diff --git a/science/gromacs/Makefile b/science/gromacs/Makefile index e0f23553aa1c..28a7df372742 100644 --- a/science/gromacs/Makefile +++ b/science/gromacs/Makefile @@ -1,98 +1,97 @@ # Created by: Stephen Montgomery-Smith PORTNAME= gromacs -DISTVERSION= 2021.5 -PORTREVISION= 2 +DISTVERSION= 2022.1 CATEGORIES= science MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/ MAINTAINER= yuri@FreeBSD.org COMMENT= Compute molecular dynamics LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/COPYING -BROKEN_i386= undefined reference to `__atomic_load' and `__atomic_compare_exchange' +BROKEN_i386= undefined reference to `__atomic_load' and `__atomic_compare_exchange' #` BUILD_DEPENDS= boost-libs>=1.44:devel/boost-libs LIB_DEPENDS= libhwloc.so:devel/hwloc2 -USES= cmake compiler:c++14-lang fortran gnome perl5 pkgconfig shebangfix xorg +USES= cmake compiler:c++17-lang fortran gnome perl5 pkgconfig shebangfix xorg SHEBANG_FILES= admin/*.sh scripts/*.pl scripts/*.sh src/gromacs/selection/*.sh bash_CMD= ${SH} USE_GNOME= libxml2 CMAKE_OFF= GMX_USE_RDTSCP \ USE_PYTHON_SCRIPTS USE_LDCONFIG= yes OPTIONS_DEFINE= ATLAS FLOAT LEGACY OPENCL OPENMP SIMD X11 OPTIONS_SINGLE= MP OPTIONS_SINGLE_MP= NOMP MPICH OPENMPI THREAD_MPI OPTIONS_DEFAULT= LEGACY OPENMP THREAD_MPI X11 # FLOAT should not a default because science/votca needs double precision. This is likely the same for many other uses. OPTIONS_SUB= yes ATLAS_DESC= Use ATLAS for BLAS and LAPACK ATLAS_USES= blaslapack:atlas ATLAS_USES_OFF= blaslapack ATLAS_CMAKE_ON= -DBLAS_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libcblas.so;${LOCALBASE}/lib/libf77blas.so" \ -DLAPACK_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libalapack.so" ATLAS_CMAKE_OFF= -DBLAS_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libblas.so" \ -DLAPACK_LIBRARIES:FILEPATH="${LOCALBASE}/lib/liblapack.so" FLOAT_DESC= Use single instead of double precision FLOAT_BUILD_DEPENDS= fftw3>0:math/fftw3 FLOAT_LIB_DEPENDS= libfftw3f.so:math/fftw3-float FLOAT_LIB_DEPENDS_OFF= libfftw3.so:math/fftw3 FLOAT_CMAKE_ON= -DGMX_DOUBLE:BOOL=OFF FLOAT_CMAKE_OFF= -DGMX_DOUBLE:BOOL=ON FLOAT_PLIST_SUB= SUFFIX_D="" FLOAT_PLIST_SUB_OFF= SUFFIX_D="_d" LEGACY_DESC= Install legacy API # expected by science/votca LEGACY_CMAKE_BOOL= GMX_INSTALL_LEGACY_API OPENCL_CMAKE_BOOL= GMX_USE_OPENCL OPENCL_CMAKE_ON= -DGMX_GPU:STRING=OpenCL # one of: OFF, CUDA, OpenCL, SYCL OPENCL_CMAKE_OFF= -DGMX_GPU:STRING=OFF OPENCL_LIB_DEPENDS= libOpenCL.so:devel/ocl-icd OPENMP_CMAKE_ON= -DGMX_CXX11:BOOL=OFF OPENMP_CMAKE_OFF= -DGMX_OPENMP:BOOL=OFF SIMD_CMAKE_OFF= -DGMX_SIMD:STRING="None" X11_USE= XORG=ice,sm,xext,x11 X11_CMAKE_BOOL= GMX_X11 MP_DESC= Multiprocessing NOMP_DESC= No multiprocessing support NOMP_PLIST_SUB= SUFFIX_MPI="" MPICH_LIB_DEPENDS= libmpich.so:net/mpich MPICH_CMAKE_ON= -DGMX_MPI:BOOL=ON \ -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/bin/mpicc" MPICH_PLIST_SUB= SUFFIX_MPI="_mpi" OPENMPI_BUILD_DEPENDS= openmpi>0:net/openmpi OPENMPI_RUN_DEPENDS= openmpi>0:net/openmpi OPENMPI_CMAKE_ON= -DGMX_MPI:BOOL=ON \ -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/mpi/openmpi/bin/mpicc" OPENMPI_PLIST_SUB= SUFFIX_MPI="_mpi" THREAD_MPI_DESC= Build a thread-MPI-based multithreaded version of GROMACS THREAD_MPI_CMAKE_BOOL= GMX_THREAD_MPI THREAD_MPI_PLIST_SUB= SUFFIX_MPI="" post-patch: @${FIND} ${WRKSRC} -name "CMakeLists.txt" | ${XARGS} \ ${REINPLACE_CMD} -e \ 's|share/man|man| ; \ /pkgconfig/s|LIB_INSTALL_DIR}|CMAKE_INSTALL_PREFIX}/libdata|' @${FIND} ${WRKSRC} -name "GMXRC.*" | ${XARGS} ${REINPLACE_CMD} -e \ 's|LDLIB/pkgconfig|LDLIB/../libdata/pkgconfig| ; \ s|LDLIB}/pkgconfig|LDLIB}/../libdata/pkgconfig|' @${REINPLACE_CMD} -e '/CMAKE_REQUIRED_LIBRARIES/d' \ ${WRKSRC}/cmake/gmxTestdlopen.cmake .include diff --git a/science/gromacs/distinfo b/science/gromacs/distinfo index 42ab8fafcea0..fadfb2f4ed37 100644 --- a/science/gromacs/distinfo +++ b/science/gromacs/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1642283496 -SHA256 (gromacs-2021.5.tar.gz) = eba63fe6106812f72711ef7f76447b12dd1ee6c81b3d8d4d0e3098cd9ea009b6 -SIZE (gromacs-2021.5.tar.gz) = 38023772 +TIMESTAMP = 1651109042 +SHA256 (gromacs-2022.1.tar.gz) = 85ddab5197d79524a702c4959c2c43be875e0fc471df3a35224939dce8512450 +SIZE (gromacs-2022.1.tar.gz) = 40375423 diff --git a/science/gromacs/files/patch-cmake_gmxManageSharedLibraries.cmake b/science/gromacs/files/patch-cmake_gmxManageSharedLibraries.cmake deleted file mode 100644 index cb366e776b08..000000000000 --- a/science/gromacs/files/patch-cmake_gmxManageSharedLibraries.cmake +++ /dev/null @@ -1,11 +0,0 @@ ---- cmake/gmxManageSharedLibraries.cmake.orig 2015-07-27 14:11:45 UTC -+++ cmake/gmxManageSharedLibraries.cmake -@@ -39,7 +39,7 @@ - ######################################################################## - # Determine the defaults (this block has no effect if the variables have - # already been set) --if((APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD|GNU") AND NOT GMX_BUILD_MDRUN_ONLY) -+if((APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD|DragonFly") AND NOT GMX_BUILD_MDRUN_ONLY) - # Maybe Solaris should be here? Patch this if you know! - SET(SHARED_LIBS_DEFAULT ON) - elseif(WIN32 OR ${CMAKE_SYSTEM_NAME} MATCHES "BlueGene") diff --git a/science/gromacs/pkg-plist b/science/gromacs/pkg-plist index 6c35ed2eebf8..38d4889e21b2 100644 --- a/science/gromacs/pkg-plist +++ b/science/gromacs/pkg-plist @@ -1,701 +1,720 @@ bin/GMXRC bin/GMXRC.bash bin/GMXRC.csh bin/GMXRC.zsh bin/demux.pl -bin/gmx%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/gmx-completion-gmx%%SUFFIX_MPI%%%%SUFFIX_D%%.bash +bin/gmx-completion-gmx%%SUFFIX_D%%.bash bin/gmx-completion.bash +bin/gmx%%SUFFIX_D%% bin/xplor2gmx.pl include/gmxapi/compat/mdparams.h include/gmxapi/compat/tpr.h include/gmxapi/context.h include/gmxapi/exceptions.h include/gmxapi/gmxapi.h include/gmxapi/gmxapicompat.h include/gmxapi/gromacsfwd.h include/gmxapi/md.h include/gmxapi/md/mdmodule.h include/gmxapi/md/mdsignals.h include/gmxapi/mpi/gmxapi_mpi.h include/gmxapi/mpi/resourceassignment.h include/gmxapi/session.h include/gmxapi/session/resources.h include/gmxapi/status.h include/gmxapi/system.h include/gmxapi/version.h %%LEGACY%%include/gromacs/analysisdata.h %%LEGACY%%include/gromacs/analysisdata/abstractdata.h %%LEGACY%%include/gromacs/analysisdata/analysisdata.h %%LEGACY%%include/gromacs/analysisdata/arraydata.h %%LEGACY%%include/gromacs/analysisdata/dataframe.h %%LEGACY%%include/gromacs/analysisdata/datamodule.h %%LEGACY%%include/gromacs/analysisdata/modules/average.h %%LEGACY%%include/gromacs/analysisdata/modules/displacement.h %%LEGACY%%include/gromacs/analysisdata/modules/histogram.h %%LEGACY%%include/gromacs/analysisdata/modules/lifetime.h %%LEGACY%%include/gromacs/analysisdata/modules/plot.h %%LEGACY%%include/gromacs/external/boost/stl_interfaces/fwd.hpp %%LEGACY%%include/gromacs/external/boost/stl_interfaces/iterator_interface.hpp %%LEGACY%%include/gromacs/fileio/confio.h %%LEGACY%%include/gromacs/fileio/filetypes.h %%LEGACY%%include/gromacs/fileio/oenv.h %%LEGACY%%include/gromacs/fileio/pdbio.h %%LEGACY%%include/gromacs/fileio/tpxio.h %%LEGACY%%include/gromacs/fileio/trxio.h include/gromacs/math/do_fit.h include/gromacs/math/functions.h include/gromacs/math/units.h include/gromacs/math/utilities.h include/gromacs/math/vec.h include/gromacs/math/vectypes.h include/gromacs/mdrun/simulationinputhandle.h %%LEGACY%%include/gromacs/mdtypes/inputrec.h %%LEGACY%%include/gromacs/mdtypes/md_enums.h %%LEGACY%%include/gromacs/options.h %%LEGACY%%include/gromacs/options/abstractoption.h %%LEGACY%%include/gromacs/options/basicoptions.h %%LEGACY%%include/gromacs/options/filenameoption.h %%LEGACY%%include/gromacs/options/filenameoptionmanager.h %%LEGACY%%include/gromacs/options/ioptionsbehavior.h %%LEGACY%%include/gromacs/options/ioptionscontainer.h %%LEGACY%%include/gromacs/options/ioptionscontainerwithsections.h %%LEGACY%%include/gromacs/options/ivaluestore.h %%LEGACY%%include/gromacs/options/optionfiletype.h %%LEGACY%%include/gromacs/options/optionflags.h %%LEGACY%%include/gromacs/options/options.h %%LEGACY%%include/gromacs/options/timeunitmanager.h %%LEGACY%%include/gromacs/pbcutil/pbc.h include/gromacs/restraint/restraintpotential.h %%LEGACY%%include/gromacs/selection.h %%LEGACY%%include/gromacs/selection/indexutil.h %%LEGACY%%include/gromacs/selection/nbsearch.h %%LEGACY%%include/gromacs/selection/position.h %%LEGACY%%include/gromacs/selection/selection.h %%LEGACY%%include/gromacs/selection/selectioncollection.h %%LEGACY%%include/gromacs/selection/selectionenums.h %%LEGACY%%include/gromacs/selection/selectionoption.h %%LEGACY%%include/gromacs/selection/selectionoptionbehavior.h %%LEGACY%%include/gromacs/selection/selectionoptionmanager.h %%LEGACY%%include/gromacs/topology/atomprop.h %%LEGACY%%include/gromacs/topology/atoms.h %%LEGACY%%include/gromacs/topology/block.h %%LEGACY%%include/gromacs/topology/forcefieldparameters.h %%LEGACY%%include/gromacs/topology/idef.h %%LEGACY%%include/gromacs/topology/ifunc.h %%LEGACY%%include/gromacs/topology/index.h %%LEGACY%%include/gromacs/topology/symtab.h %%LEGACY%%include/gromacs/topology/topology.h %%LEGACY%%include/gromacs/trajectory/trajectoryframe.h %%LEGACY%%include/gromacs/trajectoryanalysis.h %%LEGACY%%include/gromacs/trajectoryanalysis/analysismodule.h %%LEGACY%%include/gromacs/trajectoryanalysis/analysissettings.h %%LEGACY%%include/gromacs/trajectoryanalysis/cmdlinerunner.h %%LEGACY%%include/gromacs/trajectoryanalysis/topologyinformation.h %%LEGACY%%include/gromacs/utility/arrayref.h include/gromacs/utility/basedefinitions.h -%%LEGACY%%%%LEGACY%%include/gromacs/utility/baseversion.h -%%LEGACY%%%%LEGACY%%include/gromacs/utility/classhelpers.h +%%LEGACY%%include/gromacs/utility/baseversion.h +%%LEGACY%%include/gromacs/utility/classhelpers.h include/gromacs/utility/current_function.h %%LEGACY%%include/gromacs/utility/enumerationhelpers.h %%LEGACY%%include/gromacs/utility/exceptions.h %%LEGACY%%include/gromacs/utility/fileptr.h %%LEGACY%%include/gromacs/utility/flags.h %%LEGACY%%include/gromacs/utility/futil.h include/gromacs/utility/gmxassert.h %%LEGACY%%include/gromacs/utility/listoflists.h %%LEGACY%%include/gromacs/utility/pleasecite.h %%LEGACY%%include/gromacs/utility/programcontext.h %%LEGACY%%include/gromacs/utility/range.h include/gromacs/utility/real.h %%LEGACY%%include/gromacs/utility/smalloc.h %%LEGACY%%include/gromacs/utility/stringutil.h %%LEGACY%%include/gromacs/utility/unique_cptr.h %%LEGACY%%include/gromacs/version.h +include/muParser.h +include/muParserBase.h +include/muParserBytecode.h +include/muParserCallback.h +include/muParserDLL.h +include/muParserDef.h +include/muParserError.h +include/muParserFixes.h +include/muParserInt.h +include/muParserTemplateMagic.h +include/muParserTest.h +include/muParserToken.h +include/muParserTokenReader.h include/nblib/basicdefinitions.h include/nblib/box.h include/nblib/exception.h -include/nblib/forcecalculator.h +include/nblib/gmxcalculatorcpu.h include/nblib/integrator.h include/nblib/interactions.h include/nblib/kerneloptions.h include/nblib/listed_forces/bondtypes.h include/nblib/listed_forces/calculator.h include/nblib/listed_forces/definitions.h include/nblib/molecules.h include/nblib/nblib.h +include/nblib/nbnxmsetuphelpers.h include/nblib/particlesequencer.h include/nblib/particletype.h include/nblib/simulationstate.h include/nblib/topology.h +include/nblib/tpr.h include/nblib/util/setup.h include/nblib/util/traits.hpp include/nblib/util/util.hpp include/nblib/vector.h -lib/libgmxapi%%SUFFIX_MPI%%%%SUFFIX_D%%.so -lib/libgmxapi%%SUFFIX_MPI%%%%SUFFIX_D%%.so.0 -lib/libgmxapi%%SUFFIX_MPI%%%%SUFFIX_D%%.so.0.2.1 -lib/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.so -lib/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6 -lib/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6.0.0 -lib/libnblib.so -lib/libnblib.so.0 -lib/libnblib.so.0.1.0 -libdata/pkgconfig/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.pc +lib/libgmxapi%%SUFFIX_D%%.so +lib/libgmxapi%%SUFFIX_D%%.so.0 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