* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/gromacs/files/, sci-chemistry/gromacs/
@ 2017-12-01 14:48 Alexey Shvetsov
0 siblings, 0 replies; 6+ messages in thread
From: Alexey Shvetsov @ 2017-12-01 14:48 UTC (permalink / raw
To: gentoo-commits
commit: 697442f898e427104b40bf9b0c4941c521e2f231
Author: Alexey Shvetsov <alexxy <AT> omrb <DOT> pnpi <DOT> spb <DOT> ru>
AuthorDate: Fri Dec 1 14:45:46 2017 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri Dec 1 14:48:30 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=697442f8
sci-chemistry/gromacs: Add opencl support and 2018_beta1
Package-Manager: Portage-2.3.16, Repoman-2.3.6
sci-chemistry/gromacs/Manifest | 2 +
.../gromacs/files/gromacs-2018-fix-build.patch | 71 ++++++
sci-chemistry/gromacs/gromacs-2018.9999.ebuild | 272 ++++++++++++++++++++
sci-chemistry/gromacs/gromacs-2018_beta1.ebuild | 276 +++++++++++++++++++++
sci-chemistry/gromacs/metadata.xml | 1 +
5 files changed, 622 insertions(+)
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index fb80356088e..8f7e43c5694 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -3,6 +3,7 @@ DIST gromacs-2016.2.tar.gz 27339623 SHA256 b6ac3632b848ab0c19f8f319dd5b58fcd09b8
DIST gromacs-2016.3.tar.gz 27342692 SHA256 7bf00e74a9d38b7cef9356141d20e4ba9387289cbbfd4d11be479ef932d77d27 SHA512 16593df0a52620766fb86cfeb16328793503f860cb07cdbbd503ba7f41e6430efb4848389b7179ca3907b57311162666d05224b454e1afb1b74b220f38498d86 WHIRLPOOL dfe31f212545ae2baf7373fde31f715a8df203d098d3ace915d4269b7bf16d06a1f91ead33ccbf8a17e9e0091b593818d0ce2eff151ce532238a8c27f5e20cda
DIST gromacs-2016.4.tar.gz 27368706 SHA256 4be9d3bfda0bdf3b5c53041e0b8344f7d22b75128759d9bfa9442fe65c289264 SHA512 69661d2a7a8a5259be277de35e2baa4b688d1f7bef225fc7d733a9b00c6ee135dcbad517c7c9f751121647c2fbd085f2c9cdf22dbd941c7ebc5d3b09e7e08f1f WHIRLPOOL c1586377d2a27f0b529370efb63e09ecca64cdb3d418fe9bc4f3ea1ff82ff5293d159834f4ed5d0136d801095d6f4085722e0d91bce873776fa4549853497ff7
DIST gromacs-2016.tar.gz 27321561 SHA256 aa0a27cd13050a4b70aacfbd169ddce2fe507c7e668f460ecf6cf32afcac5771 SHA512 756771baaa85a1d16e7d5b8e4c96bbd1c04c7acdc536a253886cff186316330f06d60d206a0159efb15f47f161c779d3757dc5dbceab8c097241c1382d376201 WHIRLPOOL 1cc3d3797e1aaf93e1e0cb2e71173896e33fee2bb03f4e97e06be3ab85842e6da3feaf8701425358f1d701e00159ff6ce3b24fa1488d5e8ef70a1acbb914361c
+DIST gromacs-2018-beta1.tar.gz 29857800 BLAKE2B 221ed414c1dc73b59df27dfb6dd22ef094152bba7a8346cd0d0164e9a0aa5463a7d836dfb13e98ac8cdbef2ae4a0503763a5c445a5e1c73815b3592d8b8f97fe SHA512 6e827b7b33589ccc7ef1d237c4e8ce06749a2c47f59956d383fdb59439a34874a9e0e3a3cca1d209425353a7dcf0f963de035dd0281d4c8aad0c921e6bbc7b93
DIST gromacs-5.0.4.tar.gz 26342095 SHA256 78068eeccc0b950018ddb45c41280e53c8bedae4639dca48e17c940f8896b23b SHA512 bc62b623bf71dcaa948aaf7563a3d3afa973da0702062848a20323db202e862dcee413197dacd1472866ccb40fce7709e283177b1c6c49514064f23e6c46b5ee WHIRLPOOL d8458d3d563e015e830622ae0c924e896765a6329ffe4cb1a31c7aef3c804f392d29e3f1db5617051e85058403422f7d69a160a6c7cc810564696d88f9d50bd4
DIST gromacs-5.1.3.tar.gz 27095702 SHA256 c962d9446939a9ba9905e7ca440c9306fd310f08600da3b744806bfd0eacccde SHA512 9ab26e1b2268f8d567b89b2d99d0b75b937b28edceaec56d17ca3243c76faa31255ffc0c45d762c7c693fe500b00e36ad43b80572d1d7f92dc87f9d2d98c0ba6 WHIRLPOOL bdd9c63ceb5e61963c4edd0af815cc34a3f237d8dee410c834b9b55bb82374de65b437828390a668282e50428b9907b887cd5265caf2a2007fc7673e7ab23733
DIST regressiontests-2016.1.tar.gz 67094518 SHA256 10c9f50ff3cb32cf629aa35e35d957965dcfce4af84a6569e6d65a16c4e09eb7 SHA512 fc01c802d81400373a147171881f3b7b9309402e8ffb08287ba393aefbb701ba93bbe0b9549ff6fa264a8befbba445c2d2c7450633063a724f78ec8ca81ae8c9 WHIRLPOOL e8c54164558fcbaa1e65e9280e438882c96bbbaa6c9389a2ee5aed37d70b83b6b36e95dd5141b4e64b303e3799411ee01cf04aa919f25014d172011e49714126
@@ -10,5 +11,6 @@ DIST regressiontests-2016.2.tar.gz 67095329 SHA256 53fa9ad062cc3e269fc6186db1ccb
DIST regressiontests-2016.3.tar.gz 67093968 SHA256 a3d1b09acfc61820dddd765a381f706190b4657606488f1e676becb859ea7ecc SHA512 ee87df9f339954da0e1f1b4c8b8d4deb574f3b73d174010a295a7a0e8bc462ead7691090ea7cf8ac3d984a6cd70f1cd22c3592fa161b2967061ae5ba2796286b WHIRLPOOL 2e986136f7faf6db108bc79e6fb6db9fe81d05f5af8bc27037b80cd25869f7cd4162d5cabc03994b36c71945910be79a217ff27f61463d1548cbdff6acd99f56
DIST regressiontests-2016.4.tar.gz 67643648 SHA256 d58d1a2a53c22c06e2dc03bd98ae1eea0a0d51696a1f20f635dfc394fa3da957 SHA512 367438b897a05e1cc0dcd1d3872fb6a0e9ff6b1146e9448d941d6517dce789f0c478d20cf0a4f3565070f132dc88872441aadb8b499f59efa0e1e4a6dd6a7135 WHIRLPOOL 695a3b7f81915247a90e95c0a83823c0297fba6ae6266195e86c61ec540ca58afd8d01ba236c5ddb3f44b41fb9301ba6a836b15cad1875bae42ba6276670daff
DIST regressiontests-2016.tar.gz 66908712 SHA256 30a72362f011fd9e3a8d33004018126f938536c13fcb70f590afc74beaec5406 SHA512 59902c1973c33ea8f003f21a737dc7cc64da3258112322eedc9834b53628134a6817d5ee5b3950c9bfd97a3a0580aef88ddef0609ef2c58693c96c7575651e01 WHIRLPOOL 9d210aed00ddfa57df47733169997ef04dec84c524eb5a9c5c6dd9b05ad9ec2d7f3c8a5a43f2ade9be166d80f35a260c04b1a48ac092f5969a213475bb63ae20
+DIST regressiontests-2018-beta1.tar.gz 67870909 BLAKE2B e9aff43331394c4a50cbc626d0327498f1571cf457e6b924f0cfe8eb688a9cd8d2b66c13c900da8737b124861fb567f9129aff840a294e92233b9a2214ff20d7 SHA512 509175cbbb8528d9bb1394c726c6e89291c2077880a3c4bf99a330ff457ca233ae74e771b8a753b0c94bba8de02840b1e5460b7c226e177742b1dee289833c0f
DIST regressiontests-5.0.4.tar.gz 65193251 SHA256 89ad9bc067035ac8f340319b538c446983d937b910067e871911d7afe2ecb3f0 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65 WHIRLPOOL e15ccab0a0beefac41aeff11e2e596e971167f1590eed159ff82c4a8e3aec1d234287be597026951904ecfe6099f30ef3bcd48f2098b9f5201bde62e15fbc4f9
DIST regressiontests-5.1.3.tar.gz 66994083 SHA256 fd5797dcfd29f7ae70857a438dcd4200a8006fce222f297892c8e90123993ebc SHA512 486e86eb3b75bae822abe82dac4e1098aa13723bd04214021f835a2f0b847303f015a9ececc33aa5ae63d31a2eeae07e512f22464b6c0e26d1286b0781578022 WHIRLPOOL 6ddb76859ee8fa3aba4d995e397970e6fd270acbdd6cc07ab77de0aebb0bfdbd2bd1107ae39d4410e750641047ae4b75c703eafad95a57ff42deb3bf1c742d08
diff --git a/sci-chemistry/gromacs/files/gromacs-2018-fix-build.patch b/sci-chemistry/gromacs/files/gromacs-2018-fix-build.patch
new file mode 100644
index 00000000000..2ed6a19f31b
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-2018-fix-build.patch
@@ -0,0 +1,71 @@
+From 81e68584512b21ec572d2561c25a1b19982aa0be Mon Sep 17 00:00:00 2001
+From: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
+Date: Fri, 1 Dec 2017 17:12:36 +0300
+Subject: [PATCH] Fix build with cmake 3.10 on Linux
+
+Without this fix cmake will fail with
+
+-- Detecting CXX compiler ABI info - done
+-- Detecting CXX compile features
+-- Detecting CXX compile features - done
+CMake Error at cmake/gmxCTestUtilities.cmake:56 (file):
+ file STRINGS file
+ "/var/tmp/portage/sci-chemistry/gromacs-2018_beta1/work/gromacs-2018_beta1_float/DartConfiguration.tcl"
+ cannot be read.
+Call Stack (most recent call first):
+ CMakeLists.txt:89 (gmx_ctest_init)
+
+-- Performing Test CXXFLAG_STD_CXX0X
+-- Performing Test CXXFLAG_STD_CXX0X - Success
+-- Performing Test CXX11_SUPPORTED
+-- Performing Test CXX11_SUPPORTED - Success
+....
+....
+....
+-- Looking for inttypes.h
+-- Looking for inttypes.h - found
+-- <<< Gentoo configuration >>>
+Build type Gentoo
+Install path /usr
+Compiler flags:
+C -march=core-avx2 -O2 -pipe -march=native -mtune=native -mfpmath=sse -mavx2
+C++ -march=core-avx2 -O2 -pipe -march=native -mtune=native -mfpmath=sse -mavx2 -std=c++11
+Linker flags:
+Executable -Wl,-O1 -Wl,--as-needed
+Module -Wl,-O1 -Wl,--as-needed
+Shared -Wl,-O1 -Wl,--as-needed
+
+-- Configuring incomplete, errors occurred!
+See also "/var/tmp/portage/sci-chemistry/gromacs-2018_beta1/work/gromacs-2018_beta1_float/CMakeFiles/CMakeOutput.log".
+See also "/var/tmp/portage/sci-chemistry/gromacs-2018_beta1/work/gromacs-2018_beta1_float/CMakeFiles/CMakeError.log".
+
+Change-Id: Ie04c2e5f5884f05c3648fed7289157e73fd8d81f
+Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
+---
+ cmake/gmxCTestUtilities.cmake | 10 ++++++----
+ 1 file changed, 6 insertions(+), 4 deletions(-)
+
+diff --git a/cmake/gmxCTestUtilities.cmake b/cmake/gmxCTestUtilities.cmake
+index 89715f910..3685df648 100644
+--- a/cmake/gmxCTestUtilities.cmake
++++ b/cmake/gmxCTestUtilities.cmake
+@@ -50,10 +50,12 @@ macro (gmx_ctest_init)
+ set(MEMORYCHECK_TYPE "AddressSanitizer")
+ endif()
+ include(CTest)
+- # At least with CMake 3.4.1 on OS X, AddressSanitizer support in CTest
+- # does not work without this...
+- set(_ctest_config_file "${PROJECT_BINARY_DIR}/DartConfiguration.tcl")
+- file(STRINGS ${_ctest_config_file} _existing REGEX "^CMakeCommand: ")
++ if(APPLE)
++ # At least with CMake 3.4.1 on OS X, AddressSanitizer support in CTest
++ # does not work without this...
++ set(_ctest_config_file "${PROJECT_BINARY_DIR}/DartConfiguration.tcl")
++ file(STRINGS ${_ctest_config_file} _existing REGEX "^CMakeCommand: ")
++ endif()
+ if (NOT _existing)
+ file(APPEND ${_ctest_config_file} "\nCMakeCommand: ${CMAKE_COMMAND}\n")
+ endif()
+--
+2.15.0
+
diff --git a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild b/sci-chemistry/gromacs/gromacs-2018.9999.ebuild
new file mode 100644
index 00000000000..315835fdc60
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-2018.9999.ebuild
@@ -0,0 +1,272 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+
+if [[ $PV = *9999* ]]; then
+ EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+ https://gerrit.gromacs.org/gromacs.git
+ https://github.com/gromacs/gromacs.git
+ http://repo.or.cz/r/gromacs.git"
+ [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
+ inherit git-r3
+ KEYWORDS=""
+else
+ SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
+ test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
+ KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+fi
+
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+# see COPYING for details
+# http://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 +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+ X? (
+ x11-libs/libX11
+ x11-libs/libSM
+ x11-libs/libICE
+ )
+ blas? ( virtual/blas )
+ cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+ opencl? ( virtual/opencl )
+ fftw? ( sci-libs/fftw:3.0 )
+ hwloc? ( sys-apps/hwloc )
+ lapack? ( virtual/lapack )
+ mkl? ( sci-libs/mkl )
+ mpi? ( virtual/mpi )
+ "
+DEPEND="${CDEPEND}
+ virtual/pkgconfig
+ doc? (
+ app-doc/doxygen
+ dev-texlive/texlive-latex
+ dev-texlive/texlive-latexextra
+ media-gfx/imagemagick
+ )"
+RDEPEND="${CDEPEND}"
+
+REQUIRED_USE="
+ || ( single-precision double-precision )
+ cuda? ( single-precision )
+ cuda? ( !opencl )
+ mkl? ( !blas !fftw !lapack )"
+
+DOCS=( AUTHORS README )
+
+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"
+}
+
+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-utils_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
+
+ mycmakeargs_pre+=(
+ "${fft_opts[@]}"
+ -DGMX_X11=$(usex X)
+ -DGMX_EXTERNAL_BLAS=$(usex blas)
+ -DGMX_EXTERNAL_LAPACK=$(usex lapack)
+ -DGMX_OPENMP=$(usex openmp)
+ -DGMX_COOL_QUOTES=$(usex offensive)
+ -DGMX_USE_TNG=$(usex tng)
+ -DGMX_BUILD_MANUAL=$(usex doc)
+ -DGMX_HWLOC=$(usex hwloc)
+ -DGMX_DEFAULT_SUFFIX=off
+ -DGMX_SIMD="$acce"
+ -DGMX_LIB_INSTALL_DIR="$(get_libdir)"
+ -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+ -DBUILD_TESTING=$(usex test)
+ -DGMX_BUILD_UNITTESTS=$(usex test)
+ ${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)
+ "${opencl[@]}"
+ "${cuda[@]}"
+ "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
+ -DGMX_BINARY_SUFFIX="${suffix}"
+ -DGMX_LIBS_SUFFIX="${suffix}"
+ )
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_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 ${cuda}
+ -DGMX_OPENMM=OFF
+ -DGMX_BUILD_MDRUN_ONLY=ON
+ -DBUILD_SHARED_LIBS=OFF
+ -DGMX_BUILD_MANUAL=OFF
+ -DGMX_BINARY_SUFFIX="_mpi${suffix}"
+ -DGMX_LIBS_SUFFIX="_mpi${suffix}"
+ )
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_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-utils_src_compile
+ # not 100% necessary for rel ebuilds as available from website
+ if use doc; then
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake-utils_src_compile manual
+ fi
+ use mpi || continue
+ einfo "Compiling for ${x} precision with mpi"
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+ cmake-utils_src_compile
+ done
+}
+
+src_test() {
+ for x in ${GMX_DIRS}; do
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake-utils_src_make check
+ done
+}
+
+src_install() {
+ for x in ${GMX_DIRS}; do
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \
+ cmake-utils_src_install
+ if use doc; then
+ newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+ fi
+ use mpi || continue
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+ cmake-utils_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-2018_beta1.ebuild b/sci-chemistry/gromacs/gromacs-2018_beta1.ebuild
new file mode 100644
index 00000000000..3e0dd9b80bc
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-2018_beta1.ebuild
@@ -0,0 +1,276 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+
+if [[ $PV = *9999* ]]; then
+ EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+ https://gerrit.gromacs.org/gromacs.git
+ https://github.com/gromacs/gromacs.git
+ http://repo.or.cz/r/gromacs.git"
+ [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
+ inherit git-r3
+ KEYWORDS=""
+else
+ SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
+ test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
+ KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+fi
+
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+# see COPYING for details
+# http://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 +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+ X? (
+ x11-libs/libX11
+ x11-libs/libSM
+ x11-libs/libICE
+ )
+ blas? ( virtual/blas )
+ cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+ opencl? ( virtual/opencl )
+ fftw? ( sci-libs/fftw:3.0 )
+ hwloc? ( sys-apps/hwloc )
+ lapack? ( virtual/lapack )
+ mkl? ( sci-libs/mkl )
+ mpi? ( virtual/mpi )
+ "
+DEPEND="${CDEPEND}
+ virtual/pkgconfig
+ doc? (
+ app-doc/doxygen
+ dev-texlive/texlive-latex
+ dev-texlive/texlive-latexextra
+ media-gfx/imagemagick
+ )"
+RDEPEND="${CDEPEND}"
+
+REQUIRED_USE="
+ || ( single-precision double-precision )
+ cuda? ( single-precision )
+ cuda? ( !opencl )
+ mkl? ( !blas !fftw !lapack )"
+
+DOCS=( AUTHORS README )
+
+PATCHES=(
+ "${FILESDIR}/${PN}-2018-fix-build.patch"
+ )
+
+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"
+}
+
+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-utils_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
+
+ mycmakeargs_pre+=(
+ "${fft_opts[@]}"
+ -DGMX_X11=$(usex X)
+ -DGMX_EXTERNAL_BLAS=$(usex blas)
+ -DGMX_EXTERNAL_LAPACK=$(usex lapack)
+ -DGMX_OPENMP=$(usex openmp)
+ -DGMX_COOL_QUOTES=$(usex offensive)
+ -DGMX_USE_TNG=$(usex tng)
+ -DGMX_BUILD_MANUAL=$(usex doc)
+ -DGMX_HWLOC=$(usex hwloc)
+ -DGMX_DEFAULT_SUFFIX=off
+ -DGMX_SIMD="$acce"
+ -DGMX_LIB_INSTALL_DIR="$(get_libdir)"
+ -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+ -DBUILD_TESTING=$(usex test)
+ -DGMX_BUILD_UNITTESTS=$(usex test)
+ ${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)
+ "${opencl[@]}"
+ "${cuda[@]}"
+ "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
+ -DGMX_BINARY_SUFFIX="${suffix}"
+ -DGMX_LIBS_SUFFIX="${suffix}"
+ )
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_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 ${cuda}
+ -DGMX_OPENMM=OFF
+ -DGMX_BUILD_MDRUN_ONLY=ON
+ -DBUILD_SHARED_LIBS=OFF
+ -DGMX_BUILD_MANUAL=OFF
+ -DGMX_BINARY_SUFFIX="_mpi${suffix}"
+ -DGMX_LIBS_SUFFIX="_mpi${suffix}"
+ )
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_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-utils_src_compile
+ # not 100% necessary for rel ebuilds as available from website
+ if use doc; then
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake-utils_src_compile manual
+ fi
+ use mpi || continue
+ einfo "Compiling for ${x} precision with mpi"
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+ cmake-utils_src_compile
+ done
+}
+
+src_test() {
+ for x in ${GMX_DIRS}; do
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake-utils_src_make check
+ done
+}
+
+src_install() {
+ for x in ${GMX_DIRS}; do
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \
+ cmake-utils_src_install
+ if use doc; then
+ newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+ fi
+ use mpi || continue
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+ cmake-utils_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/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index c9beb4a5a32..844b34dd014 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -15,6 +15,7 @@
</maintainer>
<use>
<flag name="cuda">Enable cuda non-bonded kernels</flag>
+ <flag name="opencl">Enable opencl non-bonded kernels</flag>
<flag name="double-precision">More precise calculations at the expense of speed</flag>
<flag name="single-precision">Single precision version of gromacs (default)</flag>
<flag name="boost">Enable external boost library</flag>
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/gromacs/files/, sci-chemistry/gromacs/
@ 2021-04-23 11:42 Alexey Shvetsov
0 siblings, 0 replies; 6+ messages in thread
From: Alexey Shvetsov @ 2021-04-23 11:42 UTC (permalink / raw
To: gentoo-commits
commit: 58f023bcae9893f344186cb4474ec86f94653cf7
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Fri Apr 23 11:41:19 2021 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri Apr 23 11:41:19 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=58f023bc
sci-chemistry/gromacs: Update patches
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>
.../gromacs/files/gromacs-2020-pytest.patch | 35 ++++++++++++++
.../gromacs/files/gromacs-2020_beta1-pytest.patch | 12 -----
.../gromacs/files/gromacs-2021-nblib.patch | 53 ++++++++++++++++++++++
sci-chemistry/gromacs/gromacs-2020.4.ebuild | 2 +-
sci-chemistry/gromacs/gromacs-2020.5.ebuild | 2 +-
sci-chemistry/gromacs/gromacs-2020.6.ebuild | 2 +-
sci-chemistry/gromacs/gromacs-2020.9999.ebuild | 2 +-
sci-chemistry/gromacs/gromacs-2021.1.ebuild | 5 +-
sci-chemistry/gromacs/gromacs-2021.9999.ebuild | 2 -
sci-chemistry/gromacs/gromacs-2021.ebuild | 2 +-
sci-chemistry/gromacs/gromacs-9999.ebuild | 2 -
11 files changed, 97 insertions(+), 22 deletions(-)
diff --git a/sci-chemistry/gromacs/files/gromacs-2020-pytest.patch b/sci-chemistry/gromacs/files/gromacs-2020-pytest.patch
new file mode 100644
index 00000000000..cc7730afecb
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-2020-pytest.patch
@@ -0,0 +1,35 @@
+From e4e1263776844d660c471e3d1203acf54cdc855f Mon Sep 17 00:00:00 2001
+From: Alexey Shvetsov <alexxyum@gmail.com>
+Date: Fri, 23 Apr 2021 13:21:24 +0300
+Subject: [PATCH 2/2] Allow to build python part without build testing enabled
+
+Signed-off-by: Alexey Shvetsov <alexxyum@gmail.com>
+---
+ python_packaging/src/CMakeLists.txt | 6 ++++--
+ 1 file changed, 4 insertions(+), 2 deletions(-)
+
+diff --git a/python_packaging/src/CMakeLists.txt b/python_packaging/src/CMakeLists.txt
+index c75549fc82..4f983fdd5f 100644
+--- a/python_packaging/src/CMakeLists.txt
++++ b/python_packaging/src/CMakeLists.txt
+@@ -1,7 +1,7 @@
+ #
+ # This file is part of the GROMACS molecular simulation package.
+ #
+-# Copyright (c) 2019,2020, by the GROMACS development team, led by
++# Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
+ # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ # and including many others, as listed in the AUTHORS file in the
+ # top-level source directory and at http://www.gromacs.org.
+@@ -252,5 +252,7 @@ endif()
+ # to the `check` target. Normal usage is to first install the Python package,
+ # then run `pytest` on the `tests` directory. Refer to gmxapi package documentation.
+ if(NOT GMXAPI_MASTER_PROJECT)
+- add_subdirectory(test)
++ if (BUILD_TESTING)
++ add_subdirectory(test)
++ endif()
+ endif()
+--
+2.31.1
+
diff --git a/sci-chemistry/gromacs/files/gromacs-2020_beta1-pytest.patch b/sci-chemistry/gromacs/files/gromacs-2020_beta1-pytest.patch
deleted file mode 100644
index 452987f38b9..00000000000
--- a/sci-chemistry/gromacs/files/gromacs-2020_beta1-pytest.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -urN gromacs-2020-beta1/python_packaging/src/CMakeLists.txt gromacs-2020-beta1-py/python_packaging/src/CMakeLists.txt
---- gromacs-2020-beta1/python_packaging/src/CMakeLists.txt 2019-09-12 05:48:57.000000000 +0300
-+++ gromacs-2020-beta1-py/python_packaging/src/CMakeLists.txt 2019-10-09 17:01:30.845304765 +0300
-@@ -201,5 +201,7 @@
- # to the `check` target. Normal usage is to first install the Python package,
- # then run `pytest` on the `tests` directory. Refer to gmxapi package documentation.
- if(NOT GMXAPI_MASTER_PROJECT)
-- add_subdirectory(test)
-+ if (GMX_BUILD_TESTING)
-+ add_subdirectory(test)
-+ endif()
- endif()
diff --git a/sci-chemistry/gromacs/files/gromacs-2021-nblib.patch b/sci-chemistry/gromacs/files/gromacs-2021-nblib.patch
new file mode 100644
index 00000000000..67ea6f6f63c
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-2021-nblib.patch
@@ -0,0 +1,53 @@
+From 5771842a06f483ad52781f4f2cdf5311ddb5cfa1 Mon Sep 17 00:00:00 2001
+From: Alexey Shvetsov <alexxyum@gmail.com>
+Date: Fri, 23 Apr 2021 13:15:10 +0300
+Subject: [PATCH 1/2] Allow to build and install nblib without GMX TESTS
+ enabled
+
+Without it you'll get error like this:
+
+ CMake Error at api/nblib/CMakeLists.txt:79 (add_dependencies):
+ Cannot add target-level dependencies to non-existent target "tests".
+
+ The add_dependencies works for top-level logical targets created by the
+ add_executable, add_library, or add_custom_target commands. If you want to
+ add file-level dependencies see the DEPENDS option of the add_custom_target
+ and add_custom_command commands.
+
+Signed-off-by: Alexey Shvetsov <alexxyum@gmail.com>
+---
+ api/nblib/CMakeLists.txt | 18 ++++++++++--------
+ 1 file changed, 10 insertions(+), 8 deletions(-)
+
+diff --git a/api/nblib/CMakeLists.txt b/api/nblib/CMakeLists.txt
+index a2ce06596e..51211c3d70 100644
+--- a/api/nblib/CMakeLists.txt
++++ b/api/nblib/CMakeLists.txt
+@@ -76,14 +76,16 @@ add_custom_target(nblib-tests
+ )
+ # Ensure that "make tests" builds all nblib tests so the top-level
+ # "make check" will work.
+-add_dependencies(tests nblib-tests)
+-
+-# this allows all nblib tests to be run with "make check-nblib"
+-add_custom_target(check-nblib
+- COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure -R NbLib
+- COMMENT "Running nblib tests"
+- USES_TERMINAL VERBATIM)
+-add_dependencies(check-nblib nblib-tests)
++if (BUILD_TESTING)
++ add_dependencies(tests nblib-tests)
++
++ # this allows all nblib tests to be run with "make check-nblib"
++ add_custom_target(check-nblib
++ COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure -R NbLib
++ COMMENT "Running nblib tests"
++ USES_TERMINAL VERBATIM)
++ add_dependencies(check-nblib nblib-tests)
++endif()
+
+ set(NBLIB_MAJOR 0)
+ set(NBLIB_MINOR 1)
+--
+2.31.1
+
diff --git a/sci-chemistry/gromacs/gromacs-2020.4.ebuild b/sci-chemistry/gromacs/gromacs-2020.4.ebuild
index 042897ab6e1..e8417cf5947 100644
--- a/sci-chemistry/gromacs/gromacs-2020.4.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.4.ebuild
@@ -85,7 +85,7 @@ if [[ ${PV} != *9999 ]]; then
S="${WORKDIR}/${PN}-${PV/_/-}"
fi
-PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" )
+PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" )
pkg_pretend() {
[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
diff --git a/sci-chemistry/gromacs/gromacs-2020.5.ebuild b/sci-chemistry/gromacs/gromacs-2020.5.ebuild
index c891ecb0585..393fdad3162 100644
--- a/sci-chemistry/gromacs/gromacs-2020.5.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.5.ebuild
@@ -85,7 +85,7 @@ if [[ ${PV} != *9999 ]]; then
S="${WORKDIR}/${PN}-${PV/_/-}"
fi
-PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" )
+PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" )
pkg_pretend() {
[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
diff --git a/sci-chemistry/gromacs/gromacs-2020.6.ebuild b/sci-chemistry/gromacs/gromacs-2020.6.ebuild
index c891ecb0585..393fdad3162 100644
--- a/sci-chemistry/gromacs/gromacs-2020.6.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.6.ebuild
@@ -85,7 +85,7 @@ if [[ ${PV} != *9999 ]]; then
S="${WORKDIR}/${PN}-${PV/_/-}"
fi
-PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" )
+PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" )
pkg_pretend() {
[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
diff --git a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
index c891ecb0585..393fdad3162 100644
--- a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
@@ -85,7 +85,7 @@ if [[ ${PV} != *9999 ]]; then
S="${WORKDIR}/${PN}-${PV/_/-}"
fi
-PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" )
+PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" )
pkg_pretend() {
[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
diff --git a/sci-chemistry/gromacs/gromacs-2021.1.ebuild b/sci-chemistry/gromacs/gromacs-2021.1.ebuild
index 6bb2a501176..2a4610540b5 100644
--- a/sci-chemistry/gromacs/gromacs-2021.1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.1.ebuild
@@ -85,7 +85,10 @@ if [[ ${PV} != *9999 ]]; then
S="${WORKDIR}/${PN}-${PV/_/-}"
fi
-PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" )
+PATCHES=(
+ "${FILESDIR}/${PN}-2020-pytest.patch"
+ "${FILESDIR}/${PN}-2021-nblib.patch"
+)
pkg_pretend() {
[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
diff --git a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
index 6bb2a501176..dbeed6f4fec 100644
--- a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
@@ -85,8 +85,6 @@ if [[ ${PV} != *9999 ]]; then
S="${WORKDIR}/${PN}-${PV/_/-}"
fi
-PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" )
-
pkg_pretend() {
[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
use openmp && ! tc-has-openmp && \
diff --git a/sci-chemistry/gromacs/gromacs-2021.ebuild b/sci-chemistry/gromacs/gromacs-2021.ebuild
index 6bb2a501176..06979262614 100644
--- a/sci-chemistry/gromacs/gromacs-2021.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.ebuild
@@ -85,7 +85,7 @@ if [[ ${PV} != *9999 ]]; then
S="${WORKDIR}/${PN}-${PV/_/-}"
fi
-PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" )
+PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" )
pkg_pretend() {
[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 6bb2a501176..dbeed6f4fec 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -85,8 +85,6 @@ if [[ ${PV} != *9999 ]]; then
S="${WORKDIR}/${PN}-${PV/_/-}"
fi
-PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" )
-
pkg_pretend() {
[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
use openmp && ! tc-has-openmp && \
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/gromacs/files/, sci-chemistry/gromacs/
@ 2022-02-21 16:37 Alexey Shvetsov
0 siblings, 0 replies; 6+ messages in thread
From: Alexey Shvetsov @ 2022-02-21 16:37 UTC (permalink / raw
To: gentoo-commits
commit: 3be10d9efadf209bd58dc917671b4584c49824a6
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 21 16:33:29 2022 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Mon Feb 21 16:36:36 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3be10d9e
sci-chemistry/gromacs: Fix build for musl
Closes: https://bugs.gentoo.org/828673
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>
.../gromacs/files/gromacs-2021-musl-stdint.patch | 25 ++++++++++++++++++++++
sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild | 2 ++
sci-chemistry/gromacs/gromacs-2021.5.ebuild | 2 ++
3 files changed, 29 insertions(+)
diff --git a/sci-chemistry/gromacs/files/gromacs-2021-musl-stdint.patch b/sci-chemistry/gromacs/files/gromacs-2021-musl-stdint.patch
new file mode 100644
index 000000000000..c94fc5598f91
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-2021-musl-stdint.patch
@@ -0,0 +1,25 @@
+From 8a38303c52fbca07c850e0c4cd03a783aabf9e49 Mon Sep 17 00:00:00 2001
+From: Paul Bauer <paul.bauer.q@gmail.com>
+Date: Mon, 21 Feb 2022 09:53:46 +0100
+Subject: [PATCH] Fix missing includes for musl libc
+
+Fixes #4404
+---
+ src/gromacs/math/vectypes.h | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/src/gromacs/math/vectypes.h b/src/gromacs/math/vectypes.h
+index d4d5211d11..bd9d31de20 100644
+--- a/src/gromacs/math/vectypes.h
++++ b/src/gromacs/math/vectypes.h
+@@ -40,6 +40,7 @@
+
+ #include <cassert>
+ #include <cmath>
++#include <cstdint>
+
+ #include <algorithm>
+ #include <type_traits>
+--
+2.35.1
+
diff --git a/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild b/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild
index 304523f0caed..9ebdeb01146c 100644
--- a/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild
@@ -83,6 +83,8 @@ DOCS=( AUTHORS README )
RESTRICT="!test? ( test )"
+PATCHES=( "${FILESDIR}/${PN}-2021-musl-stdint.patch" )
+
if [[ ${PV} != *9999 ]]; then
S="${WORKDIR}/${PN}-${PV/_/-}"
fi
diff --git a/sci-chemistry/gromacs/gromacs-2021.5.ebuild b/sci-chemistry/gromacs/gromacs-2021.5.ebuild
index d9c7e8a5269e..abf5ed8ec5ef 100644
--- a/sci-chemistry/gromacs/gromacs-2021.5.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.5.ebuild
@@ -83,6 +83,8 @@ DOCS=( AUTHORS README )
RESTRICT="!test? ( test )"
+PATCHES=( "${FILESDIR}/${PN}-2021-musl-stdint.patch" )
+
if [[ ${PV} != *9999 ]]; then
S="${WORKDIR}/${PN}-${PV/_/-}"
fi
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/gromacs/files/, sci-chemistry/gromacs/
@ 2023-04-25 9:50 Alexey Shvetsov
0 siblings, 0 replies; 6+ messages in thread
From: Alexey Shvetsov @ 2023-04-25 9:50 UTC (permalink / raw
To: gentoo-commits
commit: dfb5e4969403efb9f58cfea999c35f09d613c1a3
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 25 09:49:08 2023 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Tue Apr 25 09:50:01 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=dfb5e496
sci-chemistry/gromacs: Fix build with cuda-12
Thanks to pacho <AT> gentoo.org for patch
Closes: https://bugs.gentoo.org/900204
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>
.../files/gromacs-2021-cuda-detection.patch | 339 +++++++++++++++++++++
sci-chemistry/gromacs/gromacs-2021.7.ebuild | 5 +-
2 files changed, 343 insertions(+), 1 deletion(-)
diff --git a/sci-chemistry/gromacs/files/gromacs-2021-cuda-detection.patch b/sci-chemistry/gromacs/files/gromacs-2021-cuda-detection.patch
new file mode 100644
index 000000000000..8b458e96cb53
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-2021-cuda-detection.patch
@@ -0,0 +1,339 @@
+--- gromacs-2021.7/cmake/gmxManageNvccConfig.cmake 2023-01-31 12:45:45.000000000 +0100
++++ gromacs-2022.5/cmake/gmxManageNvccConfig.cmake 2023-02-03 12:53:34.000000000 +0100
+@@ -1,11 +1,9 @@
+ #
+ # This file is part of the GROMACS molecular simulation package.
+ #
+-# Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
+-# Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
+-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+-# and including many others, as listed in the AUTHORS file in the
+-# top-level source directory and at http://www.gromacs.org.
++# Copyright 2012- The GROMACS Authors
++# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
++# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
+ #
+ # GROMACS is free software; you can redistribute it and/or
+ # modify it under the terms of the GNU Lesser General Public License
+@@ -19,7 +17,7 @@
+ #
+ # You should have received a copy of the GNU Lesser General Public
+ # License along with GROMACS; if not, see
+-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
++# https://www.gnu.org/licenses, or write to the Free Software Foundation,
+ # Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ #
+ # If you want to redistribute modifications to GROMACS, please
+@@ -28,10 +26,10 @@
+ # consider code for inclusion in the official distribution, but
+ # derived work must not be called official GROMACS. Details are found
+ # in the README & COPYING files - if they are missing, get the
+-# official version at http://www.gromacs.org.
++# official version at https://www.gromacs.org.
+ #
+ # To help us fund GROMACS development, we humbly ask that you cite
+-# the research papers on the package. Check out http://www.gromacs.org.
++# the research papers on the package. Check out https://www.gromacs.org.
+
+ # Manage CUDA nvcc compilation configuration, try to be smart to ease the users'
+ # pain as much as possible:
+@@ -51,7 +49,7 @@
+ # glibc source shows that _FORCE_INLINES is only used in this string.h
+ # feature and performance of memcpy variants is unimportant for CUDA
+ # code in GROMACS. So this workaround is good enough to keep problems
+-# away from users installing GROMACS. See Issue #1942.
++# away from users installing GROMACS. See Issue #1982.
+ function(work_around_glibc_2_23)
+ try_compile(IS_GLIBC_2_23_OR_HIGHER ${CMAKE_BINARY_DIR} ${CMAKE_SOURCE_DIR}/cmake/TestGlibcVersion.cpp)
+ if(IS_GLIBC_2_23_OR_HIGHER)
+@@ -83,67 +81,158 @@
+ mark_as_advanced(CUDA_HOST_COMPILER CUDA_HOST_COMPILER_OPTIONS)
+ endif()
+
++# We would like to be helpful and reject the host compiler with a
++# clear error message at configure time, rather than let nvcc
++# later reject the host compiler as not supported when the first
++# CUDA source file is built. We've implemented that for current
++# nvcc running on Unix-like systems, but e.g. changes to nvcc
++# will further affect the limited portability of this checking
++# code. Set the CMake variable GMX_NVCC_WORKS on if you want to
++# bypass this check.
++if((_cuda_nvcc_executable_or_flags_changed OR CUDA_HOST_COMPILER_CHANGED OR NOT GMX_NVCC_WORKS) AND NOT WIN32)
++ message(STATUS "Check for working NVCC/C++ compiler combination with nvcc '${CUDA_NVCC_EXECUTABLE}'")
++ execute_process(COMMAND ${CUDA_NVCC_EXECUTABLE} --compiler-bindir=${CUDA_HOST_COMPILER} -c ${CUDA_NVCC_FLAGS} ${CUDA_NVCC_FLAGS_${_build_type}} ${CMAKE_SOURCE_DIR}/cmake/TestCUDA.cu
++ RESULT_VARIABLE _cuda_test_res
++ OUTPUT_VARIABLE _cuda_test_out
++ ERROR_VARIABLE _cuda_test_err
++ OUTPUT_STRIP_TRAILING_WHITESPACE)
++
++ if(${_cuda_test_res})
++ message(STATUS "Check for working NVCC/C compiler combination - broken")
++ message(STATUS "${CUDA_NVCC_EXECUTABLE} standard output: '${_cuda_test_out}'")
++ message(STATUS "${CUDA_NVCC_EXECUTABLE} standard error: '${_cuda_test_err}'")
++ if(${_cuda_test_err} MATCHES "nsupported")
++ message(FATAL_ERROR "NVCC/C++ compiler combination does not seem to be supported. CUDA frequently does not support the latest versions of the host compiler, so you might want to try an earlier C++ compiler version and make sure your CUDA compiler and driver are as recent as possible. Set the GMX_NVCC_WORKS CMake cache variable to bypass this check if you know what you are doing.")
++ elseif(CMAKE_CXX_COMPILER_ID MATCHES "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 11.2 AND CUDA_VERSION VERSION_GREATER 11.4 AND CUDA_VERSION VERSION_LESS 11.7) # Issue #4574, #4641
++ # Above, we should be checking for VERSION_LESS 11.6.2, but CUDA_VERSION is only "major.minor"
++ message(FATAL_ERROR "CUDA versions 11.5-11.6.1 are known to be incompatible with some GCC 11.x. Use a different GCC or update your CUDA installation to at least CUDA 11.6.2")
++ else()
++ message(FATAL_ERROR "CUDA compiler does not seem to be functional or is not compatible with the host compiler. Set the GMX_NVCC_WORKS CMake cache variable to bypass this check if you know what you are doing.")
++ endif()
++ elseif(NOT GMX_CUDA_TEST_COMPILER_QUIETLY)
++ message(STATUS "Check for working NVCC/C++ compiler combination - works")
++ set(GMX_NVCC_WORKS TRUE CACHE INTERNAL "Nvcc can compile a trivial test program")
++ endif()
++endif() # GMX_CHECK_NVCC
++
++# Tests a single flag to use with nvcc.
++#
++# If the flags are accepted, they are appended to the variable named
++# in the first argument. The cache variable named in the second
++# argument is used to avoid rerunning the check in future invocations
++# of cmake. The list of flags to check follows these two required
++# arguments.
++#
++# Note that a space-separated string of flags, or a flag-value pair
++# separated by spaces will not work. Use the single-argument forms
++# accepted by nvcc, like "--arg=value".
++#
++# As this code is not yet tested on Windows, it always accepts the
++# flags in that case.
++function(gmx_add_nvcc_flag_if_supported _output_variable_name_to_append_to _flags_cache_variable_name)
++ # If the check has already been run, do not re-run it
++ if (NOT ${_flags_cache_variable_name} AND NOT WIN32)
++ message(STATUS "Checking if nvcc accepts flags ${ARGN}")
++ # See detailed comment about gcc 7 below
++ if (CMAKE_CXX_COMPILER_ID MATCHES "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 8)
++ set(_cache_variable_value TRUE)
++ message(STATUS "Checking if nvcc accepts flags ${ARGN} - Assuming success when using gcc 7")
++ else()
++ if(NOT(CMAKE_CXX_COMPILER_ID MATCHES "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 11))
++ set(CCBIN "--compiler-bindir=${CUDA_HOST_COMPILER}")
++ endif()
++ execute_process(
++ COMMAND ${CUDA_NVCC_EXECUTABLE} ${ARGN} ${CCBIN} "${CMAKE_SOURCE_DIR}/cmake/TestCUDA.cu"
++ RESULT_VARIABLE _cuda_success
++ OUTPUT_QUIET
++ ERROR_QUIET
++ )
++ # Convert the success value to a boolean and report status
++ if (_cuda_success EQUAL 0)
++ set(_cache_variable_value TRUE)
++ message(STATUS "Checking if nvcc accepts flags ${ARGN} - Success")
++ else()
++ set(_cache_variable_value FALSE)
++ message(STATUS "Checking if nvcc accepts flags ${ARGN} - Failed")
++ endif()
++ endif()
++ set(${_flags_cache_variable_name} ${_cache_variable_value} CACHE BOOL "Whether NVCC supports flag(s) ${ARGN}")
++ endif()
++ # Append the flags to the output variable if they have been tested to work
++ if (${_flags_cache_variable_name} OR WIN32)
++ list(APPEND ${_output_variable_name_to_append_to} ${ARGN})
++ set(${_output_variable_name_to_append_to} ${${_output_variable_name_to_append_to}} PARENT_SCOPE)
++ endif()
++endfunction()
++
++# Versions of gcc 7 have differing behavior when executing
++#
++# nvcc $args --compiler-bindir=gcc TestCUDA.cu
++#
++# and would need e.g. adding -lstdc++ to the command line so that
++# linking of a C++/CUDA object by the C-compiler flavor of gcc works.
++# This means we can't reliably test compiler flags in this case
++# without risking creating other problems. Instead we assume (above)
++# that all compiler flags will work, and issue this warning.
++# We also want to skip this warning during GROMACS CI testing.
++if (CMAKE_CXX_COMPILER_ID MATCHES "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 8
++ AND NOT DEFINED ENV{GITLAB_CI})
++ message(WARNING "You are using gcc version 7 with the CUDA compiler nvcc. GROMACS cannot reliably test compiler arguments for this combination, so if you later experience errors in building GROMACS, please use a more recent version of gcc.")
++endif()
++
+ # If any of these manual override variables for target CUDA GPU architectures
+ # or virtual architecture is set, parse the values and assemble the nvcc
+ # command line for these. Otherwise use our defaults.
+ # Note that the manual override variables require a semicolon separating
+ # architecture codes.
++set(GMX_CUDA_NVCC_GENCODE_FLAGS)
+ if (GMX_CUDA_TARGET_SM OR GMX_CUDA_TARGET_COMPUTE)
+- set(GMX_CUDA_NVCC_GENCODE_FLAGS)
+ set(_target_sm_list ${GMX_CUDA_TARGET_SM})
+ foreach(_target ${_target_sm_list})
+- list(APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_${_target},code=sm_${_target}")
++ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_${_target} "--generate-code=arch=compute_${_target},code=sm_${_target}")
++ if (NOT NVCC_HAS_GENCODE_COMPUTE_AND_SM_${_target} AND NOT WIN32)
++ message(FATAL_ERROR "Your choice of ${_target} in GMX_CUDA_TARGET_SM was not accepted by nvcc, please choose a target that it accepts")
++ endif()
+ endforeach()
+ set(_target_compute_list ${GMX_CUDA_TARGET_COMPUTE})
+ foreach(_target ${_target_compute_list})
+- list(APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_${_target},code=compute_${_target}")
++ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_${_target} --generate-code=arch=compute_${_target},code=compute_${_target})
++ if (NOT NVCC_HAS_GENCODE_COMPUTE_${_target} AND NOT WIN32)
++ message(FATAL_ERROR "Your choice of ${_target} in GMX_CUDA_TARGET_COMPUTE was not accepted by nvcc, please choose a target that it accepts")
++ endif()
+ endforeach()
+ else()
+ # Set the CUDA GPU architectures to compile for:
+- # - with CUDA >=9.0 CC 7.0 is supported and CC 2.0 is no longer supported
+- # => compile sm_30, sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70 SASS, and compute_35, compute_70 PTX
+- # - with CUDA >=10.0 CC 7.5 is supported
+- # => compile sm_30, sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70, sm_75 SASS, and compute_35, compute_75 PTX
+ # - with CUDA >=11.0 CC 8.0 is supported
+ # => compile sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70, sm_75, sm_80 SASS, and compute_35, compute_80 PTX
+
+ # First add flags that trigger SASS (binary) code generation for physical arch
+- if(CUDA_VERSION VERSION_LESS "11.0")
+- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_30,code=sm_30")
+- endif()
+- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_35,code=sm_35")
+- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_37,code=sm_37")
+- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_50,code=sm_50")
+- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_52,code=sm_52")
+- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_60,code=sm_60")
+- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_61,code=sm_61")
+- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_70,code=sm_70")
+- if(NOT CUDA_VERSION VERSION_LESS "10.0")
+- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_75,code=sm_75")
+- endif()
+- if(NOT CUDA_VERSION VERSION_LESS "11.0")
+- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_80,code=sm_80")
+- # Requesting sm or compute 35, 37, or 50 triggers deprecation messages with
+- # nvcc 11.0, which we need to suppress for use in CI
+- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-Wno-deprecated-gpu-targets")
+- endif()
+- if(NOT CUDA_VERSION VERSION_LESS "11.1")
+- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_86,code=sm_86")
++ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_35 --generate-code=arch=compute_35,code=sm_35)
++ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_37 --generate-code=arch=compute_37,code=sm_37)
++ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_50 --generate-code=arch=compute_50,code=sm_50)
++ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_52 --generate-code=arch=compute_52,code=sm_52)
++ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_60 --generate-code=arch=compute_60,code=sm_60)
++ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_61 --generate-code=arch=compute_61,code=sm_61)
++ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_70 --generate-code=arch=compute_70,code=sm_70)
++ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_75 --generate-code=arch=compute_75,code=sm_75)
++ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_80 --generate-code=arch=compute_80,code=sm_80)
++ # Don't attempt to add newest architectures with old GNU compiler, to avoid issues in CI
++ # related to being unable to test which flags are supported
++ if (NOT (CMAKE_CXX_COMPILER_ID MATCHES "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 8))
++ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_86 --generate-code=arch=compute_86,code=sm_86)
++ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_89 --generate-code=arch=compute_89,code=sm_89)
++ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_AND_SM_90 --generate-code=arch=compute_90,code=sm_90)
+ endif()
++ # Requesting sm or compute 35, 37, or 50 triggers deprecation messages with
++ # nvcc 11.0, which we need to suppress for use in CI
++ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_WARNING_NO_DEPRECATED_GPU_TARGETS -Wno-deprecated-gpu-targets)
+
+ # Next add flags that trigger PTX code generation for the
+ # newest supported virtual arch that's useful to JIT to future architectures
+ # as well as an older one suitable for JIT-ing to any rare intermediate arch
+ # (like that of Jetson / Drive PX devices)
+- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_35,code=compute_35")
+- if(CUDA_VERSION VERSION_LESS "11.0")
+- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_32,code=compute_32")
+- else()
+- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_53,code=compute_53")
+- endif()
+- if(NOT CUDA_VERSION VERSION_LESS "11.0")
+- list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_80,code=compute_80")
+- endif()
++ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_53 --generate-code=arch=compute_53,code=sm_53)
++ gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_GENCODE_FLAGS NVCC_HAS_GENCODE_COMPUTE_80 --generate-code=arch=compute_80,code=sm_80)
+ endif()
+
+ if (GMX_CUDA_TARGET_SM)
+@@ -158,27 +247,20 @@
+ # FindCUDA.cmake is unaware of the mechanism used by cmake to embed
+ # the compiler flag for the required C++ standard in the generated
+ # build files, so we have to pass it ourselves
+-if (CUDA_VERSION VERSION_LESS 11.0)
+- # CUDA doesn't formally support C++17 until version 11.0, so for
+- # now host-side code that compiles with CUDA is restricted to
+- # C++14. This needs to be expressed formally for older CUDA
+- # version.
++
++# gcc-7 pre-dated C++17, so uses the -std=c++1z compiler flag for it,
++# which modern nvcc does not recognize. So we work around that by
++# compiling in C++14 mode. Clang doesn't have this problem because nvcc
++# only supports version of clang that already understood -std=c++17
++if (CMAKE_CXX_COMPILER_ID MATCHES "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 8)
+ list(APPEND GMX_CUDA_NVCC_FLAGS "${CMAKE_CXX14_STANDARD_COMPILE_OPTION}")
+ else()
+- # gcc-7 pre-dated C++17, so uses the -std=c++1z compiler flag for it,
+- # which modern nvcc does not recognize. So we work around that by
+- # compiling in C++14 mode. Clang doesn't have this problem because nvcc
+- # only supports version of clang that already understood -std=c++17
+- if (CMAKE_CXX_COMPILER_ID MATCHES "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 8)
+- list(APPEND GMX_CUDA_NVCC_FLAGS "${CMAKE_CXX14_STANDARD_COMPILE_OPTION}")
+- else()
+- list(APPEND GMX_CUDA_NVCC_FLAGS "${CMAKE_CXX17_STANDARD_COMPILE_OPTION}")
+- endif()
++ list(APPEND GMX_CUDA_NVCC_FLAGS "${CMAKE_CXX17_STANDARD_COMPILE_OPTION}")
+ endif()
+
+ # assemble the CUDA flags
+ list(APPEND GMX_CUDA_NVCC_FLAGS "${GMX_CUDA_NVCC_GENCODE_FLAGS}")
+-list(APPEND GMX_CUDA_NVCC_FLAGS "-use_fast_math")
++gmx_add_nvcc_flag_if_supported(GMX_CUDA_NVCC_FLAGS NVCC_HAS_USE_FAST_MATH -use_fast_math)
+
+ # assemble the CUDA host compiler flags
+ list(APPEND GMX_CUDA_NVCC_FLAGS "${CUDA_HOST_COMPILER_OPTIONS}")
+@@ -187,12 +269,18 @@
+ # CUDA header cuda_runtime_api.h in at least CUDA 10.1 uses 0
+ # where nullptr would be preferable. GROMACS can't fix these, so
+ # must suppress them.
+- GMX_TEST_CXXFLAG(CXXFLAGS_NO_ZERO_AS_NULL_POINTER_CONSTANT "-Wno-zero-as-null-pointer-constant" NVCC_CLANG_SUPPRESSIONS_CXXFLAGS)
++ GMX_TEST_CXXFLAG(HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT "-Wno-zero-as-null-pointer-constant" NVCC_CLANG_SUPPRESSIONS_CXXFLAGS)
+
+ # CUDA header crt/math_functions.h in at least CUDA 10.x and 11.1
+ # used throw() specifications that are deprecated in more recent
+ # C++ versions. GROMACS can't fix these, so must suppress them.
+- GMX_TEST_CXXFLAG(CXXFLAGS_NO_DEPRECATED_DYNAMIC_EXCEPTION_SPEC "-Wno-deprecated-dynamic-exception-spec" NVCC_CLANG_SUPPRESSIONS_CXXFLAGS)
++ GMX_TEST_CXXFLAG(HAS_WARNING_NO_DEPRECATED_DYNAMIC_EXCEPTION_SPEC "-Wno-deprecated-dynamic-exception-spec" NVCC_CLANG_SUPPRESSIONS_CXXFLAGS)
++
++ # CUDA headers cuda_runtime.h and channel_descriptor.h in at least
++ # CUDA 11.0 uses many C-style casts, which are ncessary for this
++ # header to work for C. GROMACS can't fix these, so must suppress
++ # the warnings they generate
++ GMX_TEST_CXXFLAG(HAS_WARNING_NO_OLD_STYLE_CAST "-Wno-old-style-cast" NVCC_CLANG_SUPPRESSIONS_CXXFLAGS)
+
+ # Add these flags to those used for the host compiler. The
+ # "-Xcompiler" prefix directs nvcc to only use them for host
+@@ -205,37 +293,6 @@
+ string(TOUPPER "${CMAKE_BUILD_TYPE}" _build_type)
+ gmx_check_if_changed(_cuda_nvcc_executable_or_flags_changed CUDA_NVCC_EXECUTABLE CUDA_NVCC_FLAGS CUDA_NVCC_FLAGS_${_build_type})
+
+-# We would like to be helpful and reject the host compiler with a
+-# clear error message at configure time, rather than let nvcc
+-# later reject the host compiler as not supported when the first
+-# CUDA source file is built. We've implemented that for current
+-# nvcc running on Unix-like systems, but e.g. changes to nvcc
+-# will further affect the limited portability of this checking
+-# code. Set the CMake variable GMX_NVCC_WORKS on if you want to
+-# bypass this check.
+-if((_cuda_nvcc_executable_or_flags_changed OR CUDA_HOST_COMPILER_CHANGED OR NOT GMX_NVCC_WORKS) AND NOT WIN32)
+- message(STATUS "Check for working NVCC/C++ compiler combination with nvcc '${CUDA_NVCC_EXECUTABLE}'")
+- execute_process(COMMAND ${CUDA_NVCC_EXECUTABLE} -ccbin ${CUDA_HOST_COMPILER} -c ${CUDA_NVCC_FLAGS} ${CUDA_NVCC_FLAGS_${_build_type}} ${CMAKE_SOURCE_DIR}/cmake/TestCUDA.cu
+- RESULT_VARIABLE _cuda_test_res
+- OUTPUT_VARIABLE _cuda_test_out
+- ERROR_VARIABLE _cuda_test_err
+- OUTPUT_STRIP_TRAILING_WHITESPACE)
+-
+- if(${_cuda_test_res})
+- message(STATUS "Check for working NVCC/C compiler combination - broken")
+- message(STATUS "${CUDA_NVCC_EXECUTABLE} standard output: '${_cuda_test_out}'")
+- message(STATUS "${CUDA_NVCC_EXECUTABLE} standard error: '${_cuda_test_err}'")
+- if(${_cuda_test_err} MATCHES "nsupported")
+- message(FATAL_ERROR "NVCC/C++ compiler combination does not seem to be supported. CUDA frequently does not support the latest versions of the host compiler, so you might want to try an earlier C++ compiler version and make sure your CUDA compiler and driver are as recent as possible.")
+- else()
+- message(FATAL_ERROR "CUDA compiler does not seem to be functional.")
+- endif()
+- elseif(NOT GMX_CUDA_TEST_COMPILER_QUIETLY)
+- message(STATUS "Check for working NVCC/C++ compiler combination - works")
+- set(GMX_NVCC_WORKS TRUE CACHE INTERNAL "Nvcc can compile a trivial test program")
+- endif()
+-endif() # GMX_CHECK_NVCC
+-
+
+ # The flags are set as local variables which shadow the cache variables. The cache variables
+ # (can be set by the user) are appended. This is done in a macro to set the flags when all
diff --git a/sci-chemistry/gromacs/gromacs-2021.7.ebuild b/sci-chemistry/gromacs/gromacs-2021.7.ebuild
index 8cb244317617..1a6dbcab47f4 100644
--- a/sci-chemistry/gromacs/gromacs-2021.7.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.7.ebuild
@@ -85,7 +85,10 @@ DOCS=( AUTHORS README )
RESTRICT="!test? ( test )"
-PATCHES=( "${FILESDIR}/${PN}-2021-musl-stdint.patch" )
+PATCHES=(
+ "${FILESDIR}/${PN}-2021-musl-stdint.patch"
+ "${FILESDIR}/${PN}-2021-cuda-detection.patch"
+)
if [[ ${PV} != *9999 ]]; then
S="${WORKDIR}/${PN}-${PV/_/-}"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/gromacs/files/, sci-chemistry/gromacs/
@ 2023-10-20 13:14 Pacho Ramos
0 siblings, 0 replies; 6+ messages in thread
From: Pacho Ramos @ 2023-10-20 13:14 UTC (permalink / raw
To: gentoo-commits
commit: 05f1ec32b757a08781ce81f883ec0873b7ee6d99
Author: Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Fri Oct 20 12:11:55 2023 +0000
Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Fri Oct 20 13:14:37 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=05f1ec32
sci-chemistry/gromacs: Fix compilation with gcc-13
Closes: https://bugs.gentoo.org/915694
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>
.../gromacs/files/gromacs-2021-cstdint-include.patch | 12 ++++++++++++
sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild | 1 +
2 files changed, 13 insertions(+)
diff --git a/sci-chemistry/gromacs/files/gromacs-2021-cstdint-include.patch b/sci-chemistry/gromacs/files/gromacs-2021-cstdint-include.patch
new file mode 100644
index 000000000000..5952aa3dd8e8
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-2021-cstdint-include.patch
@@ -0,0 +1,12 @@
+# https://bugs.gentoo.org/915694
+# Not needed for newer branches, that greatly refactored the code
+--- a/src/gromacs/utility/flags.h~ 2023-01-31 12:45:46.000000000 +0100
++++ b/src/gromacs/utility/flags.h 2023-10-16 10:15:24.087340444 +0200
+@@ -42,7 +42,7 @@
+ */
+ #ifndef GMX_UTILITY_FLAGS_H
+ #define GMX_UTILITY_FLAGS_H
+-
++#include <cstdint>
+ namespace gmx
+ {
diff --git a/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild b/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild
index f209fdeadb3e..ba32eebe7d85 100644
--- a/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild
@@ -88,6 +88,7 @@ RESTRICT="!test? ( test )"
PATCHES=(
"${FILESDIR}/${PN}-2021-musl-stdint.patch"
"${FILESDIR}/${PN}-2021-cuda-detection.patch"
+ "${FILESDIR}/${PN}-2021-cstdint-include.patch"
)
if [[ ${PV} != *9999 ]]; then
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/gromacs/files/, sci-chemistry/gromacs/
@ 2024-10-25 11:08 Alexey Shvetsov
0 siblings, 0 replies; 6+ messages in thread
From: Alexey Shvetsov @ 2024-10-25 11:08 UTC (permalink / raw
To: gentoo-commits
commit: 2aa68c469487247f00d2d76f56c6e41cd45d2ace
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Fri Oct 25 11:07:42 2024 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri Oct 25 11:07:42 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2aa68c46
sci-chemistry/gromacs: drop upstreamed patch
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>
.../files/gromacs-9999-Fix-build-with-torch.patch | 40 ----------------------
sci-chemistry/gromacs/gromacs-9999.ebuild | 2 --
2 files changed, 42 deletions(-)
diff --git a/sci-chemistry/gromacs/files/gromacs-9999-Fix-build-with-torch.patch b/sci-chemistry/gromacs/files/gromacs-9999-Fix-build-with-torch.patch
deleted file mode 100644
index 3a42ba4000ed..000000000000
--- a/sci-chemistry/gromacs/files/gromacs-9999-Fix-build-with-torch.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-From d997978fc0c644784ed929b0c48e153d5c1f1408 Mon Sep 17 00:00:00 2001
-From: Alexey Shvetsov <alexxyum@gmail.com>
-Date: Sat, 19 Oct 2024 21:22:07 +0300
-Subject: [PATCH] Fix build with torch if non default C{XX}_FLAGS set
-MIME-Version: 1.0
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-
-This should fix build colvars with torch if torch was built with non
-default C{,XX}_FLAGS
-
-Erorr info:
-
-FAILED: src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o
-/usr/bin/x86_64-pc-linux-gnu-g++ -DCOLVARS_TORCH -DGMX_DOUBLE=0 -I/usr/include/torch/csrc/api/include -O2 -pipe -march=skylake -mtune=skylake -std=c++17 -fPIC "-O2 -pipe -march=skylake -mtune=skylake" -D_GLIBCXX_USE_CXX11_ABI=1 -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-9999/work/gromacs-9999/src/external/colvars/colvar.cpp
-cc1plus: error: argument to ‘-O’ should be a non-negative integer, ‘g’, ‘s’, ‘z’ or ‘fast’
-
-This caused by doubling quoted C{,XX}_FLAGS
-
-Signed-off-by: Alexey Shvetsov <alexxyum@gmail.com>
----
- cmake/gmxManageColvars.cmake | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/cmake/gmxManageColvars.cmake b/cmake/gmxManageColvars.cmake
-index 509d56e116..f49c820fa0 100644
---- a/cmake/gmxManageColvars.cmake
-+++ b/cmake/gmxManageColvars.cmake
-@@ -52,7 +52,7 @@ function(gmx_manage_colvars)
- target_link_libraries(colvars_objlib PRIVATE OpenMP::OpenMP_CXX)
- endif()
- if(GMX_TORCH)
-- target_compile_options(colvars_objlib PRIVATE ${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS})
-+ target_compile_options(colvars_objlib PRIVATE ${TORCH_CXX_FLAGS})
- target_include_directories(colvars_objlib PRIVATE ${TORCH_INCLUDE_DIRS})
- target_compile_definitions(colvars_objlib PRIVATE -DCOLVARS_TORCH)
- endif()
---
-2.47.0
-
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 9de42117f102..a05143862722 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -94,8 +94,6 @@ DOCS=( AUTHORS README )
RESTRICT="!test? ( test )"
-PATCHES=( "${FILESDIR}/${P}-Fix-build-with-torch.patch" )
-
if [[ ${PV} != *9999 ]]; then
S="${WORKDIR}/${PN}-${PV/_/-}"
fi
^ permalink raw reply related [flat|nested] 6+ messages in thread
end of thread, other threads:[~2024-10-25 11:08 UTC | newest]
Thread overview: 6+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2023-04-25 9:50 [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/gromacs/files/, sci-chemistry/gromacs/ Alexey Shvetsov
-- strict thread matches above, loose matches on Subject: below --
2024-10-25 11:08 Alexey Shvetsov
2023-10-20 13:14 Pacho Ramos
2022-02-21 16:37 Alexey Shvetsov
2021-04-23 11:42 Alexey Shvetsov
2017-12-01 14:48 Alexey Shvetsov
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox