diff --git a/devel/ga/Makefile b/devel/ga/Makefile index a946c61d67d7..02c473486f10 100644 --- a/devel/ga/Makefile +++ b/devel/ga/Makefile @@ -1,54 +1,54 @@ PORTNAME= ga DISTVERSION= 5.8.2 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= devel MASTER_SITES= https://github.com/GlobalArrays/ga/releases/download/v${DISTVERSION}/ MAINTAINER= yuri@FreeBSD.org COMMENT= Partitioned Global Address Space (PGAS) library for distributed arrays WWW= https://hpc.pnl.gov//globalarrays/ LICENSE= BSD3CLAUSE LIB_DEPENDS= libblas.so:math/blas \ liblapack.so:math/lapack \ libscalapack.so:math/scalapack USES= autoreconf fortran gmake libtool localbase USE_LDCONFIG= yes GNU_CONFIGURE= yes CONFIGURE_ARGS= --enable-peigs --enable-shared --disable-static --with-scalapack LDFLAGS+= -lscalapack INSTALL_TARGET= install-strip TEST_TARGET= check # test asserts, see https://github.com/GlobalArrays/ga/issues/312 MPIEXEC_ARGS= -np 2 OPTIONS_RADIO= BLAS_SIZE MPI OPTIONS_RADIO_BLAS_SIZE= BLAS_SIZE_4 BLAS_SIZE_8 # the default BLAS_SIZE below should be same as the same choice in science/nwchem and in math/blas or math/openblas OPTIONS_RADIO_MPI= MPICH OPENMPI # the default MPI choice below should be the same as for the MPI option in math/scalapack OPTIONS_DEFAULT= BLAS_SIZE_4 MPICH BLAS_SIZE_DESC= BLAS_SIZE value to use during build (should be same as in devel/ga) BLAS_SIZE_4_DESC= BLAS_SIZE=4 BLAS_SIZE_4_CONFIGURE_ON= --with-blas4 BLAS_SIZE_8_DESC= BLAS_SIZE=8 BLAS_SIZE_8_CONFIGURE_ON= --with-blas8 MPICH_LIB_DEPENDS= libmpich.so:net/mpich MPICH_VARS= TEST_ARGS+=MPIEXEC="${LOCALBASE}/bin/mpiexec ${MPIEXEC_ARGS}" OPENMPI_BUILD_DEPENDS= openmpi>0:net/openmpi OPENMPI_RUN_DEPENDS= openmpi>0:net/openmpi OPENMPI_CONFIGURE_ENV= CC=${LOCALBASE}/mpi/openmpi/bin/mpicc MPICC=${LOCALBASE}/mpi/openmpi/bin/mpicc \ CXX=${LOCALBASE}/mpi/openmpi/bin/mpic++ MPICXX=${LOCALBASE}/mpi/openmpi/bin/mpic++ \ F77=${LOCALBASE}/mpi/openmpi/bin/mpif77 MPIF77=${LOCALBASE}/mpi/openmpi/bin/mpif77 \ FC=${LOCALBASE}/mpi/openmpi/bin/mpif90 MPIFC=${LOCALBASE}/mpi/openmpi/bin/mpif90 \ LDFLAGS="-L${LOCALBASE}/mpi/openmpi/lib -Wl,-rpath,${LOCALBASE}/mpi/openmpi/lib" OPENMPI_MAKE_ARGS= FREEBSD_LINK_FLAGS="-L${LOCALBASE}/mpi/openmpi/lib -Wl,-rpath,${LOCALBASE}/mpi/openmpi/lib -lmpi" OPENMPI_VARS= TEST_ARGS+=MPIEXEC="${LOCALBASE}/mpi/openmpi/bin/mpiexec ${MPIEXEC_ARGS}" .include diff --git a/math/costa/Makefile b/math/costa/Makefile index 19322ee58b5c..7a0ba2039147 100644 --- a/math/costa/Makefile +++ b/math/costa/Makefile @@ -1,43 +1,43 @@ PORTNAME= costa DISTVERSIONPREFIX= v DISTVERSION= 2.2.2 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Distributed Communication-Optimal Shuffle and Transpose Algorithm WWW= https://github.com/eth-cscs/COSTA LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libopenblas.so:math/openblas \ libscalapack.so:math/scalapack USES= cmake:testing pkgconfig USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= eth-cscs GH_PROJECT= COSTA CMAKE_ON= BUILD_SHARED_LIBS CMAKE_ARGS= -DCOSTA_SCALAPACK=CUSTOM CMAKE_OFF= COSTA_WITH_TESTS CMAKE_TESTING_ON= COSTA_WITH_TESTS OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_DEFAULT= MPICH MPICH_USES= mpi:mpich OPENMPI_USES= mpi:openmpi post-install: # workaround for https://github.com/eth-cscs/COSTA/issues/9 @cd ${STAGEDIR}${PREFIX} && ${RMDIR} \ include/costa/pxtran \ include/costa/pxtranc \ include/costa/pxtranu .include diff --git a/math/deal.ii/Makefile b/math/deal.ii/Makefile index c79bf9792ed5..3b874d7d07c3 100644 --- a/math/deal.ii/Makefile +++ b/math/deal.ii/Makefile @@ -1,118 +1,118 @@ PORTNAME= deal.II DISTVERSION= 9.6.2 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math MASTER_SITES= https://github.com/dealii/dealii/releases/download/v${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= ${LOCALBASE}/include/boost/config.hpp:devel/boost-libs LIB_DEPENDS= libblis.so:math/blis \ libboost_serialization.so:devel/boost-libs \ libhdf5.so:science/hdf5 \ libmetis.so:math/metis \ libvtkCommonCore-${VTK_VER}.so:math/vtk${VTK_VER:R} # libkokkoscore.so:devel/kokkos TMP commented out for bundled kokkos, tests fail for non-bundled kokkos, see https://github.com/dealii/dealii/issues/15692 USES= blaslapack cmake:testing compiler:c++17-lang localbase:ldflags xorg USE_LDCONFIG= yes CMAKE_OFF= DEAL_II_ALLOW_BUNDLED DEAL_II_COMPONENT_EXAMPLES \ DEAL_II_WITH_P4EST DEAL_II_WITH_TRILINOS DEAL_II_WITH_UMFPACK \ DEAL_II_WITH_NANOFLANN DEAL_II_WITH_MUPARSER DEAL_II_WITH_ASSIMP \ DEAL_II_WITH_HDF5 CMAKE_ON= DEAL_II_FORCE_BUNDLED_TBB # instead of LIB_DEPENDS+=libtbb.so:devel/onetbb, pending https://github.com/dealii/dealii/issues/11561 CMAKE_ON+= FORCE_BUNDLED_KOKKOS # TMP turn on bundled kokkos CMAKE_TESTING_ON= FREEBSD_ENABLE_TESTS LDFLAGS+= -lomp LDFLAGS+= -lexecinfo # TMP for bundled kokkos XARCH!= uname -p OPTIONS_DEFINE= ADOLC ARPACK GSL LAPACK MPI OPENCASCADE PETSC SCALAPACK SLEPC SUNDIALS # for all options see contrib/docker/Dockerfile, TODO some of them need to be enabled here OPTIONS_DEFAULT= GSL LAPACK MPI OPENCASCADE PETSC SCALAPACK SLEPC SUNDIALS ADOLC_DESC= Compile with ADOL-C ADOLC_CMAKE_BOOL= DEAL_II_WITH_ADOLC ADOLC_LIB_DEPENDS= libadolc.so:math/adol-c ADOLC_BROKEN= requires the development version: see https://github.com/dealii/dealii/issues/7293 ARPACK_DESC= Compile with Arpack and PArpack (only with MPI, LAPACK) ARPACK_CMAKE_BOOL= DEAL_II_WITH_ARPACK ARPACK_CMAKE_ON= -DARPACK_LINKER_FLAGS:STRING="${LDFLAGS}" ARPACK_BUILD_DEPENDS= arpack-ng>0:math/arpack-ng ARPACK_RUN_DEPENDS= arpack-ng>0:math/arpack-ng # 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_USES= xorg 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 ${XARCH:M*64*} # match index size width being set to 64 in science/PETSc and math/metis PETSC_CMAKE_BOOL+= DEAL_II_WITH_64BIT_INDICES # as opposed to 32-bit indices that are default in deal.II .endif SCALAPACK_DESC= Compile with ScaLAPACK (only with MPI) SCALAPACK_CMAKE_BOOL= DEAL_II_WITH_SCALAPACK SCALAPACK_IMPLIES= MPI LAPACK SCALAPACK_LIB_DEPENDS= libscalapack.so:math/scalapack SLEPC_DESC= Compile with Slepc (only with MPI) SLEPC_USES= xorg SLEPC_USE= XORG=x11 # SLEPc adds x11 through interface libraries SLEPC_CMAKE_BOOL= DEAL_II_WITH_SLEPC SLEPC_LIB_DEPENDS= libslepc.so:math/slepc SLEPC_IMPLIES= MPI # has to use the same MPI as PETSc uses SUNDIALS_DESC= Compile with SUNDIALS SUNDIALS_CMAKE_BOOL= DEAL_II_WITH_SUNDIALS SUNDIALS_LIB_DEPENDS= libsundials_arkode.so:math/sundials post-patch: # unbundle boost @${RM} -r ${WRKSRC}/dealii/bundled/boost-* post-stage: @${RM} ${STAGEDIR}${PREFIX}/*.log # the testsuite is excluded from the tarball: https://github.com/dealii/dealii/issues/17951 .include <../../math/vtk9/Makefile.version> .include diff --git a/math/scalapackfx/Makefile b/math/scalapackfx/Makefile index a9f9b8284c7e..0d4e7d640914 100644 --- a/math/scalapackfx/Makefile +++ b/math/scalapackfx/Makefile @@ -1,33 +1,33 @@ PORTNAME= scalapackfx DISTVERSION= 1.2 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Modern Fortran wrappers around ScaLAPACK routines WWW= https://github.com/dftbplus/scalapackfx LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= fypp:devel/py-fypp@${PY_FLAVOR} LIB_DEPENDS= libmpi.so:net/mpich \ libmpifort.so:net/mpich \ libopenblas.so:math/openblas \ libscalapack.so:math/scalapack USES= cmake fortran python:build USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= dftbplus CMAKE_ARGS= -DSCALAPACK_LIBRARY=${LOCALBASE} LDFLAGS+= -lscalapack CMAKE_ON= BUILD_SHARED_LIBS do-test: @cd ${WRKSRC}/test && mpirun -n 2 ${BUILD_WRKSRC}/test/test_det .include diff --git a/science/bagel/Makefile b/science/bagel/Makefile index c19a49b3cb0b..f273c507104d 100644 --- a/science/bagel/Makefile +++ b/science/bagel/Makefile @@ -1,62 +1,62 @@ PORTNAME= bagel DISTVERSIONPREFIX= v DISTVERSION= 1.2.2-132 -PORTREVISION= 13 +PORTREVISION= 14 DISTVERSIONSUFFIX= -g2955e4d1a CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Brilliantly Advanced General Electronic-structure Library WWW= https://nubakery.org/ \ https://github.com/qsimulate-open/bagel LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING BROKEN_armv7= error: static_assert failed "size_t is assumed to be the same size as unsigned long long" BROKEN_i386= error: static_assert failed "size_t is assumed to be the same size as unsigned long long" LIB_DEPENDS= libboost_serialization.so:devel/boost-libs TEST_DEPENDS= cblas>0:math/cblas USES= autoreconf blaslapack:openblas compiler:c++11-lang fortran gmake libtool localbase python:build USE_CXXSTD= c++11 USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= qsimulate-open GNU_CONFIGURE= yes CONFIGURE_ARGS= --datarootdir=${DATADIR} INSTALL_TARGET= install-strip OPTIONS_DEFINE= MPI LIBXC SCALAPACK SMITH # SLATER (needs a separate lib) OPTIONS_DEFAULT= MPI LIBXC SCALAPACK SMITH MPI_CONFIGURE_ON= --with-mpi=openmpi MPI_CONFIGURE_OFF= --with-mpi=no MPI_LIB_DEPENDS= libmpicxx.so:net/mpich # openmpi option erroneously links to mpich (due to a name clash) LIBXC_DESC= Build DFT with libxc LIBXC_CONFIGURE_WITH= libxc LIBXC_LIB_DEPENDS= libxc.so:science/libxc SCALAPACK_DESC= Use ScaLapack library for parallelized linear algebra SCALAPACK_CONFIGURE_ENABLE= scalapack SCALAPACK_VARS= LDFLAGS+="-lscalapack" SCALAPACK_VARS_OFF= LDFLAGS+="${BLASLIB} ${LAPACKLIB}" # -llapack -lblas are a replacement of libscalapack SCALAPACK_LIB_DEPENDS= libscalapack.so:math/scalapack SCALAPACK_IMPLIES= MPI SMITH_DESC= Compile SMITH generated code SMITH_CONFIGURE_ENABLE= smith SMITH_IMPLIES= MPI TEST_TARGET= check TEST_ARGS= LDFLAGS+="-lcblas -lblas" ${TEST_TARGET} post-test: # tests fail, see https://github.com/qsimulate-open/bagel/issues/248 @cd ${WRKSRC}/src && ./TestSuite --log_level=all .include diff --git a/science/cp2k/Makefile b/science/cp2k/Makefile index 64785f94adae..f6b05741f098 100644 --- a/science/cp2k/Makefile +++ b/science/cp2k/Makefile @@ -1,65 +1,65 @@ PORTNAME= cp2k DISTVERSIONPREFIX= v DISTVERSION= 2025.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Quantum chemistry and solid state physics software package WWW= https://www.cp2k.org/ LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/LICENSE .if !exists(/usr/include/omp.h) BROKEN= requires OpenMP support that is missing on this architecture .endif BUILD_DEPENDS= fypp:devel/py-fypp@${PY_FLAVOR} LIB_DEPENDS= libdbcsr.so:math/dbcsr \ libfftw3.so:math/fftw3 \ libopenblas.so:math/openblas RUN_DEPENDS= cp2k-data>0:science/cp2k-data TEST_DEPENDS= bash:shells/bash USES= cmake fortran localbase:ldflags python:build,test shebangfix tar:bz2 USE_GCC= yes # OpenMP is used from both Fortan and C code, therefore C code should be compiled with GCC, otherwise it fails at run-time (same in dbcsr) USE_GITHUB= yes SHEBANG_GLOB= *.py GCC_VERSION= ${GCC_DEFAULT} MAKE_ARGS= XARCH=FreeBSD-gfortran VERSION=${VERSION} FC=gfortran${GCC_VERSION} CC=${CC} LD=gfortran${GCC_VERSION} \ DATA_DIR=${DATADIR} FFLAGS+= -D__NO_STATM_ACCESS BINARY_ALIAS= python=${PYTHON_CMD} python3=${PYTHON_CMD} OPTIONS_DEFINE= LIBINT MPIX OPTIONS_DEFAULT= MPIX # LIBINT LIBINT_DESC= Use libint to evaluate integrals LIBINT_CMAKE_BOOL= CP2K_USE_LIBINT2 LIBINT_LIB_DEPENDS= libint2.so:science/libint2 LIBINT_BROKEN= missing fortran support MPIX_DESC= Enable MPI MPIX_CMAKE_BOOL= CP2K_USE_MPI MPIX_USES= mpi:mpich MPIX_LIB_DEPENDS= libscalapack.so:math/scalapack MPIX_VARS= EXE_VERSION=psmp MPIX_VARS_OFF= EXE_VERSION=ssmp PLIST_SUB= SUFFIX=.${EXE_VERSION} do-test: install @cd ${WRKSRC}/ && \ ${SETENV} ${MAKE_ENV} CP2K_STEM=${PREFIX}/bin/cp2k \ ./tests/do_regtest.py ${BUILD_WRKSRC}/bin ${EXE_VERSION} # build instructions: https://github.com/cp2k/cp2k/blob/master/INSTALL.md .include diff --git a/science/dftbplus/Makefile b/science/dftbplus/Makefile index dcb852823317..f504de4af01a 100644 --- a/science/dftbplus/Makefile +++ b/science/dftbplus/Makefile @@ -1,110 +1,110 @@ PORTNAME= dftbplus DISTVERSION= 24.1 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= DFTB+: Package for performing fast atomistic simulations WWW= https://dftbplus.org/ LICENSE= GPLv3 # main code is under LGPL3+, the bundled dftd3-lib is under GPLv1+, this makes the result GPLv3 (based on https://www.gnu.org/licenses/gpl-faq.html#AllCompatibility) BROKEN_aarch64= Lack of IEEE754 support in gcc causes "Cannot find an intrinsic module named 'ieee_arithmetic'", see bug\#255890 LIB_DEPENDS= libblas.so:math/blas \ liblapack.so:math/lapack \ libopenblas.so:math/openblas RUN_DEPENDS= ${PYNUMPY} TEST_DEPENDS= bash:shells/bash USES= cmake compiler:gcc-c++11-lib fortran pkgconfig python:build shebangfix USE_LDCONFIG= yes SHEBANG_FILES= tools/dptools/bin/* tools/misc/* utils/srcmanip/* utils/build/* external/fypp/bin/* utils/get_opt_externals \ external/fypp/bin/fypp utils/test/testlist_to_fypp SHEBANG_GLOB= *.py *.sh USE_GITHUB= yes GH_TUPLE= \ aradi:fytest:94e05ac:aradi_fytest/external/fytest/origin \ dftbplus:testparams:cd7536f:testparams/external/slakos/origin \ dftd4:dftd4:056491b:dftd4_dftd4/external/dftd4/origin TEST_TARGET= test BINARY_ALIAS= git=false CMAKE_ON= BLAS_DETECTION BUILD_SHARED_LIBS WITH_API ENABLE_DYNAMIC_LOADING CMAKE_ARGS= -DLAPACK_LIBRARY=lapack -DSCALAPACK_LIBRARY=scalapack BINARY_ALIAS= git=false python=${PYTHON_CMD} python3=${PYTHON_CMD} OPTIONS_DEFINE= ARPACK CHIMES DFTD3 MBD MPIX PLUMED POISSON PYTHON SOCKETS TBLITE TRANSPORT # see config.cmake for a complete list OPTIONS_DEFAULT= CHIMES DFTD3 MBD MPIX PLUMED POISSON TRANSPORT SOCKETS # PYTHON TBLITE OPTIONS_SUB= yes ARPACK_DESC= Build with ARPACK for large eigenvalue problems ARPACK_CMAKE_BOOL= WITH_ARPACK ARPACK_LIB_DEPENDS= libarpack.so:math/arpack-ng ARPACK_PREVENTS= MPIX # ARPACK is only used in a single-core application CHIMES_DESC= Build with ChIMES CHIMES_CMAKE_BOOL= WITH_CHIMES CHIMES_LIB_DEPENDS= libchimescalc.so:science/chimes-calculator DFTD3_DESC= Build with s-dft3 DFTD3_CMAKE_BOOL= WITH_SDFTD3 DFTD3_LIB_DEPENDS= libs-dftd3.so:science/simple-dftd3 \ libmctc-lib.so:science/mctc-lib \ libmstore.so:science/mstore \ libtoml-f.so:textproc/toml-f # binaries not linked with libtoml-f.so, see https://github.com/dftbplus/dftbplus/issues/1040 MBD_DESC= Build with many-body-dispersion support MBD_CMAKE_BOOL= WITH_MBD MBD_LIB_DEPENDS= libmbd.so:science/libmbd MPIX_DESC= MPI (Message Passing Interface) support # the MPI option name causes failure in MPI_USES=mpi:openmpi MPIX_CMAKE_BOOL= WITH_MPI MPIX_USES= mpi:mpich MPIX_LIB_DEPENDS= libmpich.so:net/mpich \ libmpifx.so:net/mpifx \ libscalapack.so:math/scalapack \ libscalapackfx.so:math/scalapackfx MPIX_LDFLAGS= ${LOCALBASE}/lib/libmpich.so ${LOCALBASE}/lib/libmpifort.so ${LOCALBASE}/lib/libmpi.so PLUMED_DESC= Do metadynamics via the PLUMED2 library PLUMED_CMAKE_BOOL= WITH_PLUMED PLUMED_LIB_DEPENDS= libplumed.so:science/plumed POISSON_DESC= Include Poisson-solver POISSON_CMAKE_BOOL= WITH_POISSON PYTHON_USES= python PYTHON_CMAKE_BOOL= WITH_PYTHON PYTHON_BROKEN= fails to install into stage directory: https://github.com/dftbplus/dftbplus/issues/931 SOCKETS_DESC= Build with sockets library SOCKETS_CMAKE_BOOL= WITH_SOCKETS SOCKETS_BINARY_ALIAS= gcc=${CC} TBLITE_DESC= Include xTB support via tblite TBLITE_CMAKE_BOOL= WITH_TBLITE TBLITE_BROKEN= fails to build, see https://github.com/dftbplus/dftbplus/issues/1041 TRANSPORT_DESC= Transport via libNEGF TRANSPORT_CMAKE_BOOL= WITH_TRANSPORT TRANSPORT_LIB_DEPENDS= libnegf.so:science/libnegf \ libmpi.so:net/mpich \ libmpifx.so:net/mpifx .include .if ${GCC_DEFAULT} >= 10 # workaround for Type mismatch between actual argument at (1) and actual argument at (2) (COMPLEX(8)/CHARACTER(*)). # in theory, this should set FCFLAGS, but the port does not conform FFLAGS+= -fallow-argument-mismatch .endif # 5 tests fail, see https://github.com/dftbplus/dftbplus/issues/1474 .include diff --git a/science/fleur/Makefile b/science/fleur/Makefile index 1ad5d6a1c62f..f8e5cc7bf64b 100644 --- a/science/fleur/Makefile +++ b/science/fleur/Makefile @@ -1,87 +1,87 @@ PORTNAME= fleur DISTVERSION= 7.2 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= FLAPW code for atomic computations in quantum chemistry and physics WWW= https://www.flapw.de/master/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_aarch64= Fatal Error: Cannot find an intrinsic module named 'ieee_arithmetic' at (1) LIB_DEPENDS= libfftw3.so:math/fftw3 \ libhdf5.so:science/hdf5 \ liblapack.so:math/lapack \ libopenblas.so:math/openblas TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \ USES= cmake:noninja fortran gnome localbase:ldflags python:test tar:tgz USE_GNOME= libxml2 USE_GITLAB= yes GL_SITE= https://iffgit.fz-juelich.de GL_TAGNAME= 447eed3b7ec3de5fcdfbd232cd1eda4caefb51d3 FFLAGS= -I${LOCALBASE}/include LDFLAGS+= -llapack -lopenblas -lxml2 # to fix missing symbols, see https://iffgit.fz-juelich.de/fleur/fleur/-/issues/670 OPTIONS_DEFINE= HDF5 KPLIB MPI SCALAPACK ELPA LIBXC WANNIER OPTIONS_DEFAULT= MPI SCALAPACK ELPA WANNIER # HDF5 KPLIB LIBXC HDF5_CMAKE_BOOL= CLI_FLEUR_USE_HDF5 HDF5_CMAKE_ON= -DHDF5_INCLUDE_DIRS=${LOCALBASE}/include HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 HDF5_BROKEN= Missing hdf5.mod in hdf5 # hdf5 doesn't include Fortran binding KPLIB_DESC= Use kpLib library #KPLIB_CMAKE_BOOL= CLI_FLEUR_USE_KPLIB KPLIB_DEPENDS= libkplib.so:science/kplib KPLIB_BROKEN= Fails to find the pre-installed libkplib.so library, see https://iffgit.fz-juelich.de/fleur/fleur/-/issues/691 MPI_CMAKE_BOOL= CLI_FLEUR_USE_MPI MPI_LDFLAGS= -lmpich -lmpifort MPI_LIB_DEPENDS= libmpich.so:net/mpich MPI_VARS= SUFFIX=_MPI SCALAPACK_DESC= Use the ScaLAPACK Scalable LAPACK library SCALAPACK_CMAKE_BOOL= FLEUR_USE_SCALAPACK # no such variable, see https://iffgit.fz-juelich.de/fleur/fleur/-/issues/692, it works only through LDFLAGS set below SCALAPACK_VARS= FFLAGS+=-fallow-argument-mismatch SCALAPACK_LDFLAGS= -lscalapack SCALAPACK_LIB_DEPENDS= libscalapack.so:math/scalapack SCALAPACK_IMPLIES= MPI ELPA_DESC= Use libelpa, Eigenvalue SoLver for Petaflop Applications ELPA_CMAKE_BOOL= FLEUR_USE_ELPA # no such variable, see https://iffgit.fz-juelich.de/fleur/fleur/-/issues/689, it works only through FFLAGS set below ELPA_VARS= FFLAGS+=-I${LOCALBASE}/include/elpa-2021.11.001/modules ELPA_LDFLAGS= -lelpa ELPA_LIB_DEPENDS= libelpa.so:math/elpa LIBXC_DESC= Use libxc library LIBXC_CMAKE_BOOL= CLI_FLEUR_USE_LIBXC LIBXC_LIB_DEPENDS= libxc.so:science/libxc LIBXC_BROKEN= Silently links with libxc when CLI_FLEUR_USE_LIBXC=OFF, see https://iffgit.fz-juelich.de/fleur/fleur/-/issues/690 WANNIER_DESC= Use Wannier library WANNIER_CMAKE_BOOL= CLI_FLEUR_USE_WANNIER WANNIER_LIB_DEPENDS= libwannier.so:science/wannier90 EXECUTABLES= bin/fleur${SUFFIX} \ bin/inpgen PLIST_FILES= ${EXECUTABLES} CONFLICTS_BUILD= libxc # see https://iffgit.fz-juelich.de/fleur/fleur/-/issues/690 post-install: # strip @cd ${STAGEDIR}${PREFIX} && ${STRIP_CMD} ${EXECUTABLES} do-test: # now: some tests fail or freeze, possibly because of missing hdf5 and kplib dependencies # was: 9 testcases are known to fail, see https://iffgit.fz-juelich.de/fleur/fleur/-/issues/671 @cd ${WRKSRC}/testing && pytest tests --build_dir=${TEST_WRKSRC} # tests fail to run: INTERNALERROR> pluggy._manager.PluginValidationError: unknown hook 'pytest_html_report_title' in plugin .include diff --git a/science/frontistr/Makefile b/science/frontistr/Makefile index 2cf27d500822..cc8be06a48af 100644 --- a/science/frontistr/Makefile +++ b/science/frontistr/Makefile @@ -1,56 +1,56 @@ PORTNAME= FrontISTR PORTVERSION= 5.2 -PORTREVISION= 5 +PORTREVISION= 6 DISTVERSIONPREFIX= v CATEGORIES= science cad MAINTAINER= thierry@FreeBSD.org COMMENT= Large-Scale Parallel FEM Program for Nonlinear Structural Analysis WWW= https://gitlab.com/FrontISTR-Commons/FrontISTR LICENSE= MIT LIB_DEPENDS= libmetis.so:math/metis \ libscotch.so:cad/scotch \ libcmumps.so.5:math/mumps \ libscalapack.so:math/scalapack TEST_DEPENDS= bash:shells/bash \ gawk:lang/gawk USE_GITLAB= yes GL_ACCOUNT= ${PORTNAME}-Commons GL_TAGNAME= c66bdc397de319ca59a0565b3f3b1a3b33f0c50c USES= blaslapack:openblas cmake:testing fortran mpi shebangfix SHEBANG_GLOB= *.sh FFLAGS+= -fallow-argument-mismatch ALL_TARGET= all OPTIONS_DEFINE= DOCS EXAMPLES DOCS_USES= python:build DOCS_BUILD_DEPENDS= doxygen:devel/doxygen \ dot:graphics/graphviz \ ${PYTHON_PKGNAMEPREFIX}mkdocs>0:textproc/py-mkdocs@${PY_FLAVOR} DOCS_CMAKE_BOOL= WITH_DOC DOCS_ALL_TARGET= doc PORTDOCS= * PORTEXAMPLES= * pre-configure: ${REINPLACE_CMD} -e 's/awk/gawk/' ${WRKSRC}/tests/test.sh do-install-DOCS-on: ${FIND} ${BUILD_WRKSRC}/doc/html -type d -empty -delete ${MKDIR} ${STAGEDIR}${DOCSDIR} cd ${BUILD_WRKSRC}/doc/html && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR} do-install-EXAMPLES-on: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} do-test: (cd ${TEST_WRKSRC} && ctest) .include diff --git a/science/openmx/Makefile b/science/openmx/Makefile index dd7ac75395ff..4b1ef46ed92f 100644 --- a/science/openmx/Makefile +++ b/science/openmx/Makefile @@ -1,83 +1,83 @@ PORTNAME= openmx DISTVERSION= 3.9.9 # the 18June12 patch upgrades 3.9 -> 3.9.9 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MASTER_SITES= https://www.openmx-square.org/ \ https://www.openmx-square.org/bugfixed/21Oct17/:patch DISTFILES= ${PORTNAME}${DISTVERSION:R}${EXTRACT_SUFX} \ patch${DISTVERSION}${EXTRACT_SUFX}:patch # this patch isn't a patch, but a set of file updates DIST_SUBDIR= ${PORTNAME} EXTRACT_ONLY= ${PORTNAME}${DISTVERSION:R}${EXTRACT_SUFX} MAINTAINER= yuri@FreeBSD.org COMMENT= Nanoscale material simulations using density functional theories (DFT) WWW= https://www.openmx-square.org/ LICENSE= GPLv2 .if !exists(/usr/include/omp.h) BROKEN= requires OpenMP support that is missing on this architecture .endif BROKEN_i386= undefined reference to `__atomic_load', see bug#229605 and https://reviews.llvm.org/D42154 LIB_DEPENDS= libblas.so:math/blas \ libcblas.so:math/cblas \ libfftw3.so:math/fftw3 \ liblapack.so:math/lapack \ libmpich.so:net/mpich \ libscalapack.so:math/scalapack USES= dos2unix fortran gmake localbase:ldflags USE_CXXSTD= c++11 DOS2UNIX_FILES= openmx_common.h MAKEFILE= makefile WRKSRC= ${WRKDIR}/${PORTNAME}${DISTVERSION:R} CFLAGS+= -Dkcomp -fcommon LDFLAGS+= -lmpifort FFLAGS+= -fallow-argument-mismatch WRKSRC_SUBDIR= source MAKE_ENV= MPICH_CC=${CC} BINARY_ALIAS= gcc=${CXX} UTIL_PROGS= DosMain jx analysis_example esp polB bandgnu13 bin2txt cube2xsf intensity_map md2axsf PLIST_FILES= bin/${PORTNAME} ${UTIL_PROGS:C/^/bin\//} OPTIONS_DEFINE_amd64= SIMD OPTIONS_DEFINE_i386= SIMD OPTIONS_DEFAULT_amd64= SIMD OPTIONS_DEFAULT_i386= SIMD SIMD_CFLAGS= -msse -msse2 -mfpmath=sse SIMD_CFLAGS_OFF= -Dnosse CFLAGS+= ${ARCH:S/amd64//:S/i386//:S/${ARCH}/-Dnosse/} MAKE_JOBS_UNSAFE= yes pre-patch: # overlay files before patching @cd ${WRKSRC} && \ ${TAR} xzf ${DISTDIR}/${DIST_SUBDIR}/patch${DISTVERSION}${EXTRACT_SUFX} post-patch: @cd ${WRKSRC} && \ ${ECHO} "const char DFT_DATA_PATH[YOUSO10] = \"${DATADIR}/DFT_DATA19\";" >> ${WRKSRC}/Input_std.c do-install: ${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME} ${STAGEDIR}${PREFIX}/bin .for u in ${UTIL_PROGS} ${INSTALL_PROGRAM} ${WRKSRC}/${u} ${STAGEDIR}${PREFIX}/bin .endfor cd ${WRKSRC}/.. && ${COPYTREE_SHARE} DFT_DATA19 ${STAGEDIR}${DATADIR} # autoplist for potentials: about 500 files in DATADIR @cd ${STAGEDIR}${PREFIX} && \ ${FIND} ${DATADIR:S/^${PREFIX}\///} -type f >> ${TMPPLIST} .include diff --git a/science/qbox/Makefile b/science/qbox/Makefile index 40e086f55ff2..57551d8d58f7 100644 --- a/science/qbox/Makefile +++ b/science/qbox/Makefile @@ -1,44 +1,44 @@ PORTNAME= qbox DISTVERSIONPREFIX= rel DISTVERSION= 1_78_2 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= First-principles molecular dynamics code WWW= http://qboxcode.org/ LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/../COPYING LIB_DEPENDS= libblas.so:math/blas \ libcurl.so:ftp/curl \ libfftw3.so:math/fftw3 \ liblapack.so:math/lapack \ libmpicxx.so:net/mpich \ libscalapack.so:math/scalapack \ libuuid.so:misc/e2fsprogs-libuuid \ libxerces-c.so:textproc/xerces-c3 USES= compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags USE_GITHUB= yes GH_ACCOUNT= qboxcode GH_PROJECT= qbox-public WRKSRC_SUBDIR= src MAKE_ARGS= TARGET=freebsd ALL_TARGET= qb TEST_TARGET= tests # only builds tests, but doesn't run them: https://github.com/qboxcode/qbox-public/issues/6, tests fail to link, see https://github.com/qboxcode/qbox-public/issues/11 PLIST_FILES= bin/qb post-extract: @${SED} -e 's|%%LOCALBASE%%|${LOCALBASE}|; s|%%CXXFLAGS%%|${CXXFLAGS}|; s|%%LDFLAGS%%|${LDFLAGS}|' < ${FILESDIR}/freebsd.mk.in > ${WRKSRC}/freebsd.mk do-install: ${INSTALL_PROGRAM} ${WRKSRC}/qb ${STAGEDIR}${PREFIX}/bin .include