commit: cd794bcbb79b594e8056e86af835aaac6e14ee2e Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> AuthorDate: Mon Oct 22 21:28:06 2018 +0000 Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> CommitDate: Mon Oct 22 21:28:39 2018 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=cd794bcb
sci-chemistry/gromacs: New beta version Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org> Package-Manager: Portage-2.3.51, Repoman-2.3.11 sci-chemistry/gromacs/Manifest | 2 ++ ...romacs-9999.ebuild => gromacs-2019.9999.ebuild} | 26 +++++++++++--- ...omacs-9999.ebuild => gromacs-2019_beta1.ebuild} | 40 +++++++++++++++------- sci-chemistry/gromacs/gromacs-9999.ebuild | 26 +++++++++++--- sci-chemistry/gromacs/metadata.xml | 2 ++ 5 files changed, 74 insertions(+), 22 deletions(-) diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 71ac5f61019..eafd2138713 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,10 +1,12 @@ DIST gromacs-2016.2.tar.gz 27339623 BLAKE2B c3548f4abdc4c1b09a79a3da99d7ca8060daca7307e4c5b81bd97d54adfb9621fbccf1ea7fd96c3676d6b44c20f9f4cd2168ce131799792512fad3b8b1ac0522 SHA512 f5e74bb8c126823c90d205ac0f0835e61fdd13a4550bc15aa9c972ee9b187f6451cdc90877c17276d2f889d61abb5eaa5ea1b54f7cbf3da67074146c749c1aa6 DIST gromacs-2016.5.tar.gz 27369491 BLAKE2B 4a8bf1ae3e298ac2e26ec476130720dc3ef00db5d999e3a45fdbfd7fbfe7e94fbc86be6ff0f2f23552769c8bc851ce49c73f6fc1ab13f372523279b93e7794d7 SHA512 9cb8ff88871aa5df0967c60ba303c03296c6fa3c215cd01b26259df7753f0014f04222078ab4b84a66a1f709997837134d5c0f74da19b78322e410010c9d9e10 DIST gromacs-2018.3.tar.gz 29915626 BLAKE2B 6e6eeafecdd923a25b4a2a78a8e89f793639b57ffbd63f19d133d8474302f9a381041f138a509dadb42b36e25fe508729e860efb6b0c75cdbf01d924b0a8fd83 SHA512 3c4d6eb3942d7b54d01c94c6f6f5ae706e0f5d4f9901ea11a56fde4df97b1a9112007f2cb13feea0f19f30c89f57ae80ff53a8f5203b8cdff103aa903cd0dc8f +DIST gromacs-2019-beta1.tar.gz 33549950 BLAKE2B 667246f9a7cb136efca3fbda21aabe5ab0a759aa42896f8a9ddc86fafbfb1906e31fe46688c98477a5841e8fe5708b960c2a26abe754b8d793046734cd509377 SHA512 9f8bec3671f6f7421dc45cab1b5edb8ba8f2ebc34cd19ebd3d5d534be1f84135a112f49733a3f8c79e93ffc2b09c5053ae0dea31e95832a2b98acaee47f7d1af DIST gromacs-5.0.4.tar.gz 26342095 BLAKE2B 27a2483e23533ad627114c0005fa0d49a311b359c31aed6378bdd768c9dda03c3b19f11d961f0bd3b82a1711737d4b7dce13cad5fc56d058dd0110fe21421ee3 SHA512 bc62b623bf71dcaa948aaf7563a3d3afa973da0702062848a20323db202e862dcee413197dacd1472866ccb40fce7709e283177b1c6c49514064f23e6c46b5ee DIST gromacs-5.1.3.tar.gz 27095702 BLAKE2B b7fd8fa10e8c4f4368ac551338c59374dc35f85c9fdae5d64eec62929b8f04ea724a084959b3618cd8a151bf3e0a0c84c8f75de953722effca82a4928941ce73 SHA512 9ab26e1b2268f8d567b89b2d99d0b75b937b28edceaec56d17ca3243c76faa31255ffc0c45d762c7c693fe500b00e36ad43b80572d1d7f92dc87f9d2d98c0ba6 DIST regressiontests-2016.2.tar.gz 67095329 BLAKE2B fec8a663845ad67374c8a230d1590fa9e5079460198f41cee3b788aaa1c72e8ec9dcda48bc68a594f15003d11bf6617d46cc1a09c16b7a333587b43904a16ba6 SHA512 e0aceb56d1f38a7e6ab9fdaac5063fd20c5b3a162ffb6eddd0e6dc7dff9b724bfe31363493a9437e9f9d5421a534b375960fcb31e903a4901a0fa94ed8511294 DIST regressiontests-2016.5.tar.gz 67641413 BLAKE2B 4fcd30c198f3acbbabf1104c040d9a686de49536a97dbeb14732bfa0ed3cf37aa61b1b0f45393668985b993d1f1862a8985e416af819cf9793f5964f3e4f43cc SHA512 31764fd99cc4185d61de5d4443ee482c27b13533451a24aa0e4899997ce275a63685424eafacae38b1a3ffd4ce0d5ebe02a90348953b04c104f91376f0edfdff DIST regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b +DIST regressiontests-2019-beta1.tar.gz 67604794 BLAKE2B 163046e54206d3406d39e6bd9552dcce5a9a05a73e14249bf371d2432d902a3e336c0caa3e0c83353ac4566d91f4f805724f8eb996a831f8d3b712f65b1d1c42 SHA512 eef7eaacf56ba9358bfb0a3e34da4bc00d2a65564da81d144f57ee8a732081882b8e1c96f7006b966455105b834271715273e7590d3d4310209ee0324e7fa585 DIST regressiontests-5.0.4.tar.gz 65193251 BLAKE2B c5e5f23adcc2639fe652bc252533307c7fda44453d506603242968bd8588c7394028b2c3c7a9252f807a050d40e8f78735e904dfe517d3db8ae962051f4826c1 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65 DIST regressiontests-5.1.3.tar.gz 66994083 BLAKE2B 7009f65ad0138664ac84e57f8bc7cce5d18a59f99943e56b6642583120bfce279e005ac0bacd2db8904ea477a48e2b938c64de46a65fa5d08fce6009d53583c3 SHA512 486e86eb3b75bae822abe82dac4e1098aa13723bd04214021f835a2f0b847303f015a9ececc33aa5ae63d31a2eeae07e512f22464b6c0e26d1286b0781578022 diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-2019.9999.ebuild similarity index 91% copy from sci-chemistry/gromacs/gromacs-9999.ebuild copy to sci-chemistry/gromacs/gromacs-2019.9999.ebuild index d1dccde65eb..8a643e0fb30 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2019.9999.ebuild @@ -31,7 +31,7 @@ HOMEPAGE="http://www.gromacs.org/"; # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( @@ -40,10 +40,12 @@ CDEPEND=" x11-libs/libICE ) blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) + opencl? ( virtual/opencl ) fftw? ( sci-libs/fftw:3.0 ) - hwloc? ( <sys-apps/hwloc-2 ) + hwloc? ( sys-apps/hwloc ) lapack? ( virtual/lapack ) + lmfit? ( sci-libs/lmfit ) mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) " @@ -51,6 +53,8 @@ DEPEND="${CDEPEND} virtual/pkgconfig doc? ( app-doc/doxygen + dev-python/sphinx + media-gfx/mscgen dev-texlive/texlive-latex dev-texlive/texlive-latexextra media-gfx/imagemagick @@ -60,6 +64,7 @@ RDEPEND="${CDEPEND}" REQUIRED_USE=" || ( single-precision double-precision ) cuda? ( single-precision ) + cuda? ( !opencl ) mkl? ( !blas !fftw !lapack )" DOCS=( AUTHORS README ) @@ -144,8 +149,15 @@ src_configure() { fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) fi + if use lmfit; then + local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) + else + local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) + fi + mycmakeargs_pre+=( "${fft_opts[@]}" + "${lmfit_opts[@]}" -DGMX_X11=$(usex X) -DGMX_EXTERNAL_BLAS=$(usex blas) -DGMX_EXTERNAL_LAPACK=$(usex lapack) @@ -156,7 +168,6 @@ src_configure() { -DGMX_HWLOC=$(usex hwloc) -DGMX_DEFAULT_SUFFIX=off -DGMX_SIMD="$acce" - -DGMX_LIB_INSTALL_DIR="$(get_libdir)" -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" -DBUILD_TESTING=$(usex test) -DGMX_BUILD_UNITTESTS=$(usex test) @@ -173,11 +184,15 @@ src_configure() { [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" local cuda=( "-DGMX_GPU=OFF" ) [[ ${x} = "float" ]] && use cuda && \ - cuda=( -DGMX_GPU=ON ) + cuda=( "-DGMX_GPU=ON" ) + local opencl=( "-DGMX_USE_OPENCL=OFF" ) + use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF -DGMX_THREAD_MPI=$(usex threads) + -DGMXAPI=$(usex gmxapi) + "${opencl[@]}" "${cuda[@]}" "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" -DGMX_BINARY_SUFFIX="${suffix}" @@ -193,6 +208,7 @@ src_configure() { -DGMX_THREAD_MPI=OFF -DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF + -DGMXAPI=OFF -DGMX_BUILD_MDRUN_ONLY=ON -DBUILD_SHARED_LIBS=OFF -DGMX_BUILD_MANUAL=OFF diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-2019_beta1.ebuild similarity index 88% copy from sci-chemistry/gromacs/gromacs-9999.ebuild copy to sci-chemistry/gromacs/gromacs-2019_beta1.ebuild index d1dccde65eb..b59d3312f44 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2019_beta1.ebuild @@ -31,7 +31,7 @@ HOMEPAGE="http://www.gromacs.org/"; # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( @@ -40,10 +40,12 @@ CDEPEND=" x11-libs/libICE ) blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) + opencl? ( virtual/opencl ) fftw? ( sci-libs/fftw:3.0 ) - hwloc? ( <sys-apps/hwloc-2 ) + hwloc? ( sys-apps/hwloc ) lapack? ( virtual/lapack ) + lmfit? ( sci-libs/lmfit ) mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) " @@ -51,6 +53,8 @@ DEPEND="${CDEPEND} virtual/pkgconfig doc? ( app-doc/doxygen + dev-python/sphinx + media-gfx/mscgen dev-texlive/texlive-latex dev-texlive/texlive-latexextra media-gfx/imagemagick @@ -60,6 +64,7 @@ RDEPEND="${CDEPEND}" REQUIRED_USE=" || ( single-precision double-precision ) cuda? ( single-precision ) + cuda? ( !opencl ) mkl? ( !blas !fftw !lapack )" DOCS=( AUTHORS README ) @@ -144,8 +149,15 @@ src_configure() { fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) fi + if use lmfit; then + local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) + else + local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) + fi + mycmakeargs_pre+=( "${fft_opts[@]}" + "${lmfit_opts[@]}" -DGMX_X11=$(usex X) -DGMX_EXTERNAL_BLAS=$(usex blas) -DGMX_EXTERNAL_LAPACK=$(usex lapack) @@ -156,7 +168,6 @@ src_configure() { -DGMX_HWLOC=$(usex hwloc) -DGMX_DEFAULT_SUFFIX=off -DGMX_SIMD="$acce" - -DGMX_LIB_INSTALL_DIR="$(get_libdir)" -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" -DBUILD_TESTING=$(usex test) -DGMX_BUILD_UNITTESTS=$(usex test) @@ -173,11 +184,15 @@ src_configure() { [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" local cuda=( "-DGMX_GPU=OFF" ) [[ ${x} = "float" ]] && use cuda && \ - cuda=( -DGMX_GPU=ON ) + cuda=( "-DGMX_GPU=ON" ) + local opencl=( "-DGMX_USE_OPENCL=OFF" ) + use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF -DGMX_THREAD_MPI=$(usex threads) + -DGMXAPI=$(usex gmxapi) + "${opencl[@]}" "${cuda[@]}" "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" -DGMX_BINARY_SUFFIX="${suffix}" @@ -193,6 +208,7 @@ src_configure() { -DGMX_THREAD_MPI=OFF -DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF + -DGMXAPI=OFF -DGMX_BUILD_MDRUN_ONLY=ON -DBUILD_SHARED_LIBS=OFF -DGMX_BUILD_MANUAL=OFF @@ -211,10 +227,10 @@ src_compile() { BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake-utils_src_compile # not 100% necessary for rel ebuilds as available from website - if use doc; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile manual - fi + #if use doc; then + # BUILD_DIR="${WORKDIR}/${P}_${x}"\ + # cmake-utils_src_compile manual + #fi use mpi || continue einfo "Compiling for ${x} precision with mpi" BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ @@ -233,9 +249,9 @@ src_install() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}" \ cmake-utils_src_install - if use doc; then - newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" - fi + #if use doc; then + # newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + #fi use mpi || continue BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ cmake-utils_src_install diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index d1dccde65eb..8a643e0fb30 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -31,7 +31,7 @@ HOMEPAGE="http://www.gromacs.org/"; # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( @@ -40,10 +40,12 @@ CDEPEND=" x11-libs/libICE ) blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) + opencl? ( virtual/opencl ) fftw? ( sci-libs/fftw:3.0 ) - hwloc? ( <sys-apps/hwloc-2 ) + hwloc? ( sys-apps/hwloc ) lapack? ( virtual/lapack ) + lmfit? ( sci-libs/lmfit ) mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) " @@ -51,6 +53,8 @@ DEPEND="${CDEPEND} virtual/pkgconfig doc? ( app-doc/doxygen + dev-python/sphinx + media-gfx/mscgen dev-texlive/texlive-latex dev-texlive/texlive-latexextra media-gfx/imagemagick @@ -60,6 +64,7 @@ RDEPEND="${CDEPEND}" REQUIRED_USE=" || ( single-precision double-precision ) cuda? ( single-precision ) + cuda? ( !opencl ) mkl? ( !blas !fftw !lapack )" DOCS=( AUTHORS README ) @@ -144,8 +149,15 @@ src_configure() { fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) fi + if use lmfit; then + local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) + else + local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) + fi + mycmakeargs_pre+=( "${fft_opts[@]}" + "${lmfit_opts[@]}" -DGMX_X11=$(usex X) -DGMX_EXTERNAL_BLAS=$(usex blas) -DGMX_EXTERNAL_LAPACK=$(usex lapack) @@ -156,7 +168,6 @@ src_configure() { -DGMX_HWLOC=$(usex hwloc) -DGMX_DEFAULT_SUFFIX=off -DGMX_SIMD="$acce" - -DGMX_LIB_INSTALL_DIR="$(get_libdir)" -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" -DBUILD_TESTING=$(usex test) -DGMX_BUILD_UNITTESTS=$(usex test) @@ -173,11 +184,15 @@ src_configure() { [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" local cuda=( "-DGMX_GPU=OFF" ) [[ ${x} = "float" ]] && use cuda && \ - cuda=( -DGMX_GPU=ON ) + cuda=( "-DGMX_GPU=ON" ) + local opencl=( "-DGMX_USE_OPENCL=OFF" ) + use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF -DGMX_THREAD_MPI=$(usex threads) + -DGMXAPI=$(usex gmxapi) + "${opencl[@]}" "${cuda[@]}" "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" -DGMX_BINARY_SUFFIX="${suffix}" @@ -193,6 +208,7 @@ src_configure() { -DGMX_THREAD_MPI=OFF -DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF + -DGMXAPI=OFF -DGMX_BUILD_MDRUN_ONLY=ON -DBUILD_SHARED_LIBS=OFF -DGMX_BUILD_MANUAL=OFF diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml index 844b34dd014..0dcc6a6c4d7 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -22,6 +22,8 @@ <flag name="hwloc">Enable HWLoc lib support</flag> <flag name="tng">Enable new trajectory format - tng</flag> <flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag> + <flag name="lmfit">Use external <pkg>sci-libs/lmfit</pkg></flag> + <flag name="gmxapi">Add support for gmxapi library</flag> <!-- acceleration optimization flags --> <flag name="offensive">Enable gromacs partly offensive quotes</flag> <flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
