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authorAlexey Shvetsov <alexxy@gentoo.org>2024-02-29 22:43:41 +0300
committerAlexey Shvetsov <alexxy@gentoo.org>2024-02-29 22:43:41 +0300
commit6f41d89cd7d9db011c7f63ca92e7468e3a14ec9e (patch)
tree139e63b057e14a8cb5fbc75938c352099c76e50b /sci-chemistry
parentsci-chemistry/gromacs: add 2024.1 (diff)
downloadgentoo-6f41d89cd7d9db011c7f63ca92e7468e3a14ec9e.tar.gz
gentoo-6f41d89cd7d9db011c7f63ca92e7468e3a14ec9e.tar.bz2
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sci-chemistry/gromacs: drop 2023.1-r1, 2023.2
Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
Diffstat (limited to 'sci-chemistry')
-rw-r--r--sci-chemistry/gromacs/Manifest6
-rw-r--r--sci-chemistry/gromacs/gromacs-2023.1-r1.ebuild335
-rw-r--r--sci-chemistry/gromacs/gromacs-2023.2.ebuild335
3 files changed, 0 insertions, 676 deletions
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 719de00e3ba2..6a240bd34e99 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -5,8 +5,6 @@ DIST gromacs-2021.6.tar.gz 38012702 BLAKE2B 023ae37dc53643758afa050fd179cd66f3c6
DIST gromacs-2021.7.tar.gz 38028032 BLAKE2B 2dc1b15ca8692ca5cf4ad1c7a266b9e2ced064d34a63cef61fea69e48231dd0310cfd8484d29c56cdb599f795d7655959f40038ac933b46ad2841d57bf2b3646 SHA512 ca478533da3bcb377fda30682660db8eb13beef6456fac6013a1a97ec3be60b5594567412e1e2a31392e484f9a40a22da1f12336f4738cf0422ff4f3e8814609
DIST gromacs-2022.5.tar.gz 40362776 BLAKE2B e77c96cd995fb6c8284bcf9728e2f95e265911f643c69d00cc5910c6d22ada41293a1cb74033e708957776551b253453f64dba46497d68b2f73c675e94f30ddd SHA512 79310d6fd39a160e7bbc661a04540c9bcb89f40c133d1031ca16998ef0a67fc4a023f57950b22793f0c91b5fe47fd78cb2e7afedb50fe9251b1c920c9267344d
DIST gromacs-2022.6.tar.gz 40330705 BLAKE2B fdafbd5b2a92d6022dec3e79e961fef220f1eba42850916e7cb70ef459a8d9c6ebc8c1bbe3c105f5b23161dd5c552ec00505d7c0036649b782cf52c311498743 SHA512 91217394f534ca8f78f73189059712e1c2cd354b658722f23768b12748f7bfaf1a5e95227c5ed1b69c1a9b72c3174e9600a712c157ea2f27156387efb823dd67
-DIST gromacs-2023.1.tar.gz 41934072 BLAKE2B 6d04642ba37a8563fafc10e0be83e33aab5ce25ef43ec2c9555e84328096bbe61426558a1433b086028f3c6637a5b3ae82241e67f206c0dd0b5254f5ec27ae4c SHA512 4bddbbc56f26487db9d35f371d65725289d1355dc4c295d32698499e05eb74e31d4db579fc1f665edb55a68b002bddacf37c0f05d3f970b1111c149990d434b1
-DIST gromacs-2023.2.tar.gz 41930578 BLAKE2B ee115ba45711867ced4ad08cede0e87dffd7c4e7a45ff3ee0c06b2f46b0dec838e4b532e092ce3abd993e231ca7d517d9941b371fd6d9d64d581862dc67c449c SHA512 9bc17f310e6be6fd51b7c07bde0b58e8fa15085b2c073eb7bed0db917646586dee5d7cf9b4b178e9b4cedd40d4bcd967edcc4b26debaec6f4ca94399b13b9186
DIST gromacs-2023.3.tar.gz 42071770 BLAKE2B dea0f6b0ccd67bfa4fc58c06bd3eda6d17a7f4b1c6746c2743860cf00ba514884a27140b65b7830ca340c233510ace1734ecc09e393be3e9761e31b9e4abfeb6 SHA512 016181be78887b0e31bc7fd124ac7c25c923c6bab1ffe43d3b4a744ae68203bb9d9f976c4c81bce344f4ea8e9d610ebd5b631b2202fcd6cfefd8c1ad0ebfe10d
DIST gromacs-2024.1.tar.gz 42324773 BLAKE2B 6600c802c39bf7c36d8e388ced202504dcceb3ec018d5f48af4f55e43dd170157a9b6335ce1b20a73623d05a391787936c2ab6ee48ab031d17078256eb7153c5 SHA512 fea88fac28ec142201eec1cea984eabd9db43346254ac555954a13fdbae5a5b00281a17efc8dba8ab0ac42794e3cce41b314c5cb36fb4292a1c6d2668b2ba192
DIST gromacs-2024.tar.gz 42455653 BLAKE2B 86446c5e95f9ddaf718126c409389730ee1642f36c3e0d844eb4b3a640c275e7979581365dacb57ac66daec296bbd94be6d5c0376f7255d3d3950f6759f8d69a SHA512 d64bf3cbe579003ce37dfd3d27c68746a04360d9d5491c638f3f2bd9af2c938504b0c9710c62e85225370ddf5418e6ebc2422033e46af5eee6e4aaa53699fed7
@@ -17,8 +15,6 @@ DIST manual-2021.6.pdf 12256595 BLAKE2B 5d808e38571b38c1f6e0d115f6e604238206cc00
DIST manual-2021.7.pdf 12256526 BLAKE2B 6f298d7dac142f66914bbc2ea7d6ca70c4aeafaf33ccf12336d5cec64b1f1097b5332c767bb411ccef706ec6184479a84bcf59bda21c4249d45d8ce3dea08e79 SHA512 197765accb8ab6c5f1cc94b2697ff1817e157d85fa231dfe36a85036076e04da2a8035de66aba4f46c6dd7f553176357b94c92e1da5d1dabc574c627deee5279
DIST manual-2022.5.pdf 13081119 BLAKE2B 7a0ffd086d98527d42da4a22984d8351ad7861e32951e8b65c88e7d0df1559303750886ae31a7c158b4e22f616f6dd5deed9a63b0ed114bb1e0adfda9350a487 SHA512 707869ee6052f1b7f75376b0f78fcc4859035234957cc740bd770ea3bea3a591f7fc1fbc0b8526baab48eebfa506d03927df94ddc9c412c75dc2f2864574dd82
DIST manual-2022.6.pdf 13081140 BLAKE2B e7ae3f23ddc076c295be2c464fe2177d6d6848d070ee5eba2b572e996ae08adead898ec6432b123802907f64983aa4d2e17426be8d540c48d12398a479519f9e SHA512 4724888b3c33c4fa4a035d5fb2f8c51496f67e1ee312676510d5ba74bc3cc1571e71e84464585b87ad0133e8e736343ae382bf8f7b556633f86a99560213d271
-DIST manual-2023.1.pdf 13526498 BLAKE2B a9aabcb722954c9c83a8f5945c85e634b0b82ace8b9b077c3f2b9ff432ca71d3e2d5ca2dd52d6ce489d77d3d4ca7b41d75e5566205bb8855caa650fa2722e5ec SHA512 b6ca6c822ac5b3cbe3c84d8fd51d3ed465268c00bb5f96e2afa557d45f9c534b0de278f33a0fdf43080c9c619344b98cd71847e17b297a789eec4c8b42dea7b2
-DIST manual-2023.2.pdf 13547562 BLAKE2B 17155c82d968003706f974e2fb513dced28987e4630c455674d4088dcb827136e2b7b66836a2bf7f9be472254c11ab4ec98cace1462e85a7a18b0f1eb1760781 SHA512 b8026422fb367bf58d6ddb727afe2f1b208c9abb4eb513d85d395a19a82a7fcf362390f4ae5718fa17b0aeb7bf2c90567f40913fdc3cfc51c63d3757ab5a4905
DIST manual-2023.3.pdf 13565055 BLAKE2B 0332b5c4de863e9f33d7ae7404741ee8f7f503ee0d2dc723e9cc42e9fd3fb8fc74313b43589cbfc7127daec24b721ba79a3c53ff509e718992ccbde14889ea2f SHA512 144220f18bfab6fefec738a7af743bd01733a896c853963ce113354da05514941862412786f0e2183de77634b31b334814d42daae87a9009ec0211118ed87685
DIST manual-2024.1.pdf 13651959 BLAKE2B d76e112d3d22e6638e733dec7db713aa65e16099e98935e0bfe8842966a51a04ca370e9afb62ad5b30f3adced1c67574a21445b61f3ce5a753e5d8680f87967e SHA512 3f1aa3433095983cf7ce5c54383bc384d25d9f3b22357e0360639f619c740df37ec0c827ccc9d48b8f93e3877315ee82f740c486b231f777e1be35e44fd823fe
DIST manual-2024.pdf 13644437 BLAKE2B 19d547686d5c5be5e1236aba648e8afb174b281802ab76e020466953ab5d2dd98701f21eb4736cb449b61960b5b7aadce6711b2b0309a41dd1997d7383bce09e SHA512 b00048651f1f81f9024ba5c4c02ad66d2b07eb7b816f0489568fb64859cac515b885a5cb4640c8b5bd7c3620655a7ebc5fc2e4e4cbb8e952ffb0c9b5815ae661
@@ -29,8 +25,6 @@ DIST regressiontests-2021.6.tar.gz 48537070 BLAKE2B 982fad6b23da5c1e6d32009f9f08
DIST regressiontests-2021.7.tar.gz 48537500 BLAKE2B b0c97fa652cb9b972c50f29822f530fcaa2ec9acb6d6442114fc6446c54aade5eb1bfa153c69a7e8bf64b66e8b041d7f8e0d51e7f7b0516f9e03f3d9ad626193 SHA512 7cbead90aa6d62346dcf7c2249c3cfa179884b987a749624444d2f59d93e0322f7721143bf6eb44d26102635dc70a73546ef82d4647558b6320bfdd459074017
DIST regressiontests-2022.5.tar.gz 48615858 BLAKE2B 6655946155291eb24f76832c76e21b5c606905e94426fd057ecdaa44d74844613ba288b651f94120553ef7d7f938de345ddaac7c3738d67bdad148359b7b4500 SHA512 8dd0c8a9b30f4c047fb756dee8eee1cb667803c231fd114717e3156c5694a195dec2b57d80b50b417312949bc4cb7da90027cc98102d84fa154a93862bc69790
DIST regressiontests-2022.6.tar.gz 48615697 BLAKE2B 566adafbc36d3c1faae322fca9cf451f57245c4ceed63f90f26208025937dae0c1bbb8c372bce618f63305d0368113fecd96c7275a75d8b9c19c22a6e5aa9b96 SHA512 68aa9bedffbea37fb7703c18c3f66f607a91f16ece4bec58ced6e42a481156b2fe83760d0e40cecbdcaf87b168441b8ebde27cec30d98c89f516360ea45ddd43
-DIST regressiontests-2023.1.tar.gz 48613205 BLAKE2B b64716e08e5597676794209a0a951d2a5a46aab2b05bc1615d6f4ba666d5c81a7fe9247fc90ce8d9a5da1a9d52eea73d3d3cd4a4072a8bad66b8de0e06dfa599 SHA512 c6924ec75e456950cef0809ea9718be1bf9d85fe6e9ba5553b2df86ef604b0c7f54d41476f45cbc0ccf801ee0290a829bf4f9eb8d0773586bb8385efc5242d4d
-DIST regressiontests-2023.2.tar.gz 48621115 BLAKE2B bc19380e7adaef5246d5620b611546fcd31e1b92129b78c6a8b9acf58bcebab8427aca1b71434b9d6f44535aeb7c2053ada941a8851435f3949aab43316ec136 SHA512 ecb275b93b72bc862c1c9f87c7c1b3abbe535c770e86c020f0f5684a60c6edeb19a193719f338d42576b9c40ec213b915f4c2b3c206dca574eccb8f9ade2c261
DIST regressiontests-2023.3.tar.gz 48620623 BLAKE2B e664bde0dab4bc27f1c8c1b6a24f4a9cba1164a7978d169be091945dc1cabfe821f983a7b7c891cd983d5b05bb3f27c07cdb180c0bfadb93751618cab57671e7 SHA512 0a5bd7a502973c2f658faca159ed0677907a1ca30eae3912a624e58e7cae9965c17c94ce65e94886d92444d34eb63b5b88a578459e6063687c43188031c0f836
DIST regressiontests-2024.1.tar.gz 48136131 BLAKE2B 600b2d11916152b1a29db5b67de61752137e507d5b3634325c034b3ae16c96ca039762f74fe961912b728592d6940bb0aa1f409cc58b0b0d18e616c429e680c4 SHA512 1649a6a42be2887b4d494733d5a969df735904fba39f2532969435d99f8fc900e9234d3d0f2a34a90bc0961716c335bbbe322566d14974a9d8fb50932f6a36b0
DIST regressiontests-2024.tar.gz 48142685 BLAKE2B e24c29c2b534f2fe42e4abc122578ba618279f3182f83be604516e6ee2a34ff037b2604b4cda7a9b7e2ea9fce0a386b3efb7c8aa0cac378d6d8c1595be884c76 SHA512 6c4a847c379603590f618a4da7c691b51bbe180ca9dc59abf885ef8599e1b66758171eb05b7d7709d968f559b209c2fa4cfec8f15cc5d072fafe952567002c2e
diff --git a/sci-chemistry/gromacs/gromacs-2023.1-r1.ebuild b/sci-chemistry/gromacs/gromacs-2023.1-r1.ebuild
deleted file mode 100644
index a3319899d419..000000000000
--- a/sci-chemistry/gromacs/gromacs-2023.1-r1.ebuild
+++ /dev/null
@@ -1,335 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-PYTHON_COMPAT=( python3_{10..12} )
-
-DISTUTILS_OPTIONAL=1
-DISTUTILS_USE_PEP517=no
-DISTUTILS_SINGLE_IMPL=1
-
-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils
-
-if [[ ${PV} = *9999* ]]; then
- EGIT_REPO_URI="
- https://gitlab.com/gromacs/gromacs.git
- https://github.com/gromacs/gromacs.git
- "
- [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
- inherit git-r3
-else
- SRC_URI="
- https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
- doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
- test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
- # since 2022 arm support was dropped (but not arm64)
- KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-fi
-
-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"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="https://www.gromacs.org/"
-
-# see COPYING for details
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-# 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="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}"
-
-CDEPEND="
- blas? ( virtual/blas )
- cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
- opencl? ( virtual/opencl )
- fftw? ( sci-libs/fftw:3.0= )
- hwloc? ( sys-apps/hwloc:= )
- lapack? ( virtual/lapack )
- mkl? ( sci-libs/mkl )
- mpi? ( virtual/mpi[cxx] )
- sci-libs/lmfit:=
- >=dev-cpp/muParser-2.3:=
- ${PYTHON_DEPS}
- "
-BDEPEND="${CDEPEND}
- virtual/pkgconfig
- clang? ( >=sys-devel/clang-6:* )
- build-manual? (
- app-text/doxygen
- $(python_gen_cond_dep '
- dev-python/sphinx[${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}]
- ')
- media-gfx/mscgen
- media-gfx/graphviz
- dev-texlive/texlive-latex
- dev-texlive/texlive-latexextra
- media-gfx/imagemagick
- )"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
- || ( single-precision double-precision )
- doc? ( !build-manual )
- cuda? ( single-precision )
- opencl? ( single-precision )
- cuda? ( !opencl )
- clang-cuda? ( clang cuda )
- mkl? ( !blas !fftw !lapack )
- ${PYTHON_REQUIRED_USE}"
-
-DOCS=( AUTHORS README )
-
-RESTRICT="!test? ( test )"
-
-if [[ ${PV} != *9999 ]]; then
- S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
- python-single-r1_pkg_setup
-}
-
-src_unpack() {
- if [[ ${PV} != *9999 ]]; then
- default
- else
- git-r3_src_unpack
- if use test; then
- EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \
- EGIT_BRANCH="${EGIT_BRANCH}" \
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
- git-r3_src_unpack
- fi
- fi
-}
-
-src_prepare() {
- #notes/todos
- # -on apple: there is framework support
-
- xdg_environment_reset #591952
-
- # we can use clang as default
- if use clang && ! tc-is-clang ; then
- export CC=${CHOST}-clang
- export CXX=${CHOST}-clang++
- else
- tc-export CXX CC
- fi
- # clang-cuda need to filter mfpmath
- if use clang-cuda ; then
- filter-mfpmath sse
- filter-mfpmath i386
- fi
-
- cmake_src_prepare
-
- use cuda && cuda_src_prepare
-
- GMX_DIRS=""
- use single-precision && GMX_DIRS+=" float"
- use double-precision && GMX_DIRS+=" double"
-
- if use test; then
- for x in ${GMX_DIRS}; do
- mkdir -p "${WORKDIR}/${P}_${x}" || die
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
- done
- fi
-
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
- if use build-manual; then
- # try to create policy for imagemagik
- mkdir -p "${HOME}"/.config/ImageMagick
- cat >> "${HOME}"/.config/ImageMagick/policy.xml <<- EOF
- <?xml version="1.0" encoding="UTF-8"?>
- <!DOCTYPE policymap [
- <!ELEMENT policymap (policy)+>
- !ATTLIST policymap xmlns CDATA #FIXED ''>
- <!ELEMENT policy EMPTY>
- <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
- name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
- stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
- ]>
- <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
-}
-
-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
-}
diff --git a/sci-chemistry/gromacs/gromacs-2023.2.ebuild b/sci-chemistry/gromacs/gromacs-2023.2.ebuild
deleted file mode 100644
index a3319899d419..000000000000
--- a/sci-chemistry/gromacs/gromacs-2023.2.ebuild
+++ /dev/null
@@ -1,335 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-PYTHON_COMPAT=( python3_{10..12} )
-
-DISTUTILS_OPTIONAL=1
-DISTUTILS_USE_PEP517=no
-DISTUTILS_SINGLE_IMPL=1
-
-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils
-
-if [[ ${PV} = *9999* ]]; then
- EGIT_REPO_URI="
- https://gitlab.com/gromacs/gromacs.git
- https://github.com/gromacs/gromacs.git
- "
- [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
- inherit git-r3
-else
- SRC_URI="
- https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
- doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
- test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
- # since 2022 arm support was dropped (but not arm64)
- KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-fi
-
-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"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="https://www.gromacs.org/"
-
-# see COPYING for details
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-# 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="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}"
-
-CDEPEND="
- blas? ( virtual/blas )
- cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
- opencl? ( virtual/opencl )
- fftw? ( sci-libs/fftw:3.0= )
- hwloc? ( sys-apps/hwloc:= )
- lapack? ( virtual/lapack )
- mkl? ( sci-libs/mkl )
- mpi? ( virtual/mpi[cxx] )
- sci-libs/lmfit:=
- >=dev-cpp/muParser-2.3:=
- ${PYTHON_DEPS}
- "
-BDEPEND="${CDEPEND}
- virtual/pkgconfig
- clang? ( >=sys-devel/clang-6:* )
- build-manual? (
- app-text/doxygen
- $(python_gen_cond_dep '
- dev-python/sphinx[${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}]
- ')
- media-gfx/mscgen
- media-gfx/graphviz
- dev-texlive/texlive-latex
- dev-texlive/texlive-latexextra
- media-gfx/imagemagick
- )"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
- || ( single-precision double-precision )
- doc? ( !build-manual )
- cuda? ( single-precision )
- opencl? ( single-precision )
- cuda? ( !opencl )
- clang-cuda? ( clang cuda )
- mkl? ( !blas !fftw !lapack )
- ${PYTHON_REQUIRED_USE}"
-
-DOCS=( AUTHORS README )
-
-RESTRICT="!test? ( test )"
-
-if [[ ${PV} != *9999 ]]; then
- S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
- python-single-r1_pkg_setup
-}
-
-src_unpack() {
- if [[ ${PV} != *9999 ]]; then
- default
- else
- git-r3_src_unpack
- if use test; then
- EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \
- EGIT_BRANCH="${EGIT_BRANCH}" \
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
- git-r3_src_unpack
- fi
- fi
-}
-
-src_prepare() {
- #notes/todos
- # -on apple: there is framework support
-
- xdg_environment_reset #591952
-
- # we can use clang as default
- if use clang && ! tc-is-clang ; then
- export CC=${CHOST}-clang
- export CXX=${CHOST}-clang++
- else
- tc-export CXX CC
- fi
- # clang-cuda need to filter mfpmath
- if use clang-cuda ; then
- filter-mfpmath sse
- filter-mfpmath i386
- fi
-
- cmake_src_prepare
-
- use cuda && cuda_src_prepare
-
- GMX_DIRS=""
- use single-precision && GMX_DIRS+=" float"
- use double-precision && GMX_DIRS+=" double"
-
- if use test; then
- for x in ${GMX_DIRS}; do
- mkdir -p "${WORKDIR}/${P}_${x}" || die
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
- done
- fi
-
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
- if use build-manual; then
- # try to create policy for imagemagik
- mkdir -p "${HOME}"/.config/ImageMagick
- cat >> "${HOME}"/.config/ImageMagick/policy.xml <<- EOF
- <?xml version="1.0" encoding="UTF-8"?>
- <!DOCTYPE policymap [
- <!ELEMENT policymap (policy)+>
- !ATTLIST policymap xmlns CDATA #FIXED ''>
- <!ELEMENT policy EMPTY>
- <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
- name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
- stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
- ]>
- <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
-}
-
-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
-}