commit: e68b66464b330e1d2915293eaf8b07f45ca00b9d
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 12 20:08:19 2021 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Tue Jan 12 20:16:46 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e68b6646
sci-chemistry/gromacs: Version bump
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>
sci-chemistry/gromacs/Manifest | 2 +
sci-chemistry/gromacs/gromacs-2020.5.ebuild | 342 ++++++++++++++++++++++++++++
2 files changed, 344 insertions(+)
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index dea62ed45c3..bcaf2073dc5 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,10 +1,12 @@
DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B
8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015
SHA512
6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122
DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B
adc21fb6b841b06d499607f8c0166a673645ef5af0b40bd823d0fff5ea24397e6301c5e1e0070986ae1ce1deba8a42052b66da148b071c1e21f2fe3908fee275
SHA512
7c227a9539e5775d5d128ae9e872a24181d79cdcd2852b86453597987e8d7332ecec371da65d089f6e610c54aafbccc8824ce298743383dd6240719ebee692a8
DIST gromacs-2020.4.tar.gz 29149899 BLAKE2B
a07c8efd96137d58c1edf4ac9b5aafeb16d9e65234b9459b71471827032654acacb58ed6ae87ec6e0e593a0acd799683cc4461b06cc883b089d740708619345e
SHA512
0c56f058741af70660baf0177724ec940dd984c05ea141ede91ee51ce3744f76d00e31bdb5db907e46fa1639de5dca637b3ace26e89f908c2e74c69f0c21ed3a
+DIST gromacs-2020.5.tar.gz 29148909 BLAKE2B
ea439ae95d4af67a77d53182f7ddab702799edab8527c1b6ad20625d21a81f3e3c0cc699fa0b656625bffcca0bdd5a1e104aea4f592ee2db92b4f1a460ad0e80
SHA512
fe38fda36d31aef5ce01a3dbc29c9f50d3cc05b20bb34a9a8f10fda5aecde4f93ca8a3f85433139e1bb88fc23d77916a4aff5a292abaa528bd0e6138e84cba18
DIST gromacs-2021-beta3.tar.gz 30138154 BLAKE2B
4abea01663c743f70489f6fb874802496605ab1a9bc08f09547409fde370b0388fab826e0d2492e5447654bcb1ae9e5cf22fcdf5e2bd2306e83868b62ef9ec1f
SHA512
f36799c5538b0c04d7406a2886c29a95593481e06835885fcd9de2d668a68015d2aeb7865f3050cc0451b1aac37b25b5d41b0b227ac9a33067322cc7ef9ce1c2
DIST manual-2018.8.pdf 10025023 BLAKE2B
afb0a6e6a72d78df743fcb57e7c1716848589e571dd35167b957a9b407ca27978ccfb6cb9e0df9c9439b888f352501a00ba32281ed1e0b4193bd606f1d77152e
SHA512
b1972f7ce965bfc9377542993c5943ea4868a8ed23a969d4203264746d6bea3a7a65c6379196ece37fd6d68ec7ec80f827bde87d1049284af7082759a124f1d5
DIST manual-2019.6.pdf 12702376 BLAKE2B
c350127bc06a9eb3dee73da39037c84daeb89500e23cb131bd19a150bf60602d4dde7611e0c6f0f344af4093e96a899303dac71b4df56fd0c44c3a48a56606b7
SHA512
dfdff67c2c1c9ce1f1c236b7686c5331b0fe86951da6c98eddd6a3e748815e0be0a9653ae4318469fcdd913c4e7c355d64a997cc80b9d9fbe6282ef6d98e61eb
DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B
34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275
SHA512
3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb
DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B
1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386
SHA512
eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036
DIST regressiontests-2020.4.tar.gz 48542144 BLAKE2B
1dcde67525d40ababa74d9e8ba2dd3fdef1de7d1018491e102edd71d3a622925f213b5a0812e5448882b4cb5fb578317e8e5029bdc4bd53008aa8441a3d9dea1
SHA512
7c71f36a1cef22562f14dcd233e90ad2fe370ae1a7d3b5268727259b374e12d4754253735ac8745d3738bdbc1cc2067780fda5e393be2ff264f632fe4e0c1978
+DIST regressiontests-2020.5.tar.gz 48541167 BLAKE2B
81f0505090203c970178ca4eba8dfd54d942a20970525cad954833481cd79141fa33fc97e8940ca83cee104ef6b017bc0f7bbed9eddc620a86c818760b3fc261
SHA512
aba67542ed00145cae8de040e4a9074a8a359a529135180e6083b2330934962302349d382d6626bddc6971ae6d44e09c8ea44d5df55ca5fcd038055a1c3e5cc3
DIST regressiontests-2021-beta3.tar.gz 48513481 BLAKE2B
b39685e7a43dbcd83c0ffc28b15e3aca5c82c18dd817c543262787ac40466c88f72c2a350fd3e945d62e1f9ef6f938db916650315612a5d1e27d4c6b70f8d5e2
SHA512
183bebf3c44805efa5a90ae8b7a34d701ffbe3a5c5b37e80359cbdf61c8492fbe6ca24f10575b8e8061aa1ae38f2a3ea1bac8b723503b1b6ab706faeace9e411
diff --git a/sci-chemistry/gromacs/gromacs-2020.5.ebuild
b/sci-chemistry/gromacs/gromacs-2020.5.ebuild
new file mode 100644
index 00000000000..bf0d38276e2
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-2020.5.ebuild
@@ -0,0 +1,342 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+PYTHON_COMPAT=( python3_{6,7,8,9} )
+
+DISTUTILS_SINGLE_IMPL=1
+
+inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic
multilib 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
+ git://git.gromacs.org/gromacs.git"
+ [[ $PV = 9999 ]] && EGIT_BRANCH="master" ||
EGIT_BRANCH="release-${PV:0:4}"
+ inherit git-r3
+else
+ SRC_URI="
+ http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+ test? (
http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
+ KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+fi
+
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4
cpu_flags_x86_avx cpu_flags_x86_avx2"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/";
+
+# see COPYING for details
+# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+# base, vmd plugins, fftpack from numpy, blas/lapck from netlib,
memtestG80 library, mpi_thread lib
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? (
BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
+SLOT="0/${PV}"
+IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi
+gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python
+single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+ X? (
+ x11-libs/libX11
+ x11-libs/libSM
+ x11-libs/libICE
+ )
+ blas? ( virtual/blas )
+ cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
+ opencl? ( virtual/opencl )
+ fftw? ( sci-libs/fftw:3.0 )
+ hwloc? ( sys-apps/hwloc )
+ lapack? ( virtual/lapack )
+ lmfit? ( sci-libs/lmfit )
+ mkl? ( sci-libs/mkl )
+ mpi? ( virtual/mpi )
+ ${PYTHON_DEPS}
+ !sci-chemistry/gmxapi
+ "
+BDEPEND="${CDEPEND}
+ virtual/pkgconfig
+ doc? (
+ app-doc/doxygen
+ $(python_gen_cond_dep '
+ dev-python/sphinx[${PYTHON_MULTI_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 )
+ cuda? ( single-precision )
+ cuda? ( !opencl )
+ mkl? ( !blas !fftw !lapack )
+ ${PYTHON_REQUIRED_USE}"
+
+DOCS=( AUTHORS README )
+
+RESTRICT="!test? ( test )"
+
+if [[ ${PV} != *9999 ]]; then
+ S="${WORKDIR}/${PN}-${PV/_/-}"
+fi
+
+PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" )
+
+pkg_pretend() {
+ [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by
gromacs"
+ use openmp && ! tc-has-openmp && \
+ die "Please switch to an openmp compatible compiler"
+}
+
+pkg_setup() {
+ python-single-r1_pkg_setup
+}
+
+src_unpack() {
+ if [[ ${PV} != *9999 ]]; then
+ default
+ else
+ git-r3_src_unpack
+ if use test; then
+
EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+ EGIT_BRANCH="${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
+
+ 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"
+
+ # 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
+}
+
+src_configure() {
+ local mycmakeargs_pre=( ) extra fft_opts=( )
+
+ if use custom-cflags; then
+ #go from slowest to fastest acceleration
+ local acce="None"
+ 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"
+ else
+ strip-flags
+ fi
+
+ #to create man pages, build tree binaries are executed (bug #398437)
+ [[ ${CHOST} = *-darwin* ]] && \
+ extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
+ if use fftw; then
+ fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
+ elif use mkl && has_version "=sci-libs/mkl-10*"; then
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl
+ -DMKL_INCLUDE_DIR="${MKLROOT}/include"
+ -DMKL_LIBRARIES="$(echo
/opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo
/opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
+ )
+ 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
+
+ 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=$(usex lapack)
+ -DGMX_OPENMP=$(usex openmp)
+ -DGMX_COOL_QUOTES=$(usex offensive)
+ -DGMX_USE_TNG=$(usex tng)
+ -DGMX_BUILD_MANUAL=$(usex doc)
+ -DGMX_HWLOC=$(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 cuda=( "-DGMX_GPU=OFF" )
+ [[ ${x} = "float" ]] && use cuda && \
+ 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=$(usex gmxapi)
+ -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
+ "${opencl[@]}"
+ "${cuda[@]}"
+ "$(use test && echo
-DREGRESSIONTEST_PATH="${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
+ use mpi || continue
+ einfo "Configuring for ${x} precision with mpi"
+ mycmakeargs=(
+ ${mycmakeargs_pre[@]} ${p}
+ -DGMX_THREAD_MPI=OFF
+ -DGMX_MPI=ON
+ -DGMX_OPENMM=OFF
+ -DGMXAPI=OFF
+ "${opencl[@]}"
+ "${cuda[@]}"
+ -DGMX_BUILD_MDRUN_ONLY=ON
+ -DBUILD_SHARED_LIBS=OFF
+ -DGMX_BUILD_MANUAL=OFF
+ -DGMX_BINARY_SUFFIX="_mpi${suffix}"
+ -DGMX_LIBS_SUFFIX="_mpi${suffix}"
+ )
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc"
cmake_src_configure
+ [[ ${CHOST} != *-darwin* ]] || \
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/'
"${WORKDIR}/${P}_${x}_mpi/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}/${P}" \
+ distutils-r1_src_compile
+ fi
+ # not 100% necessary for rel ebuilds as available from website
+ if use doc; then
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake_src_compile manual
+ fi
+ use mpi || continue
+ einfo "Compiling for ${x} precision with mpi"
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+ cmake_src_compile
+ done
+}
+
+src_test() {
+ for x in ${GMX_DIRS}; do
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake_src_make 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}_${x}" \
+ cmake_src_install python_packaging/install
+ fi
+ if use doc; then
+ newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf
"${PN}-manual-${PV}.pdf"
+ fi
+ use mpi || continue
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+ cmake_src_install
+ done
+
+ if use tng; then
+ insinto /usr/include/tng
+ doins src/external/tng_io/include/tng/*h
+ fi
+ # drop unneeded stuff
+ rm "${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:"
+ einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+ einfo "https://dx.doi.org/10.1021/ct700301q";
+ einfo
+ readme.gentoo_print_elog
+}
