diff --git a/math/deal.ii/Makefile b/math/deal.ii/Makefile index 978153ea34d6..872b5d238403 100644 --- a/math/deal.ii/Makefile +++ b/math/deal.ii/Makefile @@ -1,130 +1,130 @@ PORTNAME= deal.II DISTVERSION= 9.8.0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= math MASTER_SITES= https://github.com/dealii/dealii/releases/download/v${DISTVERSION}/ DISTNAME= dealii-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Finite element Differential Equations Analysis Library (DEAL) WWW= https://www.dealii.org/ \ https://github.com/dealii/dealii LICENSE= APACHE20 LGPL21 LICENSE_COMB= dual LICENSE_FILE_APACHE20= ${WRKSRC}/LICENSE.md LICENSE_FILE_LGPL21= ${WRKSRC}/LICENSE.md BROKEN_aarch64= error: use of undeclared identifier '__TBB_machine_fetchadd4' BROKEN_armv7= clang runs out of memory BROKEN_i386= compilation fails: Kokkos assumes 64-bit build; i.e., 8-byte pointers BUILD_DEPENDS= cgal>0:math/cgal \ taskflow>0:devel/taskflow LIB_DEPENDS= libarb.so:math/arb \ libblis.so:math/blis \ libboost_serialization.so:devel/boost-libs \ libecm.so:math/gmp-ecm \ libflint.so:math/flint2 \ libgmp.so:math/gmp \ libmpc.so:math/mpc \ libmpfr.so:math/mpfr \ libhdf5.so:science/hdf5 \ liblapack.so:math/lapack \ libmetis.so:math/metis \ libsymengine.so:math/symengine \ libtbb.so:devel/onetbb \ libvtkCommonCore-${VTK_VER}.so:math/vtk${VTK_VER:R} \ libkokkoscore.so:devel/kokkos # TMP commented out for bundled kokkos, tests fail for non-bundled kokkos, see https://github.com/dealii/dealii/issues/15692 RUN_DEPENDS= cgal>0:math/cgal \ taskflow>0:devel/taskflow USES= blaslapack:openblas cmake:testing compiler:c++23-lang localbase:ldflags xorg USE_LDCONFIG= yes CMAKE_OFF= DEAL_II_ALLOW_BUNDLED DEAL_II_COMPONENT_EXAMPLES \ DEAL_II_WITH_P4EST DEAL_II_WITH_TRILINOS DEAL_II_WITH_UMFPACK \ DEAL_II_WITH_MUPARSER DEAL_II_WITH_ASSIMP CMAKE_OFF+= DEAL_II_WITH_MUMPS # when math/mumps is installed deal fails because it expects a newer mumps (FIXME) #CMAKE_ON= FORCE_BUNDLED_KOKKOS # TMP turn on bundled kokkos CMAKE_TESTING_ON= FREEBSD_ENABLE_TESTS CMAKE_ARGS= -DCMAKE_POLICY_VERSION_MINIMUM=3.5 # CMake 4.5 compatibility, see https://github.com/dealii/dealii/issues/20250 USE_CXXSTD= c++23 LDFLAGS+= -lomp LDFLAGS+= -lexecinfo # TMP for bundled kokkos XARCH= ${ARCH} OPTIONS_DEFINE= ADOLC ARPACK GSL LAPACK MPI OPENCASCADE PETSC SCALAPACK SLEPC SUNDIALS # for all options see contrib/docker/Dockerfile, TODO some of them need to be enabled here OPTIONS_DEFAULT= GSL LAPACK MPI OPENCASCADE PETSC SCALAPACK SLEPC SUNDIALS ADOLC_DESC= Compile with ADOL-C ADOLC_CMAKE_BOOL= DEAL_II_WITH_ADOLC ADOLC_LIB_DEPENDS= libadolc.so:math/adol-c ADOLC_BROKEN= requires the development version: see https://github.com/dealii/dealii/issues/7293 ARPACK_DESC= Compile with Arpack and PArpack (only with MPI, LAPACK) ARPACK_CMAKE_BOOL= DEAL_II_WITH_ARPACK ARPACK_CMAKE_ON= -DARPACK_LINKER_FLAGS:STRING="${LDFLAGS}" ARPACK_BUILD_DEPENDS= arpack-ng@mpich>0:math/arpack-ng@mpich ARPACK_RUN_DEPENDS= arpack-ng@mpich>0:math/arpack-ng@mpich # itself doesn't link to arpack, but makes depending project link to it ARPACK_IMPLIES= LAPACK GSL_DESC= Compile with gsl GSL_CMAKE_BOOL= DEAL_II_WITH_GSL GSL_LIB_DEPENDS= libgsl.so:math/gsl LAPACK_DESC= Compile with LAPACK for matrix operations LAPACK_USES= fortran LAPACK_CMAKE_BOOL= DEAL_II_WITH_LAPACK LAPACK_CMAKE_ON= -DLAPACK_LINKER_FLAGS:STRING="${LDFLAGS}" LAPACK_LIB_DEPENDS= libopenblas.so:math/openblas MPI_DESC= MPI support (math/sundials must be compiled with MPI) MPI_USES= fortran MPI_CMAKE_BOOL= DEAL_II_WITH_MPI MPI_CMAKE_ON= -DMPI_LINKER_FLAGS:STRING="${LDFLAGS}" MPI_LIB_DEPENDS= libboost_iostreams.so:devel/boost-libs \ libmpich.so:net/mpich OPENCASCADE_DESC= Compile with OpenCascade OPENCASCADE_CMAKE_BOOL= DEAL_II_WITH_OPENCASCADE OPENCASCADE_CMAKE_ON= -DOPENCASCADE_INCLUDE_DIR:STRING=${LOCALBASE}/include/OpenCASCADE OPENCASCADE_LIB_DEPENDS= libTKernel.so:cad/opencascade PETSC_DESC= Compile with Petsc (only with MPI) PETSC_USE= XORG=x11 # PETSc adds x11 through interface libraries PETSC_CMAKE_BOOL= DEAL_II_WITH_PETSC PETSC_LIB_DEPENDS= libpetsc.so:science/PETSc PETSC_IMPLIES= MPI # has to use the same MPI as PETSc uses .if ${XARCH:M*64*} # match index size width being set to 64 in science/PETSc and math/metis PETSC_CMAKE_BOOL+= DEAL_II_WITH_64BIT_INDICES # as opposed to 32-bit indices that are default in deal.II .endif SCALAPACK_DESC= Compile with ScaLAPACK (only with MPI) SCALAPACK_CMAKE_BOOL= DEAL_II_WITH_SCALAPACK SCALAPACK_IMPLIES= MPI LAPACK SCALAPACK_LIB_DEPENDS= libscalapack.so:math/scalapack SLEPC_DESC= Compile with Slepc (only with MPI) SLEPC_USE= XORG=x11 # SLEPc adds x11 through interface libraries SLEPC_CMAKE_BOOL= DEAL_II_WITH_SLEPC SLEPC_LIB_DEPENDS= libslepc.so:math/slepc SLEPC_IMPLIES= MPI # has to use the same MPI as PETSc uses SUNDIALS_DESC= Compile with SUNDIALS SUNDIALS_CMAKE_BOOL= DEAL_II_WITH_SUNDIALS SUNDIALS_LIB_DEPENDS= libsundials_arkode.so:math/sundials pre-configure: # unbundle boost ${RM} -r ${WRKSRC}/bundled/boost-* post-stage: @${RM} ${STAGEDIR}${PREFIX}/*.log # tests as of 9.8.0: 100% tests passed, 0 tests failed out of 17 .include <../../math/vtk9/Makefile.version> .include diff --git a/math/slepc/Makefile b/math/slepc/Makefile index a88ff079465e..8ff4558744a2 100644 --- a/math/slepc/Makefile +++ b/math/slepc/Makefile @@ -1,43 +1,49 @@ PORTNAME= slepc -DISTVERSION= 3.25.1 +DISTVERSION= 3.26.0 CATEGORIES= math devel MASTER_SITES= http://slepc.upv.es/download/distrib/ MAINTAINER= yuri@FreeBSD.org COMMENT= Scalable Library for Eigenvalue Problem Computations WWW= http://slepc.upv.es/ LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.md LIB_DEPENDS= libblas.so:math/blas \ libblis.so:math/blis \ liblapack.so:math/lapack \ libmetis.so:math/metis \ libmpich.so:net/mpich \ libpetsc.so:science/PETSc USES= gmake fortran python shebangfix xorg USE_XORG= x11 # not really needed, but is inherited from the PETSc setup USE_LDCONFIG= yes SHEBANG_FILES= configure SHEBANG_GLOB= *.py MAKEFILE= makefile MAKE_ENV= PETSC_DIR=${LOCALBASE} PETSC_ARCH="" SLEPC_DIR=${WRKSRC} PYTHON=${PYTHON_CMD} PYTHONDONTWRITEBYTECODE=1 TEST_TARGET= test TEST_ENV= ${MAKE_ENV} PETSC_OPTIONS=-nox BINARY_ALIAS= python=${PYTHON_CMD} do-configure: @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ./configure --prefix=${PREFIX} post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libslepc.so.${PORTVERSION} # tests as of 3.25.1: 2480 passed, 6 skipped, 0 failed in 702s +# tests as of 3.26.0: (need to investigate 2 failures) +# success 2661/2677 tests (99.4%) +# failed 2/2677 tests (0.1%) +# todo 0/2677 tests (0.0%) +# skip 14/2677 tests (0.5%) + .include diff --git a/math/slepc/distinfo b/math/slepc/distinfo index 438e9fa9ee62..0455251a4c90 100644 --- a/math/slepc/distinfo +++ b/math/slepc/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1788944015 -SHA256 (slepc-3.25.1.tar.gz) = 906ddbe15a20774c23ddcdf13a5054889d00a26c3c37463447ee593c757d03ee -SIZE (slepc-3.25.1.tar.gz) = 1917727 +TIMESTAMP = 1791036966 +SHA256 (slepc-3.26.0.tar.gz) = a2f4cc2af76d55c078c30ad8bc66b44736dac921a7912266eb44136fc1b6029d +SIZE (slepc-3.26.0.tar.gz) = 1944740 diff --git a/math/slepc/pkg-plist b/math/slepc/pkg-plist index 439fce613962..380d3c482245 100644 --- a/math/slepc/pkg-plist +++ b/math/slepc/pkg-plist @@ -1,110 +1,112 @@ include/slepc.h include/slepc.mod include/slepc/finclude/slepc.h include/slepc/finclude/slepcblaslapack.h include/slepc/finclude/slepcblaslapack_mangle.h include/slepc/finclude/slepcbv.h include/slepc/finclude/slepccupmblas.h include/slepc/finclude/slepcds.h include/slepc/finclude/slepceps.h include/slepc/finclude/slepcfn.h include/slepc/finclude/slepclme.h include/slepc/finclude/slepcmagma.h include/slepc/finclude/slepcmat.h include/slepc/finclude/slepcmath.h include/slepc/finclude/slepcmfn.h include/slepc/finclude/slepcnep.h include/slepc/finclude/slepcpep.h include/slepc/finclude/slepcrg.h include/slepc/finclude/slepcsc.h include/slepc/finclude/slepcst.h include/slepc/finclude/slepcsvd.h include/slepc/finclude/slepcsys.h include/slepc/finclude/slepcvec.h include/slepc/private/bvimpl.h +include/slepc/private/cupmblas.h include/slepc/private/dsimpl.h include/slepc/private/epsimpl.h include/slepc/private/fnimpl.h include/slepc/private/lmeimpl.h include/slepc/private/mfnimpl.h include/slepc/private/nepimpl.h include/slepc/private/pepimpl.h include/slepc/private/rgimpl.h include/slepc/private/slepccontour.h include/slepc/private/slepcimpl.h include/slepc/private/slepcscalapack.h include/slepc/private/stimpl.h include/slepc/private/svdimpl.h include/slepc/private/vecimplslepc.h include/slepcblaslapack.h include/slepcblaslapack_mangle.h include/slepcbv.h include/slepcbv.mod include/slepcbvdef.mod include/slepcconf.h +include/slepcconfiginfo.h include/slepccupmblas.h include/slepcds.h include/slepcds.mod include/slepcdsdef.mod include/slepceps.h include/slepceps.mod include/slepcepsdef.mod include/slepcfn.h include/slepcfn.mod include/slepcfndef.mod include/slepclme.h include/slepclme.mod include/slepclmedef.mod include/slepcmagma.h include/slepcmat.h include/slepcmath.h include/slepcmfn.h include/slepcmfn.mod include/slepcmfndef.mod include/slepcnep.h include/slepcnep.mod include/slepcnepdef.mod include/slepcpep.h include/slepcpep.mod include/slepcpepdef.mod include/slepcrg.h include/slepcrg.mod include/slepcrgdef.mod include/slepcrgtypes.h include/slepcsc.h include/slepcst.h include/slepcst.mod include/slepcstdef.mod include/slepcsvd.h include/slepcsvd.mod include/slepcsvddef.mod include/slepcsys.h include/slepcsys.mod include/slepcsysdef.mod include/slepcvec.h include/slepcversion.h lib/libslepc.so -lib/libslepc.so.3.25 -lib/libslepc.so.3.25.1 -lib/slepc/conf/modules/slepc/3.25.1 +lib/libslepc.so.3.26 +lib/libslepc.so.3.26.0 +lib/slepc/conf/modules/slepc/3.26.0 lib/slepc/conf/slepc_common lib/slepc/conf/slepc_rules lib/slepc/conf/slepc_rules_util.mk lib/slepc/conf/slepc_test lib/slepc/conf/slepc_variables lib/slepc/conf/slepcrules lib/slepc/conf/slepcvariables lib/slepc/conf/uninstall.py libdata/pkgconfig/SLEPc.pc libdata/pkgconfig/slepc.pc %%DATADIR%%/CMakeLists.txt %%DATADIR%%/Makefile.user %%DATADIR%%/datafiles/graphs/README.md %%DATADIR%%/datafiles/graphs/out.moreno_taro_taro %%DATADIR%%/datafiles/matrices/README.md %%DATADIR%%/datafiles/matrices/bfw62a.petsc %%DATADIR%%/datafiles/matrices/bfw62b.petsc %%DATADIR%%/datafiles/matrices/rdb200.petsc %%DATADIR%%/datafiles/matrices/speaker107c.petsc %%DATADIR%%/datafiles/matrices/speaker107k.petsc %%DATADIR%%/datafiles/matrices/speaker107m.petsc diff --git a/science/bout++/Makefile b/science/bout++/Makefile index 7d25807edc37..258dfa807600 100644 --- a/science/bout++/Makefile +++ b/science/bout++/Makefile @@ -1,138 +1,138 @@ PORTNAME= bout++ DISTVERSIONPREFIX= v DISTVERSION= 5.1.1 -PORTREVISION= 10 +PORTREVISION= 11 CATEGORIES= science math # physics MAINTAINER= yuri@FreeBSD.org COMMENT= Plasma fluid finite-difference simulation code WWW= https://boutproject.github.io/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= gmake:devel/gmake LIB_DEPENDS= libfftw3.so:math/fftw3 \ libfmt.so:devel/libfmt \ libopenblas.so:math/openblas \ libuuid.so:misc/libuuid RUN_DEPENDS= bash:shells/bash \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.2.1:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}natsort>=8.1.0:devel/py-natsort@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}netCDF4>=0:science/py-netCDF4@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=1.22.0:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.4.1:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sympy>=1.5.1:math/py-sympy@${PY_FLAVOR} USES= cmake:testing gettext python gettext-runtime shebangfix USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= boutproject GH_PROJECT= BOUT-dev GH_TUPLE= google:googletest:0953a17a4281fc26831da647ad3fcd5e21e6473b:google_googletest/externalpackages/googletest \ meitar:git-archive-all.sh:fc86194f00b678438f9210859597f6eead28e765:meitar_git_archive_all_sh/externalpackages/git-archive-all.sh \ mpark:variant:23cb94f027d4ef33bf48133acc2695c7e5c6f1e7:mpark_variant/externalpackages/mpark.variant \ boutproject:boutdata:e458cf0cf2af6ff68db91da39ef3e15a7e9e6b3d:boutproject_boutdata/externalpackages/boutdata \ abseil:googletest:695cf7c96249de50360a7d2951dc88eb3aea0695:abseil_googletest/externalpackages/mpark.variant/3rdparty/googletest SHEBANG_GLOB= *.sh *.py SHEBANG_FILES= bin/bout-add-mod-path \ bin/bout-boutdata-restart-create \ bin/bout-pylib-cmd-to-bin \ bin/bout-sonnet \ bin/bout-stop-script \ bin/bout_3to4.py \ bin/bout_4to5 CMAKE_ON= BUILD_SHARED_LIBS \ BOUT_USE_SYSTEM_FMT CMAKE_OFF= BOUT_TESTS CMAKE_TESTING_ON= BOUT_TESTS TESTING_UNSAFE= 6 tests fail, see https://github.com/boutproject/BOUT-dev/issues/2980 CXXFLAGS+= -I${WRKSRC}/include LDFLAGS+= -lexecinfo OPTIONS_DEFINE= OPENMP PETSC SLEPC SUNDIALS OPTIONS_MULTI= FORMAT OPTIONS_MULTI_FORMAT= HDF5 NETCDF OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_DEFAULT= MPICH NETCDF # PETSC SLEPC: not compatible with the latest petsc-3.18.4 FORMAT_DESC= File format support HDF5_CMAKE_BOOL= BOUT_USE_HDF5 HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 NETCDF_USES= localbase:ldflags pkgconfig # because of the cmake patch in files/ NETCDF_CMAKE_BOOL= BOUT_USE_NETCDF NETCDF_LIB_DEPENDS= libnetcdf_c++4.so:science/netcdf-cxx \ libnetcdf.so:science/netcdf MPICH_USES= mpi:mpich OPENMP_CMAKE_BOOL= BOUT_ENABLE_OPENMP OPRNMP_BROKEN= SEGV when OpenMP is enabled, see https://github.com/boutproject/BOUT-dev/issues/2620 OPENMPI_USES= mpi:openmpi PETSC_DESC= Build with PETSc support PETSC_CMAKE_BOOL= BOUT_USE_PETSC PETSC_LIB_DEPENDS= libpetsc.so:science/PETSc SLEPC_DESC= Build with SLEPc support SLEPC_CMAKE_BOOL= BOUT_USE_SLEPC SLEPC_LIB_DEPENDS= libslepc.so:math/slepc SLEPC_IMPLIES= PETSC # build breaks w/out petsc SUNDIALS_DESC= Build with Sundials support SUNDIALS_CMAKE_BOOL= BOUT_USE_SUNDIALS SUNDIALS_CMAKE_ON= -DBOUT_DOWNLOAD_SUNDIALS=OFF SUNDIALS_BROKEN= fails to build with sundials, see https://github.com/boutproject/BOUT-dev/issues/2617 BINARY_ALIAS= make=${GMAKE} \ python3=${PYTHON_CMD} .if defined(WITH_EXAMPLES) # Build executables demonstrating BOUT++ capabilities. They aren't installed and don't need to be built for packaging. CMAKE_ON+= BOUT_BUILD_EXAMPLES .endif post-patch: # fix the version number in the code that it can't obtain from git @${REINPLACE_CMD} \ -e 's|__version__ = version(__name__)|__version__ = "${PORTVERSION}"|' \ ${WRKSRC}/tools/pylib/boutdata/__init__.py \ ${WRKSRC}/externalpackages/boutdata/src/boututils/__init__.py post-install: # workaround for /usr/local/lib/cmake/bout++/bout++Config.cmake:if @${REINPLACE_CMD} -i '' \ -e 's|${BUILD_WRKSRC}/externalpackages/mpark.variant|${PREFIX}/lib/cmake/mpark_variant|' \ -e 's|${BUILD_WRKSRC}/externalpackages/PVODE|${PREFIX}/lib/cmake/PVODE|' \ -e 's|${WRKSRC}/cmake|${PREFIX}/lib/cmake/bout++|' \ ${STAGEDIR}${PREFIX}/lib/cmake/bout++/bout++Config.cmake # remove *.orig files created by patching @${RM} ${STAGEDIR}${PREFIX}/include/*.orig # install missing PVODE cmake files @${RM} ${STAGEDIR}${PREFIX}/lib/cmake/PVODE/* ${INSTALL_DATA} ${BUILD_WRKSRC}/externalpackages/PVODE/PVODEConfig.cmake ${STAGEDIR}${PREFIX}/lib/cmake/PVODE ${INSTALL_DATA} ${BUILD_WRKSRC}/externalpackages/PVODE/PVODEConfigVersion.cmake ${STAGEDIR}${PREFIX}/lib/cmake/PVODE @${REINPLACE_CMD} -i '' \ -e 's|${BUILD_WRKSRC}/lib|${PREFIX}/lib|' \ -e 's|${PORTSDIR}/.*/BOUT-dev-${PORTVERSION}/externalpackages/PVODE/include|${PREFIX}/include|g' \ ${STAGEDIR}${PREFIX}/lib/cmake/PVODE/* @${REINPLACE_CMD} -i '' \ -e 's|INTERFACE_INCLUDE_DIRECTORIES .*|INTERFACE_INCLUDE_DIRECTORIES "${PREFIX}/include"|' \ ${STAGEDIR}${PREFIX}/lib/cmake/PVODE/PVODEConfig.cmake # remove broken link, see https://github.com/boutproject/BOUT-dev/issues/2623 @${RM} ${STAGEDIR}${PREFIX}/bin/bout-squashoutput pre-test: # build tests @cd ${BUILD_WRKSRC} && \ ${SETENVI} ${WRK_ENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} ${CMAKE_TESTING_ARGS} ${CMAKE_SOURCE_PATH} && \ ${SETENVI} ${WRK_ENV} ${MAKE_ENV} ${TEST_ENV} ${MAKE_CMD} ${_MAKE_JOBS} ${MAKE_ARGS} build-check .include