From e9d044d4b9b71200a96adfa280848858c0f468c9 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sat, 13 Nov 2021 13:10:00 +0000 Subject: gentoo resync : 13.11.2021 --- sci-chemistry/Manifest.gz | Bin 10840 -> 10848 bytes sci-chemistry/chemex/Manifest | 6 +- sci-chemistry/chemex/chemex-2021.4.0_p2.ebuild | 43 --- sci-chemistry/chemex/chemex-2021.4.0_p4.ebuild | 46 --- sci-chemistry/chemex/chemex-2021.4.0_p6.ebuild | 46 +++ sci-chemistry/dssp/Manifest | 5 +- sci-chemistry/dssp/dssp-2.2.1-r2.ebuild | 45 --- sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild | 33 -- sci-chemistry/dssp/dssp-4.0.3.ebuild | 2 +- sci-chemistry/gromacs/Manifest | 12 +- .../files/gromacs-2019.6-missing-include.patch | 38 +++ sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild | 255 +++++++++++++++ sci-chemistry/gromacs/gromacs-2021.4.ebuild | 356 +++++++++++++++++++++ sci-chemistry/gromacs/gromacs-2022.9999.ebuild | 21 +- sci-chemistry/gromacs/gromacs-2022_beta1-r2.ebuild | 349 ++++++++++++++++++++ sci-chemistry/gromacs/gromacs-2022_beta1.ebuild | 350 -------------------- sci-chemistry/gromacs/gromacs-9999.ebuild | 21 +- sci-chemistry/openbabel/Manifest | 3 - .../openbabel-2.3.2-gcc-6_and_7-backport.patch | 13 - .../openbabel/files/openbabel-2.4.1-gcc-8.patch | 15 - sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild | 102 ------ sci-chemistry/vmd/Manifest | 2 + sci-chemistry/vmd/vmd-1.9.4_alpha55.ebuild | 269 ++++++++++++++++ 23 files changed, 1348 insertions(+), 684 deletions(-) delete mode 100644 sci-chemistry/chemex/chemex-2021.4.0_p2.ebuild delete mode 100644 sci-chemistry/chemex/chemex-2021.4.0_p4.ebuild create mode 100644 sci-chemistry/chemex/chemex-2021.4.0_p6.ebuild delete mode 100644 sci-chemistry/dssp/dssp-2.2.1-r2.ebuild delete mode 100644 sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild create mode 100644 sci-chemistry/gromacs/files/gromacs-2019.6-missing-include.patch create mode 100644 sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild create mode 100644 sci-chemistry/gromacs/gromacs-2021.4.ebuild create mode 100644 sci-chemistry/gromacs/gromacs-2022_beta1-r2.ebuild delete mode 100644 sci-chemistry/gromacs/gromacs-2022_beta1.ebuild delete mode 100644 sci-chemistry/openbabel/files/openbabel-2.3.2-gcc-6_and_7-backport.patch delete mode 100644 sci-chemistry/openbabel/files/openbabel-2.4.1-gcc-8.patch delete mode 100644 sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild create mode 100644 sci-chemistry/vmd/vmd-1.9.4_alpha55.ebuild (limited to 'sci-chemistry') diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz index 1d56a1648822..5d7c52b39642 100644 Binary files a/sci-chemistry/Manifest.gz and b/sci-chemistry/Manifest.gz differ diff --git a/sci-chemistry/chemex/Manifest b/sci-chemistry/chemex/Manifest index fd297d8394a5..3d67d625423c 100644 --- a/sci-chemistry/chemex/Manifest +++ b/sci-chemistry/chemex/Manifest @@ -1,5 +1,3 @@ -DIST chemex-2021.4.0_p2.tar.gz 2384471 BLAKE2B 1eb609c4e4ad9ac0f7cac8ab523e72e8ab9c12d40671fd598cd26b8de2a3d6e68dfdcaee9202521fc583068f591377842b3e7b9f0e1f95e6cba8da9b0c6d63a4 SHA512 568072eaf0d1c666de2aedacc50cd98da15631e0ef15ba60414be671ac97a50967e5b4d6d00340b1263f730b3a803ccc8995fbb86cfc47517b9521c9920641c8 -DIST chemex-2021.4.0_p4.tar.gz 2387888 BLAKE2B 26b4467756ba1b31775c554906a2ce09556e1fb99dd2ff294620a12b92246f441a2daa07e6bad7cedf903bd18e6ecc0613b6473f54d27d89ed9117ddc6a27269 SHA512 7d93f213317e4cb5a987c0b3cfcce146fb02a15ac9efbde74f9d3fc56a5e86c89ca6b606f45013bf08ed10f3de17cc72fa010ce0e42c5cb746119ede0ce4d38f -EBUILD chemex-2021.4.0_p2.ebuild 1184 BLAKE2B a7ab020a416e46f232ce5b9bd140d7af6c925b8e0da5b2dfe629e7f50533692700c183cf1068be6fa0cee7cd3141eee6f684a936fea9b034f0a68b8f0f080358 SHA512 06067c09038bcc2629ac272a5005acd1f11fce5014ceb2fb9eb8fa9f7c6d900d9ccdc07a90e54fde11e5399baed2b12def1facdfaf7e929e603e6c334b463a04 -EBUILD chemex-2021.4.0_p4.ebuild 1279 BLAKE2B dc10ef290d4dac75119a4b215da0b1fea01cbfc7558c6fc78f46801ec5cb0514d6d2ae7cbd58028ce4da2903109d25b0fd02637d4b3a6570b819696fc4c15348 SHA512 faaa7006bd9ee86684de6afaceb25695c63dc1514abb21201172c0338068abf0787ae67c935b12e10dcacac2c30652f513458c9f6e0284d94b1b57b53dc7e310 +DIST chemex-2021.4.0_p6.tar.gz 2395324 BLAKE2B adb08fdebe816b66359c8a567d7f7a4600715015e6f9b86b568cb8e3cd5e66b040895c09688a956cedd398a7c56a6d3a73d77f647a2f4e83280a91879a6184d0 SHA512 7d20ae73a2cf52f9d21b875cd661cefc14ce36ff603402e5dacad3e21bcb0bdb28f8f111414691b99f93196a971215d0beec3fff07535d3d781b4e7bb6782c52 +EBUILD chemex-2021.4.0_p6.ebuild 1292 BLAKE2B 2264c354a978cb6e2cb77431aa491d18cb96883aa03dc06781265060b13045f26a6181a6ab19bbc81cf84dcac39ad6b5899af067917066d1db246a3a44229e87 SHA512 dbb95167c9615e44627387d5a599520bff593739e9406089f8daea0355fa309f98e27d0c297c8241db5dfe8673adfa92bf055109ac51aa83f29856a8b0e17826 MISC metadata.xml 217 BLAKE2B f8189b02494f180dac078dcd5c275d3c795f20f360f8b172c66065a2d937e396b24b8631bba4cd8567d60285ce89fc77b9539f2233bf33899c820613c48c33ba SHA512 f0c9e5b3d281fecd21b1e23a6f44c94c1c0b3220de46a177d35932111b7f1ab4399061c42833ac1ee9bd0324b139fc8db66e0d2890224d607bd3be38ae469be9 diff --git a/sci-chemistry/chemex/chemex-2021.4.0_p2.ebuild b/sci-chemistry/chemex/chemex-2021.4.0_p2.ebuild deleted file mode 100644 index 8b5e04b8b082..000000000000 --- a/sci-chemistry/chemex/chemex-2021.4.0_p2.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 -DISTUTILS_SINGLE_IMPL="yes" -PYTHON_COMPAT=( python3_{8..10} ) -DISTUTILS_USE_SETUPTOOLS=pyproject.toml - -inherit distutils-r1 - -DESCRIPTION="Program to fit chemical exchange induced shift and relaxation data" -HOMEPAGE="https://github.com/gbouvignies/chemex" -SRC_URI="https://github.com/gbouvignies/chemex/archive/${PV/_p/-dev}.tar.gz -> ${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64" -IUSE="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - $(python_gen_cond_dep ' - >=dev-python/asteval-0.9.11[${PYTHON_USEDEP}] - >=dev-python/jsonschema-3.2.0[${PYTHON_USEDEP}] - >=dev-python/lmfit-1.0.2[${PYTHON_USEDEP}] - >=dev-python/matplotlib-3.4.2[${PYTHON_USEDEP}] - >=dev-python/numpy-1.21.0[${PYTHON_USEDEP}] - dev-python/setuptools_scm[${PYTHON_USEDEP}] - >=dev-python/scipy-1.7.0[${PYTHON_USEDEP}] - >=dev-python/tomlkit-0.7.2[${PYTHON_USEDEP}] - >=dev-python/tqdm-4.61.1[${PYTHON_USEDEP}] - ') -" -DEPEND="${RDEPEND}" - -distutils_enable_tests pytest - -S="${WORKDIR}/ChemEx-${PV/_p/-dev}" - -src_prepare() { - export SETUPTOOLS_SCM_PRETEND_VERSION="${PV}" - distutils-r1_src_prepare -} diff --git a/sci-chemistry/chemex/chemex-2021.4.0_p4.ebuild b/sci-chemistry/chemex/chemex-2021.4.0_p4.ebuild deleted file mode 100644 index 3a331d48eba7..000000000000 --- a/sci-chemistry/chemex/chemex-2021.4.0_p4.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 -DISTUTILS_SINGLE_IMPL="yes" -PYTHON_COMPAT=( python3_{8..10} ) -DISTUTILS_USE_SETUPTOOLS=pyproject.toml - -inherit distutils-r1 - -DESCRIPTION="Program to fit chemical exchange induced shift and relaxation data" -HOMEPAGE="https://github.com/gbouvignies/chemex" -SRC_URI="https://github.com/gbouvignies/chemex/archive/${PV/_p/-dev}.tar.gz -> ${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64" -IUSE="test" - -#RESTRICT="!test? ( test )" -# FIXME: Restrict until we figure out how to run tests properly, bug #815079 -RESTRICT="test" - -RDEPEND=" - $(python_gen_cond_dep ' - >=dev-python/asteval-0.9.25[${PYTHON_USEDEP}] - >=dev-python/jsonschema-4.1.0[${PYTHON_USEDEP}] - >=dev-python/lmfit-1.0.3[${PYTHON_USEDEP}] - >=dev-python/matplotlib-3.4.3[${PYTHON_USEDEP}] - >=dev-python/numpy-1.21.2[${PYTHON_USEDEP}] - dev-python/setuptools_scm[${PYTHON_USEDEP}] - >=dev-python/scipy-1.7.0[${PYTHON_USEDEP}] - >=dev-python/tomlkit-0.7.2[${PYTHON_USEDEP}] - >=dev-python/tqdm-4.61.1[${PYTHON_USEDEP}] - ') -" -DEPEND="${RDEPEND}" - -distutils_enable_tests pytest - -S="${WORKDIR}/ChemEx-${PV/_p/-dev}" - -src_prepare() { - export SETUPTOOLS_SCM_PRETEND_VERSION="${PV}" - distutils-r1_src_prepare -} diff --git a/sci-chemistry/chemex/chemex-2021.4.0_p6.ebuild b/sci-chemistry/chemex/chemex-2021.4.0_p6.ebuild new file mode 100644 index 000000000000..62c958f646d3 --- /dev/null +++ b/sci-chemistry/chemex/chemex-2021.4.0_p6.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +DISTUTILS_SINGLE_IMPL="yes" +PYTHON_COMPAT=( python3_{8..10} ) +DISTUTILS_USE_SETUPTOOLS=pyproject.toml + +inherit distutils-r1 + +DESCRIPTION="Program to fit chemical exchange induced shift and relaxation data" +HOMEPAGE="https://github.com/gbouvignies/chemex" +SRC_URI="https://github.com/gbouvignies/chemex/archive/${PV/_p/-dev}.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64" +IUSE="test" + +#RESTRICT="!test? ( test )" +# FIXME: Restrict until tests are readded https://github.com/gbouvignies/ChemEx/issues/51 +RESTRICT="test" + +RDEPEND=" + $(python_gen_cond_dep ' + >=dev-python/asteval-0.9.25[${PYTHON_USEDEP}] + >=dev-python/jsonschema-4.1.0[${PYTHON_USEDEP}] + >=dev-python/lmfit-1.0.3[${PYTHON_USEDEP}] + >=dev-python/matplotlib-3.4.3[${PYTHON_USEDEP}] + >=dev-python/numpy-1.21.2[${PYTHON_USEDEP}] + dev-python/setuptools_scm[${PYTHON_USEDEP}] + >=dev-python/scipy-1.7.0[${PYTHON_USEDEP}] + >=dev-python/tomlkit-0.7.2[${PYTHON_USEDEP}] + >=dev-python/tqdm-4.61.1[${PYTHON_USEDEP}] + ') +" +DEPEND="${RDEPEND}" + +distutils_enable_tests pytest + +S="${WORKDIR}/ChemEx-${PV/_p/-dev}" + +src_prepare() { + export SETUPTOOLS_SCM_PRETEND_VERSION="${PV}" + distutils-r1_src_prepare +} diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest index cd68455be0ea..72e737bfa652 100644 --- a/sci-chemistry/dssp/Manifest +++ b/sci-chemistry/dssp/Manifest @@ -3,11 +3,8 @@ AUX dssp-2.1.0-gentoo.patch 1513 BLAKE2B aabdcfff1083d7552392c35897eb8a84b07323c AUX dssp-2.2.1-boost-1.65-tr1-removal.patch 2126 BLAKE2B dc59d21a6be26ee96b636c13645163478999d5122f09d3a72963843be773210ea225e374941bd057ef6f083a13fb77980bd4390174df2a0c715f0386da7232e0 SHA512 8f84c6e163888d6a8192683a6555f7d6003634854f5cde0f6f962744e531165c7e0b2b08c55cbfb9c396d167c44317dd2e7a8290e4defd2c8def0a6511fbbd6c DIST dssp-2.2.1.tgz 47141 BLAKE2B 34d8b2db8797a8c23763766c0214337f03584c4be52c1bc820a0df0db6a5f78ac0229aafdd47a60b8fd6f4832abf0399663c53f9e898c75f08ecbe22b141c8da SHA512 4a273714d6b3230daea166caa7f4117d5ccb225bea0cf1bc2eb61539b6cc8e227d0ba19047d61f0ad0d1d6bc2efdec9c193bd44341e15ef0950acb4a22498811 DIST dssp-3.0.11.tar.gz 168085 BLAKE2B e1c42fd22cfb2287f10b5deae48b56a4583d4a67737a3485dcbd160d1597a15c2d5105c3794c875d8001abede1c014efb4f7f5b7c250f867bdf9ed95a0860217 SHA512 a0cfe44e517ff1f909ef2928b62ae2c639c6bddfd8a0fb538883f647fd2771e00da68e0fd2521aa02ba3c6d1b0c9b784b7fe142392af3a3abf6ea89f1546bd9d -DIST dssp-4.0.1_p20210831.tar.gz 121793 BLAKE2B 1e028b086b418772a93db350f8084d1786996ff6ea935d236b1431d8f4a07c0b33ebf374a4c4d5d4d243952f3f56e29a548ce09763863a1e0c529755fba6c211 SHA512 62f1ac781dd3d6f3436e6c155ae1a470d0baf6a6d9f6d6729034a7a5ef41550f76d0473c688d235279336306c9f3598377c056cddd6d00a89a826fbb04c1bfb3 DIST dssp-4.0.3.tar.gz 122872 BLAKE2B f88c330370645b4bd4e89656ad676e443a33c38d7882145bc60e329f823eb761777713df6c7ae44550d10bcd22256ac16db358587cadd39efd6268dd869655d4 SHA512 31ca481b097c9c59f407e35eb8175638b5e4102991007090b5b4ea30db0b076f97cff45d0aa9ae01a826f7673258464b572d68714f00e210db26020cea4be094 -EBUILD dssp-2.2.1-r2.ebuild 962 BLAKE2B 4badf2ae8647aab9c5e359d9e0763d051388afe3bf5763c8eeb99cb21b30283d72ace619f1b65c5ee248c42f8264cb31c2c1c079f75eacda1568cc4352cec5e3 SHA512 4a599b6e7cd068175bd89f4ea948ad1267df783c240ab46d3c6109bf3f2853de714ecf1e5776722309688599f28af545287fe5cb98d8b7a5f46d319df953b926 EBUILD dssp-2.2.1-r3.ebuild 880 BLAKE2B 057a862fbc9ff19fbf487f9df0faf661a7db5406c28e6cb91d5e38dfaa2e9d24eead9ba78d4e92b5b5022e2be5c69b30ff6c386aeac8160062b5f7f35b449889 SHA512 747ac74fd95400759569e657db85c3dc5c5a7ee0753761bc4b4927f4d119d168f0d5dcbd9ca16f37486358e7117e773d812034fb07953aae88c63ac1e706f8f7 EBUILD dssp-3.0.11.ebuild 825 BLAKE2B 020ea517127ffc1167cbff3a9362e5ff255b25664769ef2ac8f7f3060e34e0bec29e965df46e65bab8943cbf5fb11175d70b1b9f9e7d71bdbf92a4c54a903367 SHA512 b81dbe1cb9f7b66c5268485dc262bb705b12d250e2ec778c80fddbc584a38e36b64cb93e92385c178fdeca0e593c45ce25aef16480bfa9eb230bdd2b8a82fa53 -EBUILD dssp-4.0.1_p20210831.ebuild 854 BLAKE2B 0900056de41489970920f7bc190df755478a719ee19d9afcc9bfcebd666e0e6abe3bc03ce93a6ce5b4c426401f4243114e576a7eba4b84a84ea63c0c73f1f78e SHA512 4d2deb26d537014238592d7062b7d9ad6ce3350d09c9e422c47f70df7c9320235e141e05290635b63d66c65aebc8c964604b9269bf423bf09a2e90e87e70015f -EBUILD dssp-4.0.3.ebuild 769 BLAKE2B 406a817ed8545b7b85524cd36a0f7016b75639a0dd15971639eba0e55a2eb78b68817d0892149d8b6781d6b4ed9a767d7e508d236023a1bd16663fc289bc6399 SHA512 2dbd1aa4e76d6bc58a42ed4dc848c7e87afd3079d5f2bd21652288b38ef7ad0d5c5804a52532e33cd2519652d3a94cc2f9fc462e8488aee42309edb2a40dc156 +EBUILD dssp-4.0.3.ebuild 778 BLAKE2B f550bf8d7063b30f4fe15641b92e2973288c6da16317e74a041ada8e043133e4d6d6e125882d05f0e063b60ab421f039442951f9c92b9778e5435d82a512ed8a SHA512 7d853da1d0f4a1a623acd3e801fb8fcc3c50a4006cf75a8c999d8f6aec985c3fe92d8aae50bde624d67ddb559ae7bb49d701de36800ae5d2f8abaed523f0888d MISC metadata.xml 217 BLAKE2B f8189b02494f180dac078dcd5c275d3c795f20f360f8b172c66065a2d937e396b24b8631bba4cd8567d60285ce89fc77b9539f2233bf33899c820613c48c33ba SHA512 f0c9e5b3d281fecd21b1e23a6f44c94c1c0b3220de46a177d35932111b7f1ab4399061c42833ac1ee9bd0324b139fc8db66e0d2890224d607bd3be38ae469be9 diff --git a/sci-chemistry/dssp/dssp-2.2.1-r2.ebuild b/sci-chemistry/dssp/dssp-2.2.1-r2.ebuild deleted file mode 100644 index 63075d4d4290..000000000000 --- a/sci-chemistry/dssp/dssp-2.2.1-r2.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="The protein secondary structure standard" -HOMEPAGE="http://swift.cmbi.ru.nl/gv/dssp/" -SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/${P}.tgz" - -LICENSE="Boost-1.0" -SLOT="0" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND="dev-libs/boost:=[threads(+)]" -DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}"/${PN}-2.1.0-gentoo.patch - "${FILESDIR}"/${PN}-2.2.1-boost-1.65-tr1-removal.patch -) - -src_configure() { - tc-export CXX - - cat >> make.config <<- EOF || die - BOOST_LIB_SUFFIX = -mt - BOOST_LIB_DIR = "${EPREFIX}/usr/$(get_libdir)" - BOOST_INC_DIR = "${EPREFIX}/usr/include" - EOF -} - -src_install() { - dobin mkdssp - dosym mkdssp /usr/bin/dssp - doman doc/mkdssp.1 - dodoc README.txt changelog - - cat >> "${T}"/30-${PN} <<- EOF || die - DSSP="${EPREFIX}"/usr/bin/${PN} - EOF - doenvd "${T}"/30-${PN} -} diff --git a/sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild b/sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild deleted file mode 100644 index ca051ca5a0d2..000000000000 --- a/sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -inherit cmake - -DESCRIPTION="The protein secondary structure standard" -HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp" - -COMMIT="728cc7c6c8d95460d8db453cf7adb25a89ba15f6" -SRC_URI="https://github.com/PDB-REDO/${PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" -S="${WORKDIR}/${PN}-${COMMIT}" - -LICENSE="BSD-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -BDEPEND=" - >=dev-libs/boost-1.70.0:=[bzip2,zlib,threads(+)] - >=sci-libs/libcifpp-1.1.1 -" -DEPEND="" -RDEPEND="${BDEPEND}" - -pkg_postinst() { - if has_version sci-chemistry/gromacs; then - ewarn "DSSP > 3.0.x is not compatible with gmx do_dssp:" - ewarn "https://gitlab.com/gromacs/gromacs/-/issues/4129" - ewarn - ewarn "Feel free to mask newer versions if needed." - fi -} diff --git a/sci-chemistry/dssp/dssp-4.0.3.ebuild b/sci-chemistry/dssp/dssp-4.0.3.ebuild index d9d8a5740c8d..31f86f7e3cf4 100644 --- a/sci-chemistry/dssp/dssp-4.0.3.ebuild +++ b/sci-chemistry/dssp/dssp-4.0.3.ebuild @@ -22,7 +22,7 @@ DEPEND="" RDEPEND="${BDEPEND}" pkg_postinst() { - if has_version sci-chemistry/gromacs; then + if has_version "<=sci-chemistry/gromacs-2022"; then ewarn "DSSP > 3.0.x is not compatible with gmx do_dssp:" ewarn "https://gitlab.com/gromacs/gromacs/-/issues/4129" ewarn diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index d1a7f57dddca..eb4404d4562a 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,3 +1,4 @@ +AUX gromacs-2019.6-missing-include.patch 1052 BLAKE2B 01d7e592caa1e975a1fcea99bc37dd61ea7c039ed32243852f532c87d08911f9e83d0752d3a09e46643ca433339fe7c8d510c09e4af1070060735f9ee8a151d0 SHA512 8ed2e1de98cd35d87c0a0ea6867a99d4c1b33940040506feac09da929389afd1e19f34691c9032b1f59b156986b56c49aed1d0c8f8e7e64ad7a78e6dfd521912 AUX gromacs-2020-pytest.patch 1346 BLAKE2B 4b0b34bf4f46ec1acc3d0088ac11323938ee44b700beecc32b083885727d31904649798e38b824a6cf04ea7f9129dbd40e66bdde6e5a88fa4734db51bdf4cc46 SHA512 2c05e243b0e7bb8f9d25051d7bc86463dffa722502586799f0a8ce53bebd24fd0e367b6840365ac4ebc30595ffb8bbccb10a88d0c81148ae198941966cebddb0 AUX gromacs-2021-nblib.patch 1860 BLAKE2B 3f9d8e5683fee23434ca7bd0d9264eaed5834c3e4164176006fefea27b74ea50e67b743c4d0fa329486545ac1237d9fb288a0fbe7b6a4c06a37c8e85a22cb255 SHA512 1630eacd632519d5440fcae8aba511615ac031ce9828a059308c8ec2f33588c43dc055ab3d435efd622f23a46afa5caa14a6acad5aacb15bed33b9a9be5009f9 DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122 @@ -6,6 +7,7 @@ DIST gromacs-2020.4.tar.gz 29149899 BLAKE2B a07c8efd96137d58c1edf4ac9b5aafeb16d9 DIST gromacs-2020.6.tar.gz 29196621 BLAKE2B b350fc62fd8eeb3f2b042fa74a4ed42e43a7b74efd8fddb60ec086a814048a52b8625da65fa5c4cf2cb1e22f8347562bc84d38bf34441fc5ebc6abaa38b0eea0 SHA512 4ce4d6b9ae33e9cd2a1ad3313e80acf63ded21dac897b01dbf87df2e318181796ef64c8a1d3e0a6058b972d8d88d00f710cd0277db12f38fc2c9b29772c98bea DIST gromacs-2021.2.tar.gz 37976386 BLAKE2B 8818321bbcbdee25356bbf909d9c667f9d7cf180e696a323a61017683234d1269decc8f8d72b8012a8cc207f69e5cd97e2ab48dbbff06d82bbb407bc0578854b SHA512 51b1728f41932274436ab807d569109e2b0e145abcb5cf9c9b7daf6a7396f2f8716dc28fb93cf178c97a7eaeab2a88878d0bc71dd6c6abe7e829d579e7968615 DIST gromacs-2021.3.tar.gz 37987972 BLAKE2B d71995c7d5a34978246e33dc637ac3d273e547afcf72d1a107026650f03286ecdf27e4b9a70113b3c3a01af59ad49ac5c813aa6e5d2e8eb29fd05582a7a28d34 SHA512 da420917d06de2e192dfbb4e1b9f46989ed05b5c7e641c657104ed8f2bd8b22509bffd1ecfd7c965c80544eafa6af12d6d0aba7e1e7d9d14a4a88fb3fbf394a5 +DIST gromacs-2021.4.tar.gz 38023262 BLAKE2B 4e1c9ca23f8bd89a990bac2730f846ce9fd6423aa6934866734272ac8f5ca29cdb51daec440b7ef2af56c68bdbab504c0c1b1a4d5f4af0b16666850bf286c5b2 SHA512 35b26b3df02d151373fab49022281b89e987c867257a998acc926b2b7151f5d4e46f11c398a24f4a174f668dd24a828b07d36594ac5d5506e10e40d4578427a2 DIST gromacs-2022-beta1.tar.gz 39727355 BLAKE2B 2b17684e36f1a2746bd92e4cea2f7eedfcc1770eb127663b7d643a4e9518dc90f788c0f41dcff612d06edb05eeb06a13196810714d5cdf5a8ef5056100d75eb6 SHA512 a311a95b42647819d442be2a6106f4a3bbfa792856ac88ade9ee0793dff3a3bd0e6f2982bfa37d541b3a4673a24358fa72bf9267c3d1743bb01da673d84e0fa8 DIST manual-2018.8.pdf 10025023 BLAKE2B 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12252501 BLAKE2B 0dbf9024e1516076b0eeb46e41523b966d1d81f57504fe0501c7bc8575e74fb19e3452ac584757e425bcccbc737367fe83be87fd21a4287f4675cf87184b960b SHA512 14156d3b1017990e0be3ceb7ec055777a1aec4c347ac2e821a042d51c931f84ebca862f60644a90ed7ba4070cb14ff8babcde3e4351e4dbec84df8563e350984 DIST manual-2021.3.pdf 12255076 BLAKE2B 6ca516b6832507c9d4100679d1f9bc9e3ab17d226849b050764b0d0626247dc57ce49985f9a7fc0061f3df278923a83faa367ca8ab91c37e5624dc584a51a822 SHA512 5d53798f30ea00fcb4e1b35f7eaa4bebfc05dafa4f2d0c197dcf2b57a624ad3a98b74fd90722e40d0ac13a6fff4ca231f9d6340f52ba94659c827c53c2f1cb16 +DIST manual-2021.4.pdf 12253232 BLAKE2B 0b859c08a07d5a615ac7a822b61d5a4f4296ca9773d383a07960dc629d6b1df23e1dec51561a4ac26789b84e49cc98b6d7cc10d943c61d7784052664ac1bacf9 SHA512 024f17a670518fc19a2a462186ed2a74f331c5c83b8ba4bbe148a53767515ba19e6af887a1baae3a7770af2095fad5c513784cc54f9d0f881395ad8a89760cba DIST manual-2022_beta1.pdf 13033013 BLAKE2B dda51c931e5b124d0fbd106a73b4f04d6d58374a8590b44d1f64897a2a2c97fb4a682275d2f2bd0907de5faec74d91550642bb505a3a316d2f7e20a84f0c1308 SHA512 ea7c1362fda8a4dc5b21242154daf9d9c66bdd2462d67335c56170189ed6f75a50bf51a0cdf8654886a3c0a537dfc0d364eb57f6602ce0065e4ac8ca106f5544 DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036 @@ -20,15 +23,18 @@ DIST regressiontests-2020.4.tar.gz 48542144 BLAKE2B 1dcde67525d40ababa74d9e8ba2d DIST regressiontests-2020.6.tar.gz 48541232 BLAKE2B dbb405bd9168775984de8c9fb9e3fa2398d2790e2e4de23711c51a01dc3ea570d172a35d4924742ad5eda463eb0a885e6924512801e82b241600ceaefd5db70d SHA512 497a9e7d438b0b7b0734a97cf3683baf480ecc056e96b09f1e143c362ff047a4e51e323216750501c954559579716dc024d3c51319bd2c85fa719466ce4330b2 DIST regressiontests-2021.2.tar.gz 48514312 BLAKE2B 81b007d5e5e1d054349c73dc8bc3589db328752e48a66687c0ad36be87ebe580df9cbd93b193a724669bd5765af06ec306f2e12af00a228af616de03943d6f05 SHA512 b687ddfd3dc6ec1051af2a3253633703ef1c82335d1df23379819ea47e44dfcd417e81e29610cc584d4c5fb1ee1cbc76731a3fd31b529d8cdd0b9c22f432c7ec DIST regressiontests-2021.3.tar.gz 48515038 BLAKE2B ee79d8adddc9c68f7d59d9e568b12bf4d1fe0e44c2810fee846ad6f689bbcacf60f5c266433946329e64e3127bc2d37a3f81f69c070c636b411b38067650c2cf SHA512 e14baa22ef2902a23125bbd9143ae7a9a4810498b321794ff1989f8d044d47db5db41d5225798fda08016c05e5f7f315178b5a6e35cdf01e3b6604670a8ce7a2 +DIST regressiontests-2021.4.tar.gz 48541736 BLAKE2B 37b8e65e333dcfcfc795da631475807ffa4ecc3a85426b4de6dd2ccb50f40a78159149789da13f988340a62d21e7d6b1d4f0c6e7fe69120d4c94ab2252b4c440 SHA512 18663693cf9ce2ca3bd8df0f668e7a0c8236a7f5ae4ee02f621cbe52c139c506b61ac4cab200cc59caab41e9983ea93dfa062d7b52f6558a619096a8d439fb56 DIST regressiontests-2022-beta1.tar.gz 48534065 BLAKE2B 4f0dd89b791fa11696460befa4a755dff14546abc10a4801ddb5f0286cee267ca983c082748b0ce9345a98b7fb98bb4a5387054a373acc543ff56b72e0ad9b64 SHA512 aa178a59bc7074e1d50d2cbe4d376f3593e0af6ad2a563627529fa4b0aa6a9bb29248caaace578150ab9e80feba3bf862ab964993eed183a79e35a189d10fecf EBUILD gromacs-2018.8-r1.ebuild 6946 BLAKE2B 299b68d1a3d07e2691930de85bcee504885ae160ffc44fa4c65aeffd621fb54f15db86625a4c6339214fdfdd2e0f690c147d32abacd392fdb10c4ffc6d834b0b SHA512 0a511e8367cee468c5321df6bb5fada42950df2bda4355087b4b499e869f4167e22196a7a9d4dcdc286320cc8bd465daaf8c3da9ad9d22145bdc9024b4aeed17 EBUILD gromacs-2019.6-r1.ebuild 7269 BLAKE2B c3c66eb2fed62426d80a83fece8e5c03bb5f143f786cda937f7c54fbd279a3892148d68d7147f5e8e6610b91b1521d83fd14f241819193bc6cb6be63b7e5ef80 SHA512 4c93feca7343482e6c86ad83fcabfca16c647bf85955b8d41ef9c4a684ed87f98f153e1b7bba0da47de44127ac7abf4eb955454ba03eb29ce0a9fa11eb3a76ca +EBUILD gromacs-2019.6-r2.ebuild 7326 BLAKE2B 4850899d3e4b8affe9724870215cb6a08e57ce07c7587d01e58788c509c8a8577b41e6ff8685f2f540df33d0e47bd08fad9482bf35d1c71c7f11626208897189 SHA512 c138b4a3fef43d310469cb74583aa7b12b0c565dfe07c4f9b0805bc0c1e724ccdfedbeb9fb6fdaa836e8c3eaad3f40358070054f67b6ac8655f5e715bd32824c EBUILD gromacs-2020.4-r1.ebuild 10139 BLAKE2B 3e9851ed038cdeab3896f24c3538ebea5dd46aae402c86b900c3720db15e6cd674dd38f432efb78ce4a34324241f5d9dc1881e6ab30edc1396cf2685ff0a3ebb SHA512 a422c0fd42f721cfbfaa83aa4d300ccf3c8de089ad8f7c392528c6df86898b3b25c05c9b7131a68a0aaf75995872820b61e48f54c1b878ea162f53f917c02364 EBUILD gromacs-2020.6-r1.ebuild 10142 BLAKE2B d212ebd8e184b68d0f77173467252de2587fef6babc48a602f0fd289b15a9923d7ea47fce1459451c56df5ab31e6e975e3e0c381993322a08b424b21a5c8d31d SHA512 0a14ad921a3fd48d1a980b08ce3470f9d27f6056d9bb8addb26c14adb6dc30c8933a96bdb6ecde9e491798cceb9ffb41a3c244fa67f127c3eba5095277c6baa9 EBUILD gromacs-2021.2-r1.ebuild 10364 BLAKE2B 6d9e48d7d4c75927a1f87aae70a3458d519850be2e09f5fa358f3b16a03ad3b8916ca97805257b03558a12c173d08167c4fee056de44742d85ac83859fc63c17 SHA512 68ab6dd6fdbc3fa8f628be0fd7ab05e528492a6f626ae8edcd15785ef816c47515390667d8f36c10cd1d4eeb1e73655611572d55234e9c957517f4c85df1e971 EBUILD gromacs-2021.3-r1.ebuild 10291 BLAKE2B 7a53f7c5f5365d3efb6d8a35552aa751c4e83a3ee259d315c85d0faa7117c0bc3510f9752dd76d54bd55024ad80de7ad31d2e54cccf2c651a4414e7a0d452e7a SHA512 611076dc6d41ccab6f86ed8cbc96a6ec36ad405652a2c0c4da68fa78cd3346545efd38bdedd115d4a60d657dbbafd0019e84ed9554af211005352e6d26fad5ae +EBUILD gromacs-2021.4.ebuild 10293 BLAKE2B cb2304e0355f30d2b3549aed33db6db7229458e504c4ccd3c0cf1d2d2a66751c71c33c6b3c5f46a01129b7891dfa22d7f6b2d731275dc9396f20400a7585593d SHA512 b07b8ba64de11de4ecee1c6e3ad2638ac582e93f6122ee8cd90f5430f4ea16435f7cb4778e88a5c62a7d83989c4eb13932f7ff6e61f8f4fafd691a0a30f057cc EBUILD gromacs-2021.9999.ebuild 10293 BLAKE2B eafc12c1354eaa5c641b4c41735a8abce7d385b06c4ed6b9bdf2c60b54c96396030b5a0b8bc953ee41d4426b8ba69cb776bdc0dde0dda2c9caa7d0f025247ce6 SHA512 639fa70a146044ce2be2fd18302f99589edcd0028df24c884dd536cc5a54bd24b01008346bd1f62fa6c1c854113f25370da289bd1500b1903cf4d3371db781f2 -EBUILD gromacs-2022.9999.ebuild 10220 BLAKE2B 9d3c168fd03c68aa1f17d86e81069ff0e2c0611145012a43eef335b00a3baadd11145b7761a20521ffc17b965e5f05371f3f22a9f58e7d0ccdb7684a6ae6b4c2 SHA512 c0542d7584a6db70a55d8be5af26157146689de9b1faf6276d1585181548a8d79d691086c6f7e18c8614b78d57b6dc3f71311634608095bf0e32620560bb59a4 -EBUILD gromacs-2022_beta1.ebuild 10220 BLAKE2B 9d3c168fd03c68aa1f17d86e81069ff0e2c0611145012a43eef335b00a3baadd11145b7761a20521ffc17b965e5f05371f3f22a9f58e7d0ccdb7684a6ae6b4c2 SHA512 c0542d7584a6db70a55d8be5af26157146689de9b1faf6276d1585181548a8d79d691086c6f7e18c8614b78d57b6dc3f71311634608095bf0e32620560bb59a4 -EBUILD gromacs-9999.ebuild 10220 BLAKE2B 9d3c168fd03c68aa1f17d86e81069ff0e2c0611145012a43eef335b00a3baadd11145b7761a20521ffc17b965e5f05371f3f22a9f58e7d0ccdb7684a6ae6b4c2 SHA512 c0542d7584a6db70a55d8be5af26157146689de9b1faf6276d1585181548a8d79d691086c6f7e18c8614b78d57b6dc3f71311634608095bf0e32620560bb59a4 +EBUILD gromacs-2022.9999.ebuild 10233 BLAKE2B f3dae6a5105eb9cd31c88fe9cae8c469020010cd34c11b2934b294ec32d37500a16cca5b711ab2dd02a574228f7dcda678230a8709ca8c4e5152f918085437dc SHA512 4176081090b9f3c1a95a40c88e4c6bf92a304833083ed7f350bdf9f8a6442cba3f559f80c48ebeeb197cb16fdf670fa593518a548ee35cb4fd87881203f7f74a +EBUILD gromacs-2022_beta1-r2.ebuild 10233 BLAKE2B f3dae6a5105eb9cd31c88fe9cae8c469020010cd34c11b2934b294ec32d37500a16cca5b711ab2dd02a574228f7dcda678230a8709ca8c4e5152f918085437dc SHA512 4176081090b9f3c1a95a40c88e4c6bf92a304833083ed7f350bdf9f8a6442cba3f559f80c48ebeeb197cb16fdf670fa593518a548ee35cb4fd87881203f7f74a +EBUILD gromacs-9999.ebuild 10233 BLAKE2B f3dae6a5105eb9cd31c88fe9cae8c469020010cd34c11b2934b294ec32d37500a16cca5b711ab2dd02a574228f7dcda678230a8709ca8c4e5152f918085437dc SHA512 4176081090b9f3c1a95a40c88e4c6bf92a304833083ed7f350bdf9f8a6442cba3f559f80c48ebeeb197cb16fdf670fa593518a548ee35cb4fd87881203f7f74a MISC metadata.xml 1224 BLAKE2B dc6de7f135e5cbd7bdb94bc630d3c7344f5f5387305ada4f3f0fd3f027f9fa4e2c5e44120c8eab8e983fcda314680ac3d140ab61873ab21b839f912a52b21dde SHA512 d036cffac5fd3c4b8d26efdee0f4b4db8d3520f771754a0859f8e99f64d558795b6cab1efba1d4f1700027707a05a724ae96a7e257434d3894ef5fa6eed7ccba diff --git a/sci-chemistry/gromacs/files/gromacs-2019.6-missing-include.patch b/sci-chemistry/gromacs/files/gromacs-2019.6-missing-include.patch new file mode 100644 index 000000000000..cf478d52cb67 --- /dev/null +++ b/sci-chemistry/gromacs/files/gromacs-2019.6-missing-include.patch @@ -0,0 +1,38 @@ +From 053286ff0bfb88db5c158f5f68017c4bb5d9496a Mon Sep 17 00:00:00 2001 +From: Christoph Junghans +Date: Wed, 28 Apr 2021 19:44:09 -0600 +Subject: [PATCH] fix build on F34 + +see https://gitlab.com/gromacs/gromacs/-/merge_requests/1524 +--- + src/gromacs/awh/biasparams.cpp | 1 + + src/gromacs/mdrun/minimize.cpp | 1 + + 2 files changed, 2 insertions(+) + +diff --git a/src/gromacs/awh/biasparams.cpp b/src/gromacs/awh/biasparams.cpp +index f4db497002..e762ea084a 100644 +--- a/src/gromacs/awh/biasparams.cpp ++++ b/src/gromacs/awh/biasparams.cpp +@@ -49,6 +49,7 @@ + #include + + #include ++#include + + #include "gromacs/math/functions.h" + #include "gromacs/mdtypes/awh-params.h" +diff --git a/src/gromacs/mdrun/minimize.cpp b/src/gromacs/mdrun/minimize.cpp +index 8550271325..495bcfdda0 100644 +--- a/src/gromacs/mdrun/minimize.cpp ++++ b/src/gromacs/mdrun/minimize.cpp +@@ -51,6 +51,7 @@ + #include + + #include ++#include + #include + + #include "gromacs/commandline/filenm.h" +-- +GitLab + diff --git a/sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild b/sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild new file mode 100644 index 000000000000..35bbc972de69 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild @@ -0,0 +1,255 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake cuda multilib readme.gentoo-r1 toolchain-funcs xdg-utils + +SRC_URI=" + http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + doc? ( http://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) + test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" +KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" + +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 +doc double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +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 ) + ${PYTHON_DEPS} + " +BDEPEND="${CDEPEND} + virtual/pkgconfig + " +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + cuda? ( !opencl ) + mkl? ( !blas !fftw !lapack ) + ${PYTHON_REQUIRED_USE}" + +DOCS=( AUTHORS README ) + +RESTRICT="!test? ( test )" + +S="${WORKDIR}/${PN}-${PV/_/-}" + +PATCHES=( "${FILESDIR}/${P}-missing-include.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" +} + +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" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #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" + + #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_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=$(usex gmxapi) + "${opencl[@]}" + "${cuda[@]}" + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${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 + 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_compile check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake_src_install + if use doc; then + newdoc "${DISTDIR}/manual-${PV/_/-}.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 +} diff --git a/sci-chemistry/gromacs/gromacs-2021.4.ebuild b/sci-chemistry/gromacs/gromacs-2021.4.ebuild new file mode 100644 index 000000000000..ab6c1d40dd0b --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2021.4.ebuild @@ -0,0 +1,356 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +PYTHON_COMPAT=( python3_{8,9} ) + +DISTUTILS_USE_SETUPTOOLS=no +DISTUTILS_SINGLE_IMPL=1 + +inherit bash-completion-r1 cmake cuda distutils-r1 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 + doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) + test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${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 cpu_flags_x86_avx512f cpu_flags_arm_neon" + +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 build-manual 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[profiler] ) + 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 + build-manual? ( + app-doc/doxygen + $(python_gen_cond_dep ' + dev-python/sphinx[${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 ) + cuda? ( !opencl ) + mkl? ( !blas !fftw !lapack ) + ${PYTHON_REQUIRED_USE}" + +DOCS=( AUTHORS README ) + +RESTRICT="!test? ( test )" + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +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" + if use build-manual; then + # try to create policy for imagemagik + mkdir -p ${HOME}/.config/ImageMagick + cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF + + + !ATTLIST policymap xmlns CDATA #FIXED ''> + + + ]> + + + + + + + + + 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) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${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=$(usex build-manual) + -DGMX_HWLOC=$(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" ) + use opencl && gpu=( "-DGMX_GPU=OPENCL" ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(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 + 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}/${P}" \ + distutils-r1_src_compile + fi + # not 100% necessary for rel ebuilds as available from website + if use build-manual; then + BUILD_DIR="${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_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-${PV}.pdf" + fi + fi + + use mpi || continue + BUILD_DIR="${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 +} diff --git a/sci-chemistry/gromacs/gromacs-2022.9999.ebuild b/sci-chemistry/gromacs/gromacs-2022.9999.ebuild index 2cbb7ef61eb4..8b7107ecad96 100644 --- a/sci-chemistry/gromacs/gromacs-2022.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2022.9999.ebuild @@ -24,7 +24,7 @@ else http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf -> manual-${PV}.pdf ) test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" @@ -37,7 +37,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="blas 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}" +IUSE="blas 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 ) @@ -46,9 +46,10 @@ CDEPEND=" fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) lapack? ( virtual/lapack ) - lmfit? ( sci-libs/lmfit:= ) mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi ) + mpi? ( virtual/mpi[cxx] ) + sci-libs/lmfit:= + >=dev-cpp/muParser-2.3:= ${PYTHON_DEPS} !sci-chemistry/gmxapi " @@ -65,7 +66,8 @@ BDEPEND="${CDEPEND} dev-texlive/texlive-latexextra media-gfx/imagemagick )" -RDEPEND="${CDEPEND}" +RDEPEND="${CDEPEND} + > ${HOME}/.config/ImageMagick/policy.xml <<- EOF + + + !ATTLIST policymap xmlns CDATA #FIXED ''> + + + ]> + + + + + + + + + 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) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${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 + + 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/" + -DGMX_DSSP_PROGRAM_PATH="${EPREFIX}/usr/bin/dssp" + -DBUILD_TESTING=$(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" ) + use opencl && gpu=( "-DGMX_GPU=OPENCL" ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(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 + 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}/${P}" \ + distutils-r1_src_compile + fi + # not 100% necessary for rel ebuilds as available from website + if use build-manual; then + BUILD_DIR="${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_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-${PV}.pdf" + fi + fi + + use mpi || continue + BUILD_DIR="${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 +} diff --git a/sci-chemistry/gromacs/gromacs-2022_beta1.ebuild b/sci-chemistry/gromacs/gromacs-2022_beta1.ebuild deleted file mode 100644 index 2cbb7ef61eb4..000000000000 --- a/sci-chemistry/gromacs/gromacs-2022_beta1.ebuild +++ /dev/null @@ -1,350 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -PYTHON_COMPAT=( python3_{8,9,10} ) - -DISTUTILS_USE_SETUPTOOLS=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 - 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 - doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf -> manual-${PV}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" -fi - -ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" - -# see COPYING for details -# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING -# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib -LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" -SLOT="0/${PV}" -IUSE="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}" - -CDEPEND=" - blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14[profiler] ) - 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 - build-manual? ( - app-doc/doxygen - $(python_gen_cond_dep ' - dev-python/sphinx[${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 ) - cuda? ( !opencl ) - mkl? ( !blas !fftw !lapack ) - ${PYTHON_REQUIRED_USE}" - -DOCS=( AUTHORS README ) - -RESTRICT="!test? ( test )" - -if [[ ${PV} != *9999 ]]; then - S="${WORKDIR}/${PN}-${PV/_/-}" -fi - -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" - if use build-manual; then - # try to create policy for imagemagik - mkdir -p ${HOME}/.config/ImageMagick - cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF - - - !ATTLIST policymap xmlns CDATA #FIXED ''> - - - ]> - - - - - - - - - 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) - [[ ${CHOST} = *-darwin* ]] && \ - extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" - - if use fftw; then - fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${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_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" ) - use opencl && gpu=( "-DGMX_GPU=OPENCL" ) - mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=OFF - -DGMX_THREAD_MPI=$(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 - 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}/${P}" \ - distutils-r1_src_compile - fi - # not 100% necessary for rel ebuilds as available from website - if use build-manual; then - BUILD_DIR="${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_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-${PV}.pdf" - fi - fi - - use mpi || continue - BUILD_DIR="${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 -} diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index 2cbb7ef61eb4..8b7107ecad96 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -24,7 +24,7 @@ else http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf -> manual-${PV}.pdf ) test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" @@ -37,7 +37,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="blas 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}" +IUSE="blas 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 ) @@ -46,9 +46,10 @@ CDEPEND=" fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) lapack? ( virtual/lapack ) - lmfit? ( sci-libs/lmfit:= ) mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi ) + mpi? ( virtual/mpi[cxx] ) + sci-libs/lmfit:= + >=dev-cpp/muParser-2.3:= ${PYTHON_DEPS} !sci-chemistry/gmxapi " @@ -65,7 +66,8 @@ BDEPEND="${CDEPEND} dev-texlive/texlive-latexextra media-gfx/imagemagick )" -RDEPEND="${CDEPEND}" +RDEPEND="${CDEPEND} + = 4:g' \ - -i include/openbabel/shared_ptr.h || die - cmake-utils_src_prepare -} - -src_configure() { - use wxwidgets && setup-wxwidgets - local mycmakeargs=( - -DOPENBABEL_USE_SYSTEM_INCHI=ON - -DENABLE_OPENMP=$(usex openmp) - -DBUILD_GUI=$(usex wxwidgets) - ) - - cmake-utils_src_configure -} - -src_install() { - docinto html - dodoc doc/{*.html,*.png} - if use doc ; then - docinto html/API - dodoc -r doc/API/html/* - fi - - make_desktop_entry obgui "Open Babel" "${PN}" - doicon "${DISTDIR}/${PN}.png" - - cmake-utils_src_install -} - -src_test() { - local mycmakeargs=( - -DOPENBABEL_USE_SYSTEM_INCHI=ON - -DPYTHON_EXECUTABLE=false - -DOPENMP=$(usex openmp) - -DBUILD_GUI=$(usex wxwidgets) - -DTESTS=$(usex test) - ) - - cmake-utils_src_configure - cmake-utils_src_compile - cmake-utils_src_test -E py -} - -pkg_postinst() { - optfeature "perl support" sci-chemistry/openbabel-perl - optfeature "python support" sci-chemistry/openbabel-python -} diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest index f4eeca2aa8bc..322fabca2a0e 100644 --- a/sci-chemistry/vmd/Manifest +++ b/sci-chemistry/vmd/Manifest @@ -1,4 +1,6 @@ DIST vmd-1.9.4_alpha51-gentoo-patches.tar.xz 14604 BLAKE2B f8621956785d365cc056ba53373120d8f99da1476ab9789af6bb8ef00b8dd8c2a4c3599d75e13eba2fc5630b291aed966ce64f7f408504b079e3e994e45da243 SHA512 c57fd81e667e405ab1208a4e4a1d63710e593c07f554420c32980becd3547c2df98fbf6e439a53a626121fc361559f1ba53ab7b7235c97422bba61ece59d23bc DIST vmd-1.9.4a51.src.tar.gz 42826371 BLAKE2B 239d87f975c41a71096083028c1db8bf40cc058fc687fd9fff3c14c97c9b12bd68818d4c2eaeefd8c95c661409f1f056bce42178d0ba9271aa344fdce6f81ea9 SHA512 b42af6a4a7b1d2f0d242f89bff3a1c25a608ff59b9902b90154ba82a40439afb802a2d319363fa388a5211420fdaf0ee9bfd1f0a0e6e85d89d1dd506b373ba40 +DIST vmd-1.9.4a55.src.tar.gz 43049895 BLAKE2B 311fdbf8742647d1dbba8346e8559d26b19ec445bb5df4b23f684c5769997e2261e200b8118668d296654f59ab340fc150f5aa33fc808ad55f2e78ce7030960b SHA512 1be5f50555423120fd8c5c335a346a40253fb80cc352f08907d864f6b34d3debe28d9a3fbf821c3a6c7c86c615fd09735c05aadf1b4503722075e9ab0b946378 EBUILD vmd-1.9.4_alpha51.ebuild 7598 BLAKE2B fa0cdea71d0a85069b197d40e6d3cbc54a3136646bf18c6a9a702e591f2bbaed15606499923e8d75d1996f7e99fbd48604892add5fa16dd161cacda548df784d SHA512 8c9231669f17c59892114ee3aaf5f5d32b5c1b451795d8bcd1e7366bbf9d13723938140acf7e9e7504844e996986a96343df75ad9f4204ed5c14bec63ac0d7c4 +EBUILD vmd-1.9.4_alpha55.ebuild 7532 BLAKE2B 199eca3740403900b2b0244fda566db7f95406373075544a59c8c730ff48447ed591f34649440551eb49eea472e2b67f7bb1cdab831a5fac2f2bc95618a860e6 SHA512 965d281384e5eb5df46241c015febad2b9f260a0ef66587b9ae64b06822c52f721952647770d484e2e670faeca7640c2a1c93ed1cfac316249fa6d6c99c64fca MISC metadata.xml 779 BLAKE2B 5d824ae91cfeb1b482fb2cf1e5f8968dffe1abea898d26dc6e4949d7ba86396474964c847ee511d19d00769ed2bdf0f9a4daa7bfa779985308a93636dccfba82 SHA512 05de02395a8220118a2694df845ac125e0b2eb2720a699cbda2a84b73487ae14cb44077140698c109b5f58c30a1815b2a670a02121f85b70b90f75e40a9764d9 diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha55.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha55.ebuild new file mode 100644 index 000000000000..28638554552f --- /dev/null +++ b/sci-chemistry/vmd/vmd-1.9.4_alpha55.ebuild @@ -0,0 +1,269 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +PYTHON_COMPAT=( python3_{8..10} ) + +inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg + +DESCRIPTION="Visual Molecular Dynamics" +HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" + +MY_PV="${PV/_alpha/a}" +MY_P="${PN}-${MY_PV}" +SRC_URI=" + ${MY_P}.src.tar.gz + fetch+https://dev.gentoo.org/~pacho/${PN}/${PN}-1.9.4_alpha51-gentoo-patches.tar.xz +" + +SLOT="0" +LICENSE="vmd" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +IUSE="cuda gromacs msms povray sqlite tachyon xinerama" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RESTRICT="fetch" + +CDEPEND="${PYTHON_DEPS} + $(python_gen_cond_dep ' + dev-python/numpy[${PYTHON_USEDEP}] + ') + >=dev-lang/tk-8.6.1:0= + dev-lang/perl + dev-libs/expat + sci-libs/netcdf:0= + virtual/opengl + >=x11-libs/fltk-1.1.10-r2:1 + x11-libs/libXft + x11-libs/libXi + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) + gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] ) + sqlite? ( dev-db/sqlite:3= ) + tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) + xinerama? ( x11-libs/libXinerama ) +" +DEPEND="${CDEPEND}" +BDEPEND=" + virtual/pkgconfig + dev-lang/swig +" +RDEPEND="${CDEPEND} + sci-biology/stride + sci-chemistry/chemical-mime-data + sci-chemistry/surf + x11-misc/xdg-utils + x11-terms/xterm + msms? ( sci-chemistry/msms-bin ) + povray? ( media-gfx/povray ) +" + +S="${WORKDIR}/${MY_P}" + +VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" + +# Binary only plugin!! +QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf/bin/intersurf.so" +QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil/volutil" +QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil/volutil" + +pkg_nofetch() { + elog "Please download ${MY_P}.src.tar.gz from" + elog "${VMD_DOWNLOAD}" + elog "after agreeing to the license." + elog "Place it into your DISTDIR directory." +} + +src_prepare() { + # Apply user patches from ${WORKDIR} to allow patching on patches + # subdir too + cd "${WORKDIR}" + default + + # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32121.html + # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32116.html + eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4a51-gentoo-plugins.patch + + use cuda && cuda_sanitize + + # Prepare plugins + cd plugins || die + + sed '/^.SILENT/d' -i $(find -name Makefile) + + sed \ + -e "s:CC = gcc:CC = $(tc-getCC):" \ + -e "s:CXX = g++:CXX = $(tc-getCXX):" \ + -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ + -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ + -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ + -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ + -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ + -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ + -e "s:-ltcl8.5:-ltcl:" \ + -i Make-arch || die "Failed to set up plugins Makefile" + + sed \ + -e '/^AR /s:=:?=:g' \ + -e '/^RANLIB /s:=:?=:g' \ + -i ../plugins/*/Makefile || die + + tc-export AR RANLIB + + sed \ + -e "s:\$(CXXFLAGS)::g" \ + -i hesstrans/Makefile || die + + # prepare vmd itself + cd "${S}" || die + + eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4a51-gentoo-paths.patch + + # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32122.html + eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4-tmpdir.patch + + # PREFIX + sed \ + -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ + -i configure || die + + sed \ + -e "s:gentoo-bindir:${ED}/usr/bin:g" \ + -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ + -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ + -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ + -e "s:gentoo-gcc:$(tc-getCC):g" \ + -e "s:gentoo-g++:$(tc-getCXX):g" \ + -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ + -e "s:gentoo-cflags:${CFLAGS}:g" \ + -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ + -e "s:gentoo-nvflags::g" \ + -e "s:gentoo-ldflags:${LDFLAGS}:g" \ + -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ + -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ + -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ + -e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \ + -e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \ + -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ + -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ + -i configure || die + + if use cuda; then + sed \ + -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ + -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ + -i configure src/Makefile || die + sed \ + -e '/compute_/d' \ + -i configure || die + sed \ + -e 's:-gencode .*code=sm_..::' \ + -i src/Makefile || die + fi + + sed \ + -e "s:LINUXPPC:LINUX:g" \ + -e "s:LINUXALPHA:LINUX:g" \ + -e "s:LINUXAMD64:LINUX:g" \ + -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ + -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ + -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ + -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" + + EMAKEOPTS=( + TCLINC="-I${EPREFIX}/usr/include" + TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" + TCLLDFLAGS="-shared" + NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" + NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include" + NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" + NETCDFDYNAMIC=1 + EXPATINC="-I${EPREFIX}/usr/include" + EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" + EXPATLDFLAGS="-shared" + EXPATDYNAMIC=1 + ) + if use gromacs; then + EMAKEOPTS+=( + TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" + TNGINC="-I${EPREFIX}/usr/include" + TNGLDFLAGS="-shared" + TNGDYNAMIC=1 + ) + fi + if use sqlite; then + EMAKEOPTS+=( + SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" + SQLITEINC="-I${EPREFIX}/usr/include" + SQLITELDFLAGS="-shared" + SQLITEDYNAMIC=1 + ) + fi +} + +src_configure() { + local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" + rm -f configure.options && echo $myconf >> configure.options + + use cuda && myconf+=" CUDA" +# use mpi && myconf+=" MPI" + use tachyon && myconf+=" LIBTACHYON" + use xinerama && myconf+=" XINERAMA" + + export \ + PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ + PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ + PYTHON_LIBRARY="$(python_get_LIBS)" \ + NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ + NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" + + perl ./configure LINUX \ + ${myconf} || die +} + +src_compile() { + # build plugins + cd "${WORKDIR}"/plugins || die + + emake \ + ${EMAKEOPTS[@]} \ + LINUX + + # build vmd + cd "${S}"/src || die + emake +} + +src_install() { + # install plugins + cd "${WORKDIR}"/plugins || die + emake \ + PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ + distrib + + # install vmd + cd "${S}"/src || die + emake install + + # install docs + cd "${S}" || die + dodoc Announcement README doc/ig.pdf doc/ug.pdf + + # remove some of the things we don't want and need in + # /usr/lib + cd "${ED}"/usr/$(get_libdir)/vmd || die + rm -fr doc README Announcement LICENSE || \ + die "failed to clean up /usr/lib/vmd directory" + + # adjust path in vmd wrapper + sed \ + -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ + -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ + || die "failed to set up vmd wrapper script" + + # install icon and generate desktop entry + insinto /usr/share/pixmaps + doins "${WORKDIR}"/vmd-patches/vmd.png + eprefixify "${WORKDIR}"/vmd-patches/vmd.desktop + domenu "${WORKDIR}"/vmd-patches/vmd.desktop +} -- cgit v1.2.3