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commit: 4709c2a32a83396ae5f02187336bc28dbb7d9be3 |
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Author: Christoph Junghans <junghans <AT> gentoo <DOT> org> |
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AuthorDate: Fri Feb 28 16:32:42 2020 +0000 |
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Commit: Christoph Junghans <junghans <AT> gentoo <DOT> org> |
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CommitDate: Fri Feb 28 16:33:03 2020 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4709c2a3 |
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|
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sci-chemistry/gromacs: add v2019.6 |
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|
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Package-Manager: Portage-2.3.84, Repoman-2.3.20 |
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Signed-off-by: Christoph Junghans <junghans <AT> gentoo.org> |
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|
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sci-chemistry/gromacs/Manifest | 2 + |
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sci-chemistry/gromacs/gromacs-2019.6.ebuild | 316 ++++++++++++++++++++++++++++ |
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2 files changed, 318 insertions(+) |
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|
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diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest |
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index e5351904160..ac07e91a6c4 100644 |
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--- a/sci-chemistry/gromacs/Manifest |
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+++ b/sci-chemistry/gromacs/Manifest |
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@@ -1,6 +1,8 @@ |
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DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122 |
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DIST gromacs-2019.5.tar.gz 33445791 BLAKE2B 1e2e2764b0c8774c878abf4f32c2fa7ddd9b46f464cf1256deb48335433d92ef1b315f5534cdec9f766ae928a71361b5a4dd4a4def638269eb260ff98dbbe8bb SHA512 fdd177e4dfd29629b72bfbb4d61ff7bcdb37279f534883a9df8fd57569212fe1e9f8b8c9cec347fcc607539f31412d604d11ee3c0eb797251960435962b1bec6 |
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+DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645ef5af0b40bd823d0fff5ea24397e6301c5e1e0070986ae1ce1deba8a42052b66da148b071c1e21f2fe3908fee275 SHA512 7c227a9539e5775d5d128ae9e872a24181d79cdcd2852b86453597987e8d7332ecec371da65d089f6e610c54aafbccc8824ce298743383dd6240719ebee692a8 |
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DIST gromacs-2020.tar.gz 28928068 BLAKE2B 72d4ff8f6b383284e61df9d3b2b53c51300f6961d4c19810670c8ee9ba2f1864d2a325e2774093b9338db785cb91a94461bf93f16cdf4caf0f690298a672d51c SHA512 15f0d58cd8d217eab39ef8e3535dec34127708797eaf6575fb340292cbee2303cd25deb84b3d4417a787076f4ae7be9e4958ec3a347a3aa9aed52ef337a4587c |
26 |
DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb |
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DIST regressiontests-2019.5.tar.gz 67643634 BLAKE2B c4d9535d9a8a650869d67544ad5f367324f45e55325bb5074ece9b010f232f2f0dd97c9af97924d3f2368ed63015ca7330baff1cc681310e1439ec330b70ee8d SHA512 7c0917b76e7db35ab4e3271d523d268e0e2d858091e68ead863bfe6d1e56b381e30fdbf44f479f6e065c029e2eb27cfa0dbaa1b243f185144321aaf5084c55ce |
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+DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036 |
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DIST regressiontests-2020.tar.gz 48536146 BLAKE2B 9511db78b5d6a5ea431fdb73782f28dde4b94655139886c0ad519888ef3e435fe81807f158d66c1a4284cb88fe730f62d039ac23549f17d0ce5984764ef35f10 SHA512 5a35aaf6fe2f3b146c7045e9c967dc1c8bf754748cc1f2a7300193ae3f206a9f5058329380ae7b03b181410303bcd434584571e6161a75f99e52bd48f8ba1821 |
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|
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diff --git a/sci-chemistry/gromacs/gromacs-2019.6.ebuild b/sci-chemistry/gromacs/gromacs-2019.6.ebuild |
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new file mode 100644 |
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index 00000000000..755bafef447 |
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--- /dev/null |
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+++ b/sci-chemistry/gromacs/gromacs-2019.6.ebuild |
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@@ -0,0 +1,316 @@ |
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+# Copyright 1999-2020 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=7 |
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+ |
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+CMAKE_MAKEFILE_GENERATOR="ninja" |
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+ |
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+PYTHON_COMPAT=( python2_7 ) |
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+ |
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+inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1 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="git://git.gromacs.org/gromacs.git |
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+ https://gerrit.gromacs.org/gromacs.git |
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+ https://github.com/gromacs/gromacs.git |
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+ https://repo.or.cz/r/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="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
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+ test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" |
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+ KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-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" |
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+ |
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+DESCRIPTION="The ultimate molecular dynamics simulation package" |
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+HOMEPAGE="http://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 +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +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 ) |
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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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+ ${PYTHON_DEPS} |
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+ " |
90 |
+BDEPEND="${CDEPEND} |
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+ virtual/pkgconfig |
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+ doc? ( |
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+ app-doc/doxygen |
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+ $(python_gen_cond_dep ' |
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+ dev-python/sphinx[${PYTHON_MULTI_USEDEP}] |
96 |
+ ') |
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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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+ cuda? ( 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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+ [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
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+ use openmp && ! tc-has-openmp && \ |
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+ die "Please switch to an openmp compatible compiler" |
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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-utils_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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+ |
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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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+ ]> |
175 |
+ <policymap> |
176 |
+ <policy domain="coder" rights="read | write" pattern="PS" /> |
177 |
+ <policy domain="coder" rights="read | write" pattern="PS2" /> |
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+ <policy domain="coder" rights="read | write" pattern="PS3" /> |
179 |
+ <policy domain="coder" rights="read | write" pattern="EPS" /> |
180 |
+ <policy domain="coder" rights="read | write" pattern="PDF" /> |
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+ <policy domain="coder" rights="read | write" pattern="XPS" /> |
182 |
+ </policymap> |
183 |
+ EOF |
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+} |
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+ |
186 |
+src_configure() { |
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+ local mycmakeargs_pre=( ) extra fft_opts=( ) |
188 |
+ |
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+ #go from slowest to fastest acceleration |
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+ local acce="None" |
191 |
+ use cpu_flags_x86_sse2 && acce="SSE2" |
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+ use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
193 |
+ 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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+ |
197 |
+ #to create man pages, build tree binaries are executed (bug #398437) |
198 |
+ [[ ${CHOST} = *-darwin* ]] && \ |
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+ extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
200 |
+ |
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+ if use fftw; then |
202 |
+ fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
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+ elif use mkl && has_version "=sci-libs/mkl-10*"; then |
204 |
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl |
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+ -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
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+ -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
207 |
+ ) |
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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=$(usex lapack) |
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+ -DGMX_OPENMP=$(usex openmp) |
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+ -DGMX_COOL_QUOTES=$(usex offensive) |
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+ -DGMX_USE_TNG=$(usex tng) |
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+ -DGMX_BUILD_MANUAL=$(usex doc) |
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+ -DGMX_HWLOC=$(usex hwloc) |
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+ -DGMX_DEFAULT_SUFFIX=off |
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+ -DGMX_SIMD="$acce" |
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+ -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
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+ -DBUILD_TESTING=$(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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+ |
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+ for x in ${GMX_DIRS}; do |
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+ einfo "Configuring for ${x} precision" |
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+ local suffix="" |
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+ #if we build single and double - double is suffixed |
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+ use double-precision && use single-precision && \ |
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+ [[ ${x} = "double" ]] && suffix="_d" |
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+ local p |
251 |
+ [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
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+ local cuda=( "-DGMX_GPU=OFF" ) |
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+ [[ ${x} = "float" ]] && use cuda && \ |
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+ cuda=( "-DGMX_GPU=ON" ) |
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+ local opencl=( "-DGMX_USE_OPENCL=OFF" ) |
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+ use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) |
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+ mycmakeargs=( |
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+ ${mycmakeargs_pre[@]} ${p} |
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+ -DGMX_MPI=OFF |
260 |
+ -DGMX_THREAD_MPI=$(usex threads) |
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+ -DGMXAPI=$(usex gmxapi) |
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+ "${opencl[@]}" |
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+ "${cuda[@]}" |
264 |
+ "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
265 |
+ -DGMX_BINARY_SUFFIX="${suffix}" |
266 |
+ -DGMX_LIBS_SUFFIX="${suffix}" |
267 |
+ ) |
268 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
269 |
+ [[ ${CHOST} != *-darwin* ]] || \ |
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+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
271 |
+ use mpi || continue |
272 |
+ einfo "Configuring for ${x} precision with mpi" |
273 |
+ mycmakeargs=( |
274 |
+ ${mycmakeargs_pre[@]} ${p} |
275 |
+ -DGMX_THREAD_MPI=OFF |
276 |
+ -DGMX_MPI=ON |
277 |
+ -DGMX_OPENMM=OFF |
278 |
+ -DGMXAPI=OFF |
279 |
+ "${opencl[@]}" |
280 |
+ "${cuda[@]}" |
281 |
+ -DGMX_BUILD_MDRUN_ONLY=ON |
282 |
+ -DBUILD_SHARED_LIBS=OFF |
283 |
+ -DGMX_BUILD_MANUAL=OFF |
284 |
+ -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
285 |
+ -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
286 |
+ ) |
287 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
288 |
+ [[ ${CHOST} != *-darwin* ]] || \ |
289 |
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
290 |
+ done |
291 |
+} |
292 |
+ |
293 |
+src_compile() { |
294 |
+ for x in ${GMX_DIRS}; do |
295 |
+ einfo "Compiling for ${x} precision" |
296 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
297 |
+ cmake-utils_src_compile |
298 |
+ # not 100% necessary for rel ebuilds as available from website |
299 |
+ if use doc; then |
300 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
301 |
+ cmake-utils_src_compile manual |
302 |
+ fi |
303 |
+ use mpi || continue |
304 |
+ einfo "Compiling for ${x} precision with mpi" |
305 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
306 |
+ cmake-utils_src_compile |
307 |
+ done |
308 |
+} |
309 |
+ |
310 |
+src_test() { |
311 |
+ for x in ${GMX_DIRS}; do |
312 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
313 |
+ cmake-utils_src_make check |
314 |
+ done |
315 |
+} |
316 |
+ |
317 |
+src_install() { |
318 |
+ for x in ${GMX_DIRS}; do |
319 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
320 |
+ cmake-utils_src_install |
321 |
+ if use doc; then |
322 |
+ newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
323 |
+ fi |
324 |
+ use mpi || continue |
325 |
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
326 |
+ cmake-utils_src_install |
327 |
+ done |
328 |
+ |
329 |
+ if use tng; then |
330 |
+ insinto /usr/include/tng |
331 |
+ doins src/external/tng_io/include/tng/*h |
332 |
+ fi |
333 |
+ # drop unneeded stuff |
334 |
+ rm "${ED}"/usr/bin/GMXRC* || die |
335 |
+ for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do |
336 |
+ local n=${x##*/gmx-completion-} |
337 |
+ n="${n%.bash}" |
338 |
+ cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
339 |
+ newbashcomp "${T}"/"${n}" "${n}" |
340 |
+ done |
341 |
+ rm "${ED}"/usr/bin/gmx-completion*.bash || die |
342 |
+ readme.gentoo_create_doc |
343 |
+} |
344 |
+ |
345 |
+pkg_postinst() { |
346 |
+ einfo |
347 |
+ einfo "Please read and cite:" |
348 |
+ einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
349 |
+ einfo "https://dx.doi.org/10.1021/ct700301q" |
350 |
+ einfo |
351 |
+ readme.gentoo_print_elog |
352 |
+} |