ + die "Failed to enable TINKER code" + if [ "x$QMMM_GAMESS_MAXMM" == "x" ]; then + einfo "No QMMM_GAMESS_MAXMM set. Using default value = 1000" + else + einfo "Setting QMMM_GAMESS_MAXMM to $QMMM_GAMESS_MAXMM" + sed -e "s:maxatm=1000:maxatm=$QMMM_GAMESS_MAXMM:g" \ + -i tinker/sizes.i \ + || die "Setting QMMM_GAMESS_MAXMM failed" + sed -e "s:MAXATM=1000:MAXATM=$QMMM_GAMESS_MAXMM:g" \ + -i source/inputb.src \ + || die "Setting QMMM_GAMESS_MAXMM failed" + fi + sed -e "s:maxclass=250:maxclass=$QMMM_GAMESS_MAXCLASS:g" \ + -i tinker/sizes.i \ + || die "Setting QMMM_GAMESS_MAXCLASS failed" + sed -e "s:maxtyp=500:maxtyp=$QMMM_GAMESS_MAXCTYP:g" \ + -i tinker/sizes.i \ + || die "Setting QMMM_GAMESS_MAXCTYP failed" + sed -e "s:maxhess=1000000:maxhess=$QMMM_GAMESS_MAXHESS:g" \ + -i tinker/sizes.i \ + || die "Setting QMMM_GAMESS_MAXHESS failed" + fi + # greate proper activate sourcefile + cp "./tools/actvte.code" "./tools/actvte.f" || \ + die "Failed to create actvte.f" + sed -e "s/^\*UNX/ /" -i "./tools/actvte.f" || \ + die "Failed to perform UNX substitutions in actvte.f" + + # fix GAMESS' compall script to use proper CC + sed -e "s|\$CCOMP -c \$extraflags source/zunix.c|$(tc-getCC) -c \$extraflags source/zunix.c|" \ + -i compall || die "Failed setting up compall script" + + # insert proper FFLAGS into GAMESS' comp makefile + # in case we're using ifc let's strip all the gcc + # specific stuff + if [[ "${FORTRANC}" == "ifc" ]]; then + sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS} -quiet'/" \ + -e "s/gentoo-g77/${FORTRANC}/" \ + -i comp || die "Failed setting up comp script" + elif ! use x86; then + sed -e "s/-malign-double //" \ + -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \ + -e "s/gentoo-g77/${FORTRANC}/" \ + -i comp || die "Failed setting up comp script" + else + sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \ + -e "s/gentoo-g77/${FORTRANC}/" \ + -i comp || die "Failed setting up comp script" + fi + + # fix up GAMESS' linker script; + sed -e "s/gentoo-g77/${FORTRANC}/" \ + -e "s/gentoo-LDOPTS=' '/LDOPTS='${LDFLAGS}'/" \ + -i lked || die "Failed setting up lked script" + + # fix up GAMESS' ddi TCP/IP socket build + sed -e "s/gentoo-CC = 'gcc'/CC = '$(tc-getCC)'/" \ + -e "s/gentoo-g77/${FORTRANC}/" \ + -i ddi/compddi || die "Failed setting up compddi script" + + # fix up the checker scripts for gamess tests + sed -e "s:set GMSPATH:#set GMSPATH:g" \ + -e "s:\$GMSPATH/tools/checktst:.:g" \ + -i tools/checktst/checktst +} + +src_compile() { + # build actvte + cd "${S}"/tools + "${FORTRANC}" -o actvte.x actvte.f || \ + die "Failed to compile actvte.x" + + # for hardened (PAX) users and ifc we need to turn + # MPROTECT off + if [[ "${FORTRANC}" == "ifc" ]] && use hardened; then + /sbin/paxctl -PemRxS actvte.x 2> /dev/null || \ + die "paxctl failed on actvte.x" + fi + + # build gamess + cd "${S}" + ./compall || die "compall failed" + + # build the ddi TCP/IP socket stuff + cd ${S}/"ddi" + ./compddi || die "compddi failed" + + # finally, link it all together + cd "${S}" + ./lked || die "lked failed" + + # for hardened (PAX) users and ifc we need to turn + # MPROTECT off + if [[ "${FORTRANC}" == "ifc" ]] && use hardened; then + /sbin/paxctl -PemRxS ${PN}.00.x 2> /dev/null || \ + die "paxctl failed on actvte.x" + fi +} + +src_install() { + # the executables + dobin ${PN}.00.x rungms \ + || die "Failed installing binaries" + if use !mpi; then + dobin ddi/ddikick.x \ + || die "Failed installing binaries" + fi + + # the docs + dodoc *.DOC qmnuc/*.DOC || die "Failed installing docs" + + # install ericftm + insinto /usr/share/${PN}/ericfmt + doins ericfmt.dat || die "Failed installing ericfmt.dat" + + # install mcpdata + insinto /usr/share/${PN}/mcpdata + doins mcpdata/* || die "Failed installing mcpdata" + + # install tinker params in case of qmmm + if use qmmm-tinker ; then + dodoc tinker/simomm.doc || die "Failed installing docs" + insinto /usr/share/${PN} + doins -r tinker/params || die "Failed to install Tinker params" + fi + + # install the tests the user should run, and + # fix up the runscript; also grab a copy of rungms + # so the user is ready to run the tests + insinto /usr/share/${PN}/tests + insopts -m0644 + doins tests/* || die "Failed installing tests" + insopts -m0744 + doins runall || die "Failed installing tests" + doins tools/checktst/checktst tools/checktst/chkabs || \ + die "Failed to install main test checker" + doins tools/checktst/exam* || \ + die "Failed to install individual test files" + + insinto /usr/share/${PN}/neotests + insopts -m0644 + doins -r qmnuc/neotests/* || die "Failed to install NEO tests" +} + +pkg_postinst() { + echo + einfo "Before you use GAMESS for any serious work you HAVE" + einfo "to run the supplied test files located in" + einfo "/usr/share/gamess/tests and check them thoroughly." + einfo "Otherwise all scientific publications resulting from" + einfo "your GAMESS runs should be immediately rejected :)" + einfo "To do so copy the content of /usr/share/gamess/tests" + einfo "to some temporary location and execute './runall'. " + einfo "Then run the checktst script in the same directory to" + einfo "validate the tests." + einfo "Please consult TEST.DOC and the other docs!" + + if [[ "${FORTRANC}" == "ifc" ]]; then + echo + ewarn "IMPORTANT NOTE: We STRONGLY recommend to stay away" + ewarn "from ifc-9.0 for now and use the ifc-8.1 series of" + ewarn "compilers UNLESS you can run through ALL of the " + ewarn "test cases (see above) successfully." + fi + + echo + einfo "If you want to run on more than a single CPU" + einfo "you will have to acquaint yourself with the way GAMESS" + einfo "does multiprocessor runs and adjust rungms according to" + einfo "your target network architecture." + echo + + if use qmmm-tinker; then + einfo "You may want to install sci-chemistry/tinker to use addition FF" + einfo "parameters for your qmmm calculations" + echo + fi +} |