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sci-chemistry/gromacs: add 2024.5
Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
This commit is contained in:
Alexey Shvetsov
@@ -1,12 +1,15 @@
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DIST gromacs-2023.5.tar.gz 42079310 BLAKE2B e50dbe76396230f4a886280bdebcf7b131506679240e77d2a2263c3b5dbfe7ef754c4265fc04e9acad7932c7691de7f694cc23140a25d0d5be649a4120f45b0c SHA512 f3a34cf0d379d6d4964d7494af6c6617c0c092293ea38a3a248af2dd2a90cae04696d52e68126176065efc480977942b00efa441028e526e1555c7e84551fc0c
|
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DIST gromacs-2024.3.tar.gz 42373103 BLAKE2B f45af72ecdf119b423d98b84818eaca1aa2e3f43eaf1aff7435de2a5891079a880f19a654627ee2f43e3a38c9dcfa0638bc6eb6da201b3c9ce89b2dc32fc683b SHA512 13f23e581c2b63f6262e8359e7bed6a1a5f3164047ea38d2b6a44bcd2b20b61332705167435fe2ad30fe6f24f8ab49b982388550cdecb49167e4156e36286d3d
|
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DIST gromacs-2024.4.tar.gz 42356162 BLAKE2B 3a1019128a2cfd47fb3ab23962a6fcd5bac3b5519d4bfa1239956740226468986ba93e645eb3bc20117968c024823e948fd819a603315399d573275c91c6e51b SHA512 32a08e9417d4d36a29bdfde4e0448bc136bd3db79b5d5c84fa99d9f022ffca6a94b7bd1c7e7a335430fb6bdcf0181e3cbabeb46d13978c0f87b5d88787ea8d63
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DIST gromacs-2024.5.tar.gz 42353127 BLAKE2B c1fa6bd90390c9e13f11995ea9992902e136e15f6191ed47c9eac95384f97221533509ddd2bc4908f1d36fb790aab8a068fd1c00dd6f82e440f4719092b8ea37 SHA512 cb4f6bf4a6a53fb7ee4d8ed832d514d77d21eea3e1b86eec1bf51a4b6197a30aa8d68ca61919d7921c701af365077a9c84c12ef33d5584a1bc796b25709aa7af
|
||||
DIST gromacs-2025-rc.tar.gz 44424653 BLAKE2B 24f3d9ab02320604bb4e99a2bfe409061de92069684cec987355490eeeefd0cee2d665d7d1d4277904bf5025f6c59f0b3de36e6bf61b33f780c2ed2c758f6995 SHA512 0c40ea9b34b3f577ebe3843a65d5d384961224dd179434b98725a4f58190e9d0177b63407d276266a838e39b8d846f461672099787e683d7c8f4ad189cbc5571
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DIST manual-2023.5.pdf 13579081 BLAKE2B 42f687ebcdb79bfc77aabac4fd382940c23ba27da380b8eff342c2e9255a58fc11a0458220d1f71f3c13ab1cf6fdabad00ac1bad741781d0b787899165bea2cc SHA512 0661f166f7a8dc24b4244c0139f366832ddfc1298129df2a6e29800b5d1567318781ab547bc7e9ee54de7a62abba4996f8e3010c91d6917c248117e5711d7dbb
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DIST manual-2024.3.pdf 13676383 BLAKE2B fa5b310ee8977c525781492c70a18d40f8842f5fa43831ad0283c033f39968ba98e74ea618a4a9c25d88c3ed694071327220617b17f316ba2f29777c3edc95ca SHA512 8dd09913b89213a6673a5f5e3462fb963d1f30d68e0d58b846b7e2cf2f73baacb14fabab6591b680849607f4ca617cf288899729939b2c32021b4ee5ba06835f
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DIST manual-2024.4.pdf 13690684 BLAKE2B 7fac46df0da9d4cf7584599c7a71c4e1d11f75fc20a7a19ecc8069fdc2e9e35f0292e389f9c40d69dc96bdfea8d4ee370a54279b5531c0fb37c4cbd76caf7800 SHA512 5c4662527554171774adde5a3de220d775723154914838fd7fc3e40c981e1fccac0fd0def1acc500635cd39269d3bcc2edab5ec7aa85a7ea78350969d72ee13c
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DIST manual-2024.5.pdf 13693341 BLAKE2B b2e94b845f04201734c0a3ef834d013c2e65be53614329166d3b7e4ffcdfb71f3d25a4e8d9f852c4a7570b776532b7d0f00f9f62b76b1cd7fa8567ce22d44540 SHA512 b33a6689f965cfd867daee26b88693ab0696bb49db86e4f411030f36ce924e29f9cedbf3df51e3b02a223b91aa54394144795edb632336b8aa9eb164da8d4ded
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DIST manual-2025-rc.pdf 13789080 BLAKE2B e60b7199c3b97989210480b5efe1a8c339c2875cb8257d9a9898dd82282a43c9efb0fd6bc0be065df315590d0fe61fbb0869b85e526020795b6e10c6b5eff659 SHA512 20774686f02f2b2eb2e24b11d22c9d17bfe6f41be43474948285ee75778c456429316da1a9bc3bb727555295eeea4963ea49bb968e25df020ba830d304c3e6bb
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DIST regressiontests-2023.5.tar.gz 48619605 BLAKE2B f2549a34750c6866f054614a00a3360a09b82306e6bd5e5b848e18cdd3a3fabaac6203c5ca734901019403225dd47e0d662838abe9a1db7d07662f1c745b8e4f SHA512 3ccaf9db7dfba641a5e98ebff3d735cae3f679926aba443ffedec20dd6c85e67f0e9711ebad5dfa8105122d5411f5de6ded1802a7da4ddf0599657832c8c597a
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DIST regressiontests-2024.3.tar.gz 32776961 BLAKE2B 6a74977a396f8e82f7aba7a384cc840275b86d470597a4bbb93e97f1c13cd8fcf6d86ab26bdd4a89464b863954c9ed7dbd49af095e821573845f7bda43c2b90b SHA512 1c4afbbca82c9b9ad371713ef5e7e093ca766f25f6fbda55c79ea1aecb2f0a06bdb042d3c8a86e3d9bf9e8b8091244827dbff544f66037ffa56b0bcb341a9d2c
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DIST regressiontests-2024.4.tar.gz 32777006 BLAKE2B 41623de750b89410fa0a52037ea28d99a688b602b286cff732a6e8100b2b72072f579fc4f72bfe7c246ca086b6c6c1c10adb89874db6e1c9276494572e408a9f SHA512 dfbe8ee1b7c5b534842203f2295ea08875df6af3fb94798138b92ab8bc816719e3357db2935d2de4fd798d104ad7cb44860cd65887da7bb2438db422f35e6848
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DIST regressiontests-2024.5.tar.gz 32776573 BLAKE2B 5e397b6c601132ac96b826325bd0304d5939b87f0edaa89ba84d672a9df27351f26dbc9fde39fdb7a177be2743db93198316663a39145231741d08f3268d67cf SHA512 8594e8365f676f18f227b4d6b87fa6a1a8ceab8301302469a626380a7d29035a2cd8667b4d923b26491d3db9298d6660a9c9bde9274dfeba278dfabdb54ef424
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DIST regressiontests-2025-rc.tar.gz 32653300 BLAKE2B 6078855a0a2958732338f402fcce7e0cf0d117916930491977f894aa856ae40d968810f94e2f26f658201a8e00d2df782c27b942adab5d84063e4d2ed9dbfd07 SHA512 b9cfceef1495f43aaebc33d612c5c584c60418b2dab15d0ac78c8d5a52258221db7adce708f78bda70c3f9c48b6527777aceee32fafa603a4eca2d99ab166059
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341
sci-chemistry/gromacs/gromacs-2024.5.ebuild
Normal file
341
sci-chemistry/gromacs/gromacs-2024.5.ebuild
Normal file
@@ -0,0 +1,341 @@
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# Copyright 1999-2025 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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CMAKE_MAKEFILE_GENERATOR="ninja"
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PYTHON_COMPAT=( python3_{10..12} )
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DISTUTILS_OPTIONAL=1
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DISTUTILS_USE_PEP517=no
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DISTUTILS_SINGLE_IMPL=1
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inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils
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|
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if [[ ${PV} = *9999* ]]; then
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||||
EGIT_REPO_URI="
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||||
https://gitlab.com/gromacs/gromacs.git
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https://github.com/gromacs/gromacs.git
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"
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[[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
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inherit git-r3
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else
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SRC_URI="
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https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
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doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
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test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
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# since 2022 arm support was dropped (but not arm64)
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KEYWORDS="~amd64 -arm ~arm64 ~riscv -x86 ~amd64-linux -x86-linux ~x64-macos"
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fi
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ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
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DESCRIPTION="The ultimate molecular dynamics simulation package"
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HOMEPAGE="https://www.gromacs.org/"
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# see COPYING for details
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# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
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# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
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LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
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SLOT="0/${PV}"
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IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
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CDEPEND="
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blas? ( virtual/blas )
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cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
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opencl? ( virtual/opencl )
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||||
openmp? (
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sys-devel/gcc[openmp]
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llvm-core/clang-runtime[openmp]
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)
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fftw? ( sci-libs/fftw:3.0= )
|
||||
hwloc? ( sys-apps/hwloc:= )
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||||
lapack? ( virtual/lapack )
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||||
mkl? ( sci-libs/mkl )
|
||||
mpi? ( virtual/mpi[cxx] )
|
||||
sci-libs/lmfit:=
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>=dev-cpp/muParser-2.3:=
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${PYTHON_DEPS}
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"
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BDEPEND="${CDEPEND}
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||||
virtual/pkgconfig
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clang? ( >=llvm-core/clang-6:* )
|
||||
build-manual? (
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app-text/doxygen
|
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$(python_gen_cond_dep '
|
||||
dev-python/sphinx[${PYTHON_USEDEP}]
|
||||
dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
|
||||
dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
|
||||
dev-python/sphinx-argparse[${PYTHON_USEDEP}]
|
||||
dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
|
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')
|
||||
media-gfx/mscgen
|
||||
media-gfx/graphviz
|
||||
dev-texlive/texlive-latex
|
||||
dev-texlive/texlive-latexextra
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||||
media-gfx/imagemagick
|
||||
)"
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RDEPEND="${CDEPEND}"
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REQUIRED_USE="
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|| ( single-precision double-precision )
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doc? ( !build-manual )
|
||||
cuda? ( single-precision )
|
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opencl? ( single-precision )
|
||||
cuda? ( !opencl )
|
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clang-cuda? ( clang cuda )
|
||||
mkl? ( !blas !fftw !lapack )
|
||||
${PYTHON_REQUIRED_USE}"
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DOCS=( AUTHORS README )
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RESTRICT="!test? ( test )"
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|
||||
PATCHES=( "${FILESDIR}/${PN}-gcc-15.patch" )
|
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|
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if [[ ${PV} != *9999 ]]; then
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S="${WORKDIR}/${PN}-${PV/_/-}"
|
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fi
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|
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pkg_pretend() {
|
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[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
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}
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pkg_setup() {
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[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
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python-single-r1_pkg_setup
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}
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src_unpack() {
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if [[ ${PV} != *9999 ]]; then
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default
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else
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git-r3_src_unpack
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if use test; then
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EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \
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EGIT_BRANCH="${EGIT_BRANCH}" \
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EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
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git-r3_src_unpack
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fi
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||||
fi
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}
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src_prepare() {
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#notes/todos
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# -on apple: there is framework support
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|
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xdg_environment_reset #591952
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# we can use clang as default
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if use clang && ! tc-is-clang ; then
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export CC=${CHOST}-clang
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export CXX=${CHOST}-clang++
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else
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tc-export CXX CC
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fi
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# clang-cuda need to filter mfpmath
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if use clang-cuda ; then
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filter-mfpmath sse
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filter-mfpmath i386
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fi
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cmake_src_prepare
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use cuda && cuda_src_prepare
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GMX_DIRS=""
|
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use single-precision && GMX_DIRS+=" float"
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use double-precision && GMX_DIRS+=" double"
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if use test; then
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for x in ${GMX_DIRS}; do
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mkdir -p "${WORKDIR}/${P}_${x}" || die
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cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
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done
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||||
fi
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DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
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if use build-manual; then
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# try to create policy for imagemagik
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mkdir -p "${HOME}"/.config/ImageMagick
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cat >> "${HOME}"/.config/ImageMagick/policy.xml <<- EOF
|
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<?xml version="1.0" encoding="UTF-8"?>
|
||||
<!DOCTYPE policymap [
|
||||
<!ELEMENT policymap (policy)+>
|
||||
!ATTLIST policymap xmlns CDATA #FIXED ''>
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<!ELEMENT policy EMPTY>
|
||||
<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
|
||||
name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
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stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
|
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]>
|
||||
<policymap>
|
||||
<policy domain="coder" rights="read | write" pattern="PS" />
|
||||
<policy domain="coder" rights="read | write" pattern="PS2" />
|
||||
<policy domain="coder" rights="read | write" pattern="PS3" />
|
||||
<policy domain="coder" rights="read | write" pattern="EPS" />
|
||||
<policy domain="coder" rights="read | write" pattern="PDF" />
|
||||
<policy domain="coder" rights="read | write" pattern="XPS" />
|
||||
</policymap>
|
||||
EOF
|
||||
fi
|
||||
}
|
||||
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||||
src_configure() {
|
||||
local mycmakeargs_pre=( ) extra fft_opts=( )
|
||||
local acce="AUTO"
|
||||
|
||||
if use custom-cflags; then
|
||||
#go from slowest to fastest acceleration
|
||||
acce="None"
|
||||
if (use amd64 || use x86); then
|
||||
use cpu_flags_x86_sse2 && acce="SSE2"
|
||||
use cpu_flags_x86_sse4_1 && acce="SSE4.1"
|
||||
use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
|
||||
use cpu_flags_x86_avx && acce="AVX_256"
|
||||
use cpu_flags_x86_avx2 && acce="AVX2_256"
|
||||
use cpu_flags_x86_avx512f && acce="AVX_512"
|
||||
elif (use arm); then
|
||||
use cpu_flags_arm_neon && acce="ARM_NEON"
|
||||
elif (use arm64); then
|
||||
use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
|
||||
fi
|
||||
else
|
||||
strip-flags
|
||||
fi
|
||||
|
||||
#to create man pages, build tree binaries are executed (bug #398437)
|
||||
[[ ${CHOST} = *-darwin* ]] && \
|
||||
extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
|
||||
|
||||
if use fftw; then
|
||||
fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
|
||||
elif use mkl; then
|
||||
local bits=$(get_libdir)
|
||||
fft_opts=( -DGMX_FFT_LIBRARY=mkl
|
||||
-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
|
||||
-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
|
||||
)
|
||||
else
|
||||
fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
|
||||
fi
|
||||
|
||||
mycmakeargs_pre+=(
|
||||
"${fft_opts[@]}"
|
||||
"${lmfit_opts[@]}"
|
||||
-DGMX_USE_LMFIT=EXTERNAL
|
||||
-DGMX_USE_MUPARSER=EXTERNAL
|
||||
-DGMX_EXTERNAL_BLAS=$(usex blas)
|
||||
-DGMX_EXTERNAL_LAPACK=$(usex lapack)
|
||||
-DGMX_OPENMP=$(usex openmp)
|
||||
-DGMX_COOL_QUOTES=$(usex offensive)
|
||||
-DGMX_USE_TNG=$(usex tng)
|
||||
-DGMX_BUILD_MANUAL=$(usex build-manual)
|
||||
-DGMX_HWLOC=$(usex hwloc)
|
||||
-DGMX_DEFAULT_SUFFIX=off
|
||||
-DGMX_SIMD="$acce"
|
||||
-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
|
||||
-DBUILD_TESTING=$(usex test)
|
||||
-DGMX_BUILD_UNITTESTS=$(usex test)
|
||||
-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
|
||||
${extra}
|
||||
)
|
||||
|
||||
for x in ${GMX_DIRS}; do
|
||||
einfo "Configuring for ${x} precision"
|
||||
local suffix=""
|
||||
#if we build single and double - double is suffixed
|
||||
use double-precision && use single-precision && \
|
||||
[[ ${x} = "double" ]] && suffix="_d"
|
||||
local p
|
||||
[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
|
||||
local gpu=( "-DGMX_GPU=OFF" )
|
||||
[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
|
||||
[[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
|
||||
use opencl && gpu=( "-DGMX_GPU=OPENCL" )
|
||||
local mycmakeargs=(
|
||||
${mycmakeargs_pre[@]} ${p}
|
||||
-DGMX_MPI=$(usex mpi)
|
||||
-DGMX_THREAD_MPI=$(usex threads)
|
||||
-DGMXAPI=$(usex gmxapi)
|
||||
-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
|
||||
"${gpu[@]}"
|
||||
"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
|
||||
-DGMX_BINARY_SUFFIX="${suffix}"
|
||||
-DGMX_LIBS_SUFFIX="${suffix}"
|
||||
-DGMX_PYTHON_PACKAGE=$(usex python)
|
||||
)
|
||||
BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
|
||||
[[ ${CHOST} != *-darwin* ]] || \
|
||||
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
|
||||
done
|
||||
}
|
||||
|
||||
src_compile() {
|
||||
for x in ${GMX_DIRS}; do
|
||||
einfo "Compiling for ${x} precision"
|
||||
BUILD_DIR="${WORKDIR}/${P}_${x}"\
|
||||
cmake_src_compile
|
||||
if use python; then
|
||||
BUILD_DIR="${WORKDIR}/${P}_${x}"\
|
||||
cmake_src_compile python_packaging/all
|
||||
BUILD_DIR="${WORKDIR}/${P}" \
|
||||
distutils-r1_src_compile
|
||||
fi
|
||||
# not 100% necessary for rel ebuilds as available from website
|
||||
if use build-manual; then
|
||||
BUILD_DIR="${WORKDIR}/${P}_${x}"\
|
||||
cmake_src_compile manual
|
||||
fi
|
||||
done
|
||||
}
|
||||
|
||||
src_test() {
|
||||
for x in ${GMX_DIRS}; do
|
||||
BUILD_DIR="${WORKDIR}/${P}_${x}"\
|
||||
cmake_src_compile check
|
||||
done
|
||||
}
|
||||
|
||||
src_install() {
|
||||
for x in ${GMX_DIRS}; do
|
||||
BUILD_DIR="${WORKDIR}/${P}_${x}" \
|
||||
cmake_src_install
|
||||
if use python; then
|
||||
BUILD_DIR="${WORKDIR}/${P}_${x}" \
|
||||
cmake_src_install python_packaging/install
|
||||
fi
|
||||
if use build-manual; then
|
||||
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
|
||||
fi
|
||||
|
||||
if use doc; then
|
||||
if [[ ${PV} != *9999* ]]; then
|
||||
newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
|
||||
fi
|
||||
fi
|
||||
done
|
||||
|
||||
if use tng; then
|
||||
insinto /usr/include/tng
|
||||
doins src/external/tng_io/include/tng/*h
|
||||
fi
|
||||
# drop unneeded stuff
|
||||
rm "${ED}"/usr/bin/GMXRC* || die
|
||||
for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
|
||||
local n=${x##*/gmx-completion-}
|
||||
n="${n%.bash}"
|
||||
cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
|
||||
newbashcomp "${T}"/"${n}" "${n}"
|
||||
done
|
||||
rm "${ED}"/usr/bin/gmx-completion*.bash || die
|
||||
readme.gentoo_create_doc
|
||||
}
|
||||
|
||||
pkg_postinst() {
|
||||
einfo
|
||||
einfo "Please read and cite gromacs related papers from list:"
|
||||
einfo "https://www.gromacs.org/articles.html"
|
||||
einfo
|
||||
readme.gentoo_print_elog
|
||||
}
|
||||
Reference in New Issue
Block a user