From 3dc4de6331223493015f198dc61854af604da86c Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 21 Oct 2024 04:04:33 +0100 Subject: gentoo auto-resync : 21:10:2024 - 04:04:33 --- sci-chemistry/Manifest.gz | Bin 8372 -> 8365 bytes sci-chemistry/gromacs/Manifest | 19 +++++----- .../files/gromacs-9999-Fix-build-with-torch.patch | 40 +++++++++++++++++++++ sci-chemistry/gromacs/gromacs-2020.7-r1.ebuild | 4 +++ sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild | 4 +++ sci-chemistry/gromacs/gromacs-2022.6.ebuild | 4 +++ sci-chemistry/gromacs/gromacs-2023.5.ebuild | 4 +++ sci-chemistry/gromacs/gromacs-2023.9999.ebuild | 4 +++ sci-chemistry/gromacs/gromacs-2024.3.ebuild | 4 +++ sci-chemistry/gromacs/gromacs-2024.9999.ebuild | 4 +++ sci-chemistry/gromacs/gromacs-9999.ebuild | 20 +++++++++-- sci-chemistry/gromacs/metadata.xml | 1 + 12 files changed, 97 insertions(+), 11 deletions(-) create mode 100644 sci-chemistry/gromacs/files/gromacs-9999-Fix-build-with-torch.patch (limited to 'sci-chemistry') diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz index 216d239bffcc..5680eb7a4d15 100644 Binary files a/sci-chemistry/Manifest.gz and b/sci-chemistry/Manifest.gz differ diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 251eafacf63d..c0e2e17fed77 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -2,6 +2,7 @@ AUX gromacs-2020-pytest.patch 1346 BLAKE2B 4b0b34bf4f46ec1acc3d0088ac11323938ee4 AUX gromacs-2021-cstdint-include.patch 361 BLAKE2B 98c09c5c82d722fc2fcc320741d8f8ed4f661eed7acd66e72ff1423aa2f0eac316add28f5b2b8b65a3b82c160d36aef6948078d3bad3248ffbd7bd63211980d1 SHA512 decf900c565ad9afed33e9a257a2364b63f0f872a5521dc6de4bdf6c7335e15b1cadaf06041f963573c116f1ffcf289a73d0b482df86740ff0874e0ee598825f AUX gromacs-2021-cuda-detection.patch 21849 BLAKE2B 4976321e5f2c5bc9b45feeaa29206d77d04d6148ca910652bd3f7923b6e74b7b10f039b5bcc4430826745f6d64b232c536a8ef75cce61556275942e94945acc0 SHA512 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254a8fd8fd9b12cdb0afbbd98539add499934781db7a2a249b1fd5dd077227d6a50a23cadb87e409aaf51a7188491dc4662f305142ebc8388b9ef823bbe7b45d SHA512 e9d3a2346f38a64f125bb20031f37e3ffde9c17b50f7812b682818417dc2c68aef0afec206a58f91e5c9af091ce198b97e998ecf6fc5b6c64d861cfda31be755 -MISC metadata.xml 1375 BLAKE2B 321b7db8536061655a6efaa40110f4858633921292eba465b85fe0cb50280842e511f2f11385fe5d62bbdfb40e9c0c76e8e986a1efce8eac25d52c438d7ed5f4 SHA512 cc61e0b477f6576079a0f7910475b9091c1c521fbb48efab365d355e3c0a80cd19e1ea9028cb269d37c2572546b1be66a210512e40ff0f2d6314d1b0138cdba6 +EBUILD gromacs-9999.ebuild 10089 BLAKE2B c141bdd9c2bb7c3fe3dcc4ec8c8d6c22e79809f58f71a1df57b1ef3de5c76378fd8ee660ff667c3ef2ced6160003392e3a2b2b6b17bf71343c62e330a4285062 SHA512 8f9beb4b0f07642b66efcbd62c386bd3795439e940ae0c279958dff629d8387ab32dda49b012de0115ce2bf7f341c90cda3c12046381a63806e013852e3d602c +MISC metadata.xml 1461 BLAKE2B fa82d5e83fa403fe8c31d076b2cf577d4299b2c97e993b02634c32e8c74088825f8ef61417bc1294947408fddc5b831b983574dafaac5c6975c06af74d890f00 SHA512 ce2b73c332585d9cfb7d1c7cbc49e5fb94f828191c8805463c03e3f215a7137253796ab49718148ea0c5a6ab85b45794b2fe5d213e0d35b2013ea41f6079d484 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 new file mode 100644 index 000000000000..3a42ba4000ed --- /dev/null +++ b/sci-chemistry/gromacs/files/gromacs-9999-Fix-build-with-torch.patch @@ -0,0 +1,40 @@ +From d997978fc0c644784ed929b0c48e153d5c1f1408 Mon Sep 17 00:00:00 2001 +From: Alexey Shvetsov +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 +--- + 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-2020.7-r1.ebuild b/sci-chemistry/gromacs/gromacs-2020.7-r1.ebuild index fa123d04defb..c93e5baf72ef 100644 --- a/sci-chemistry/gromacs/gromacs-2020.7-r1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.7-r1.ebuild @@ -49,6 +49,10 @@ CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14:= ) opencl? ( virtual/opencl ) + openmp? ( + sys-devel/gcc[openmp] + sys-devel/clang-runtime[openmp] + ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) lapack? ( virtual/lapack ) diff --git a/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild b/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild index 1b82d86998ee..8b99117678ed 100644 --- a/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild @@ -49,6 +49,10 @@ CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14:=[profiler] ) opencl? ( virtual/opencl ) + openmp? ( + sys-devel/gcc[openmp] + sys-devel/clang-runtime[openmp] + ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) lapack? ( virtual/lapack ) diff --git a/sci-chemistry/gromacs/gromacs-2022.6.ebuild b/sci-chemistry/gromacs/gromacs-2022.6.ebuild index 8ebb3ae9a8dd..92b1f497c860 100644 --- a/sci-chemistry/gromacs/gromacs-2022.6.ebuild +++ b/sci-chemistry/gromacs/gromacs-2022.6.ebuild @@ -45,6 +45,10 @@ CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] ) opencl? ( virtual/opencl ) + openmp? ( + sys-devel/gcc[openmp] + sys-devel/clang-runtime[openmp] + ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) lapack? ( virtual/lapack ) diff --git a/sci-chemistry/gromacs/gromacs-2023.5.ebuild b/sci-chemistry/gromacs/gromacs-2023.5.ebuild index a3319899d419..4ee08b22a7f0 100644 --- a/sci-chemistry/gromacs/gromacs-2023.5.ebuild +++ b/sci-chemistry/gromacs/gromacs-2023.5.ebuild @@ -45,6 +45,10 @@ CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] ) opencl? ( virtual/opencl ) + openmp? ( + sys-devel/gcc[openmp] + sys-devel/clang-runtime[openmp] + ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) lapack? ( virtual/lapack ) diff --git a/sci-chemistry/gromacs/gromacs-2023.9999.ebuild b/sci-chemistry/gromacs/gromacs-2023.9999.ebuild index a3319899d419..4ee08b22a7f0 100644 --- a/sci-chemistry/gromacs/gromacs-2023.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2023.9999.ebuild @@ -45,6 +45,10 @@ CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] ) opencl? ( virtual/opencl ) + openmp? ( + sys-devel/gcc[openmp] + sys-devel/clang-runtime[openmp] + ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) lapack? ( virtual/lapack ) diff --git a/sci-chemistry/gromacs/gromacs-2024.3.ebuild b/sci-chemistry/gromacs/gromacs-2024.3.ebuild index 33e343e23e7c..2101629ebc36 100644 --- a/sci-chemistry/gromacs/gromacs-2024.3.ebuild +++ b/sci-chemistry/gromacs/gromacs-2024.3.ebuild @@ -45,6 +45,10 @@ CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] ) opencl? ( virtual/opencl ) + openmp? ( + sys-devel/gcc[openmp] + sys-devel/clang-runtime[openmp] + ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) lapack? ( virtual/lapack ) diff --git a/sci-chemistry/gromacs/gromacs-2024.9999.ebuild b/sci-chemistry/gromacs/gromacs-2024.9999.ebuild index 33e343e23e7c..2101629ebc36 100644 --- a/sci-chemistry/gromacs/gromacs-2024.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2024.9999.ebuild @@ -45,6 +45,10 @@ CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] ) opencl? ( virtual/opencl ) + openmp? ( + sys-devel/gcc[openmp] + sys-devel/clang-runtime[openmp] + ) fftw? ( sci-libs/fftw:3.0= ) hwloc? ( sys-apps/hwloc:= ) lapack? ( virtual/lapack ) diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index 33e343e23e7c..9de42117f102 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -18,7 +18,7 @@ if [[ ${PV} = *9999* ]]; then https://gitlab.com/gromacs/gromacs.git https://github.com/gromacs/gromacs.git " - [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${PV:0:4}" inherit git-r3 else SRC_URI=" @@ -39,17 +39,23 @@ HOMEPAGE="https://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 clang clang-cuda 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}" +IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hdf5 +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] ) opencl? ( virtual/opencl ) + openmp? ( + sys-devel/gcc[openmp] + sys-devel/clang-runtime[openmp] + ) fftw? ( sci-libs/fftw:3.0= ) + hdf5? ( sci-libs/hdf5 ) hwloc? ( sys-apps/hwloc:= ) lapack? ( virtual/lapack ) mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi[cxx] ) + nnpot? ( sci-libs/caffe2[cuda=,opencl=] ) sci-libs/lmfit:= >=dev-cpp/muParser-2.3:= ${PYTHON_DEPS} @@ -88,6 +94,8 @@ DOCS=( AUTHORS README ) RESTRICT="!test? ( test )" +PATCHES=( "${FILESDIR}/${P}-Fix-build-with-torch.patch" ) + if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi @@ -178,6 +186,11 @@ src_prepare() { src_configure() { local mycmakeargs_pre=( ) extra fft_opts=( ) local acce="AUTO" + local nnpot="OFF" + + if use nnpot; then + nnpot="TORCH" + fi if use custom-cflags; then #go from slowest to fastest acceleration @@ -225,9 +238,12 @@ src_configure() { -DGMX_COOL_QUOTES=$(usex offensive) -DGMX_USE_TNG=$(usex tng) -DGMX_BUILD_MANUAL=$(usex build-manual) + -DGMX_USE_HDF5=$(usex hdf5) -DGMX_HWLOC=$(usex hwloc) -DGMX_DEFAULT_SUFFIX=off + -DGMX_BUILD_HELP=on -DGMX_SIMD="$acce" + -DGMX_NNPOT="$nnpot" -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" -DBUILD_TESTING=$(usex test) -DGMX_BUILD_UNITTESTS=$(usex test) diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml index 44ddb19d1d9d..518711308a02 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -19,6 +19,7 @@ Enable installing lagacy headers Enable HWLoc lib support Use external sci-libs/lmfit + Allow to use sci-libs/caffe2 for NN Potentials Enable opencl non-bonded kernels Single precision version of gromacs (default) Enable new trajectory format - tng -- cgit v1.2.3