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commit: d511b69e54aa63f3ad07f7463ecc0127d0de6f6e |
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Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> |
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AuthorDate: Sat Jan 28 19:48:06 2023 +0000 |
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Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> |
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CommitDate: Wed Feb 1 19:26:34 2023 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d511b69e |
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|
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sci-chemistry/gromacs: drop 2021.9999 |
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|
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No more development? Last commit happened two years ago. |
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|
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Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org> |
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|
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sci-chemistry/gromacs/gromacs-2021.9999.ebuild | 350 ------------------------- |
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1 file changed, 350 deletions(-) |
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|
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diff --git a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild |
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deleted file mode 100644 |
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index 843c14bc04b1..000000000000 |
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--- a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild |
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+++ /dev/null |
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@@ -1,350 +0,0 @@ |
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-# Copyright 1999-2023 Gentoo Authors |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=8 |
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- |
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-CMAKE_MAKEFILE_GENERATOR="ninja" |
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- |
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-PYTHON_COMPAT=( python3_{9..11} ) |
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- |
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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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- |
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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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- git://git.gromacs.org/gromacs.git" |
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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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- KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
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-fi |
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- |
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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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- |
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-DESCRIPTION="The ultimate molecular dynamics simulation package" |
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-HOMEPAGE="https://www.gromacs.org/" |
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- |
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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="X blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" |
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- |
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-CDEPEND=" |
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- X? ( |
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- x11-libs/libX11 |
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- x11-libs/libSM |
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- x11-libs/libICE |
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- ) |
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- blas? ( virtual/blas ) |
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- cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14[profiler] ) |
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- opencl? ( virtual/opencl ) |
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- fftw? ( sci-libs/fftw:3.0= ) |
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- hwloc? ( sys-apps/hwloc:= ) |
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- lapack? ( virtual/lapack ) |
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- lmfit? ( sci-libs/lmfit:= ) |
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- mkl? ( sci-libs/mkl ) |
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- mpi? ( virtual/mpi ) |
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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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- build-manual? ( |
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- app-doc/doxygen |
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- $(python_gen_cond_dep ' |
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- dev-python/sphinx[${PYTHON_USEDEP}] |
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- ') |
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- media-gfx/mscgen |
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- media-gfx/graphviz |
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- dev-texlive/texlive-latex |
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- dev-texlive/texlive-latexextra |
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- media-gfx/imagemagick |
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- )" |
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-RDEPEND="${CDEPEND}" |
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- |
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-REQUIRED_USE=" |
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- || ( single-precision double-precision ) |
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- doc? ( !build-manual ) |
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- cuda? ( single-precision ) |
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- opencl? ( single-precision ) |
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- cuda? ( !opencl ) |
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- mkl? ( !blas !fftw !lapack ) |
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- ${PYTHON_REQUIRED_USE}" |
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- |
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-DOCS=( AUTHORS README ) |
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- |
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-RESTRICT="!test? ( test )" |
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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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- |
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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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- |
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-src_unpack() { |
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- if [[ ${PV} != *9999 ]]; then |
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- default |
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- else |
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- git-r3_src_unpack |
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- if use test; then |
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- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
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- EGIT_BRANCH="${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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- |
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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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- |
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- cmake_src_prepare |
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- |
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- use cuda && cuda_src_prepare |
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- |
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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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- |
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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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- |
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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"?> |
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- <!DOCTYPE policymap [ |
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- <!ELEMENT policymap (policy)+> |
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- !ATTLIST policymap xmlns CDATA #FIXED ''> |
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- <!ELEMENT policy EMPTY> |
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- <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED |
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- name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED |
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- stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> |
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- ]> |
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- <policymap> |
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- <policy domain="coder" rights="read | write" pattern="PS" /> |
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- <policy domain="coder" rights="read | write" pattern="PS2" /> |
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- <policy domain="coder" rights="read | write" pattern="PS3" /> |
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- <policy domain="coder" rights="read | write" pattern="EPS" /> |
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- <policy domain="coder" rights="read | write" pattern="PDF" /> |
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- <policy domain="coder" rights="read | write" pattern="XPS" /> |
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- </policymap> |
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- EOF |
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- fi |
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-} |
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- |
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-src_configure() { |
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- local mycmakeargs_pre=( ) extra fft_opts=( ) |
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- local acce="AUTO" |
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- |
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- if use custom-cflags; then |
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- #go from slowest to fastest acceleration |
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- acce="None" |
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- if (use amd64 || use x86); then |
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- use cpu_flags_x86_sse2 && acce="SSE2" |
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- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
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- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
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- use cpu_flags_x86_avx && acce="AVX_256" |
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- use cpu_flags_x86_avx2 && acce="AVX2_256" |
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- use cpu_flags_x86_avx512f && acce="AVX_512" |
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- elif (use arm); then |
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- use cpu_flags_arm_neon && acce="ARM_NEON" |
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- elif (use arm64); then |
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- use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" |
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- fi |
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- else |
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- strip-flags |
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- fi |
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- |
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- #to create man pages, build tree binaries are executed (bug #398437) |
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- [[ ${CHOST} = *-darwin* ]] && \ |
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- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
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- |
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- if use fftw; then |
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- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
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- elif use mkl; then |
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- local bits=$(get_libdir) |
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- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
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- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
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- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
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- ) |
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- else |
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- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
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- fi |
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- |
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- if use lmfit; then |
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- local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) |
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- else |
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- local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) |
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- fi |
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- |
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- mycmakeargs_pre+=( |
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- "${fft_opts[@]}" |
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- "${lmfit_opts[@]}" |
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- -DGMX_X11=$(usex X) |
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- -DGMX_EXTERNAL_BLAS=$(usex blas) |
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- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
| 235 |
- -DGMX_OPENMP=$(usex openmp) |
| 236 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
| 237 |
- -DGMX_USE_TNG=$(usex tng) |
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- -DGMX_BUILD_MANUAL=$(usex build-manual) |
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- -DGMX_HWLOC=$(usex hwloc) |
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- -DGMX_DEFAULT_SUFFIX=off |
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- -DGMX_SIMD="$acce" |
| 242 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
| 243 |
- -DBUILD_TESTING=$(usex test) |
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- -DGMX_BUILD_UNITTESTS=$(usex test) |
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- -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" |
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- ${extra} |
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- ) |
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- |
| 249 |
- for x in ${GMX_DIRS}; do |
| 250 |
- einfo "Configuring for ${x} precision" |
| 251 |
- local suffix="" |
| 252 |
- #if we build single and double - double is suffixed |
| 253 |
- use double-precision && use single-precision && \ |
| 254 |
- [[ ${x} = "double" ]] && suffix="_d" |
| 255 |
- local p |
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- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
| 257 |
- local gpu=( "-DGMX_GPU=OFF" ) |
| 258 |
- [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) |
| 259 |
- use opencl && gpu=( "-DGMX_GPU=OPENCL" ) |
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- local mycmakeargs=( |
| 261 |
- ${mycmakeargs_pre[@]} ${p} |
| 262 |
- -DGMX_MPI=OFF |
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- -DGMX_THREAD_MPI=$(usex threads) |
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- -DGMXAPI=$(usex gmxapi) |
| 265 |
- -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) |
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- "${gpu[@]}" |
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- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
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- -DGMX_BINARY_SUFFIX="${suffix}" |
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- -DGMX_LIBS_SUFFIX="${suffix}" |
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- -DGMX_PYTHON_PACKAGE=$(usex python) |
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- ) |
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- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure |
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- [[ ${CHOST} != *-darwin* ]] || \ |
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- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
| 275 |
- use mpi || continue |
| 276 |
- einfo "Configuring for ${x} precision with mpi" |
| 277 |
- local mycmakeargs=( |
| 278 |
- ${mycmakeargs_pre[@]} ${p} |
| 279 |
- -DGMX_THREAD_MPI=OFF |
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- -DGMX_MPI=ON |
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- -DGMX_OPENMM=OFF |
| 282 |
- -DGMXAPI=OFF |
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- "${opencl[@]}" |
| 284 |
- "${cuda[@]}" |
| 285 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
| 286 |
- -DBUILD_SHARED_LIBS=OFF |
| 287 |
- -DGMX_BUILD_MANUAL=OFF |
| 288 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
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- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
| 290 |
- ) |
| 291 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure |
| 292 |
- [[ ${CHOST} != *-darwin* ]] || \ |
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- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
| 294 |
- done |
| 295 |
-} |
| 296 |
- |
| 297 |
-src_compile() { |
| 298 |
- for x in ${GMX_DIRS}; do |
| 299 |
- einfo "Compiling for ${x} precision" |
| 300 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 301 |
- cmake_src_compile |
| 302 |
- if use python; then |
| 303 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 304 |
- cmake_src_compile python_packaging/all |
| 305 |
- BUILD_DIR="${WORKDIR}/${P}" \ |
| 306 |
- distutils-r1_src_compile |
| 307 |
- fi |
| 308 |
- # not 100% necessary for rel ebuilds as available from website |
| 309 |
- if use build-manual; then |
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- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 311 |
- cmake_src_compile manual |
| 312 |
- fi |
| 313 |
- use mpi || continue |
| 314 |
- einfo "Compiling for ${x} precision with mpi" |
| 315 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
| 316 |
- cmake_src_compile |
| 317 |
- done |
| 318 |
-} |
| 319 |
- |
| 320 |
-src_test() { |
| 321 |
- for x in ${GMX_DIRS}; do |
| 322 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| 323 |
- cmake_src_compile check |
| 324 |
- done |
| 325 |
-} |
| 326 |
- |
| 327 |
-src_install() { |
| 328 |
- for x in ${GMX_DIRS}; do |
| 329 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
| 330 |
- cmake_src_install |
| 331 |
- if use python; then |
| 332 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
| 333 |
- cmake_src_install python_packaging/install |
| 334 |
- fi |
| 335 |
- if use build-manual; then |
| 336 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
| 337 |
- fi |
| 338 |
- |
| 339 |
- if use doc; then |
| 340 |
- if [[ ${PV} != *9999* ]]; then |
| 341 |
- newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" |
| 342 |
- fi |
| 343 |
- fi |
| 344 |
- |
| 345 |
- use mpi || continue |
| 346 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
| 347 |
- cmake_src_install |
| 348 |
- done |
| 349 |
- |
| 350 |
- if use tng; then |
| 351 |
- insinto /usr/include/tng |
| 352 |
- doins src/external/tng_io/include/tng/*h |
| 353 |
- fi |
| 354 |
- # drop unneeded stuff |
| 355 |
- rm "${ED}"/usr/bin/GMXRC* || die |
| 356 |
- for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do |
| 357 |
- local n=${x##*/gmx-completion-} |
| 358 |
- n="${n%.bash}" |
| 359 |
- cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
| 360 |
- newbashcomp "${T}"/"${n}" "${n}" |
| 361 |
- done |
| 362 |
- rm "${ED}"/usr/bin/gmx-completion*.bash || die |
| 363 |
- readme.gentoo_create_doc |
| 364 |
-} |
| 365 |
- |
| 366 |
-pkg_postinst() { |
| 367 |
- einfo |
| 368 |
- einfo "Please read and cite gromacs related papers from list:" |
| 369 |
- einfo "https://www.gromacs.org/Gromacs_papers" |
| 370 |
- einfo |
| 371 |
- readme.gentoo_print_elog |
| 372 |
-} |
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