diff --git a/misc/lbann/Makefile b/misc/lbann/Makefile index be4656410487..2767e9e0adef 100644 --- a/misc/lbann/Makefile +++ b/misc/lbann/Makefile @@ -1,60 +1,60 @@ PORTNAME= lbann DISTVERSIONPREFIX= v DISTVERSION= 0.102-254 DISTVERSIONSUFFIX= -g2e3012a9a -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= misc # machine-learning MAINTAINER= yuri@FreeBSD.org COMMENT= Livermore Big Artificial Neural Network toolkit WWW= https://github.com/LLNL/lbann LICENSE= APACHE20 BROKEN= many C++ errors, broken until the upstream would help, see https://github.com/LLNL/lbann/issues/2407 BUILD_DEPENDS= cereal>0:devel/cereal \ dihydrogen>0:math/dihydrogen \ zstr>0:archivers/zstr LIB_DEPENDS= libconduit.so:science/conduit \ libhdf5.so:science/hdf5 \ libHydrogen_CXX.so:math/hydrogen \ libopenblas.so:math/openblas \ libprotobuf.so:devel/protobuf \ libsiloh5.so:science/silo USES= cmake:testing compiler:c++17-lang localbase:ldflags pkgconfig USE_GITHUB= yes GH_ACCOUNT= LLNL GH_TUPLE= KIwabuchi:havoqgt:100f63b:havoqgt/applications/graph/node2vec/havoqgt \ samadejacobs:moses:28932ce:moses/applications/ATOM/moses \ snap-stanford:snap:58a1e6a:snap/applications/graph/node2vec/snap \ catchorg:Clara:2bfd8b2:clara CMAKE_ARGS= -DCLARA_INCLUDE_PATH=${WRKSRC_clara}/include CMAKE_OFF= LBANN_WITH_CNPY \ LBANN_WITH_CUDNN \ LBANN_WITH_HWLOC \ LBANN_WITH_PYTHON_FRONTEND \ LBANN_WITH_EMBEDDED_PYTHON \ LBANN_WITH_VISION \ LBANN_WITH_TBINF CMAKE_ON= LBANN_USE_PROTOBUF_MODULE CMAKE_TESTING_ON= LBANN_WITH_UNIT_TESTING # requires MPI cluster LDFLAGS+= -labsl_hash -labsl_log_internal_message -labsl_log_internal_nullguard -labsl_spinlock_wait -lexecinfo USE_CXXSTD= c++17 OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_DEFAULT= MPICH # should be same as in conduit, hydrogen, dihydrogen MPICH_USES= mpi:mpich OPENMPI_USES= mpi:openmpi post-install: # remove unnecessary files @${RM} -r ${STAGEDIR}${PREFIX}/share/doc .include diff --git a/science/ascent/Makefile b/science/ascent/Makefile index 700c3175eeba..1687ea96d527 100644 --- a/science/ascent/Makefile +++ b/science/ascent/Makefile @@ -1,57 +1,58 @@ PORTNAME= ascent DISTVERSIONPREFIX= v DISTVERSION= 0.9.5 +PORTREVISION= 1 CATEGORIES= science PKGNAMESUFFIX= -visualizer MAINTAINER= yuri@FreeBSD.org COMMENT= Visualization and analysis runtime for multi-physics HPC simulations WWW= https://ascent.readthedocs.io/en/latest/ \ https://github.com/Alpine-DAV/ascent LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/../LICENSE BROKEN_FreeBSD_15= compilation fails with clang-19, see https://github.com/Alpine-DAV/ascent/issues/1422 LIB_DEPENDS= libconduit.so:science/conduit \ libhdf5.so:science/hdf5 \ libsiloh5.so:science/silo \ libsysinfo.so:devel/libsysinfo \ libsz.so:science/libaec USES= cmake:testing compiler:c++11-lang fortran localbase:ldflags USE_GITHUB= yes GH_ACCOUNT= Alpine-DAV GH_TUPLE= Alpine-DAV:spack_configs:26ea412:spack_configs/../scripts/uberenv_configs/spack_configs \ LLNL:blt:9ff7734:blt/blt \ llnl:uberenv:105e384:uberenv/../scripts/uberenv CMAKE_OFF= ENABLE_PYTHON ENABLE_DOCS ENABLE_TESTS ENABLE_EXAMPLES CMAKE_OFF+= ENABLE_UTILS # utils are installed into a non-standard path, see https://github.com/Alpine-DAV/ascent/issues/814 CMAKE_ARGS= -DCONDUIT_DIR=${LOCALBASE} CMAKE_TESTING_ON= ENABLE_TESTS # one testcase fails because conduit lacks HDF5, see https://github.com/LLNL/conduit/issues/840 LDFLAGS+= -lsysinfo WRKSRC_SUBDIR= src OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI OPTIONS_DEFAULT= MPICH OPTIONS_SUB= yes NOMPI_DESC= Build without parallel processing support NOMPI_CMAKE_ON= -DENABLE_MPI=OFF MPICH_USES= mpi:mpich MPICH_CMAKE_ON= -DENABLE_MPI=ON OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DENABLE_MPI=ON OPENMPI_BROKEN= still chooses mpich, see https://github.com/Alpine-DAV/ascent/issues/1091 # tests as of 0.9.5: 100% tests passed, 0 tests failed out of 97 .include diff --git a/science/axom/Makefile b/science/axom/Makefile index 25a79bc28304..254bf8397995 100644 --- a/science/axom/Makefile +++ b/science/axom/Makefile @@ -1,81 +1,81 @@ PORTNAME= axom DISTVERSIONPREFIX= v DISTVERSION= 0.10.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Infrastructure for development of multi-physics applications and tools WWW= https://github.com/LLNL/axom \ https://axom.readthedocs.io/en/develop LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/../LICENSE BROKEN_armv7= use of overloaded operator '[]' is ambiguous, see https://github.com/LLNL/axom/issues/743 BROKEN_i386= use of overloaded operator '[]' is ambiguous, see https://github.com/LLNL/axom/issues/743 BROKEN_powerpc= use of overloaded operator '[]' is ambiguous, see https://github.com/LLNL/axom/issues/743 LIB_DEPENDS= libconduit.so:science/conduit \ libhdf5.so:science/hdf5 \ libHYPRE.so:science/hypre \ libmetis.so:math/metis \ libsiloh5.so:science/silo RUN_DEPENDS= sparsehash>0:devel/sparsehash USES= cmake:testing,noninja compiler:c++11-lang USE_GITHUB= yes GH_ACCOUNT= LLNL GH_TUPLE= LLNL:axom_data:1bff47e:axom_data/../data \ LLNL:blt:9cfe8ae:blt/cmake/blt \ LLNL:uberenv:e7dd3d9:uberenv/../scripts/uberenv CMAKE_OFF= AXOM_ENABLE_DOCS AXOM_ENABLE_EXAMPLES AXOM_ENABLE_TESTS AXOM_ENABLE_EXAMPLES CMAKE_ON= BUILD_SHARED_LIBS CMAKE_TESTING_ON= AXOM_ENABLE_TESTS AXOM_ENABLE_EXAMPLES CMAKE_TESTING_TARGET= all test CMAKE_ARGS= -DCONDUIT_DIR=${LOCALBASE} \ -DHDF5_DIR=${LOCALBASE} \ -DBLT_CXX_STD=c++14 # BLT_CXX_STD=c++14 is required for LLNL/serac LDFLAGS+= -lexecinfo WRKSRC_SUBDIR= src CONFLICTS_INSTALL= libfmt # bundles and installs an incompatible libfmt version: https://github.com/LLNL/axom/issues/561, axom headers include fmt unnecessarily OPTIONS_DEFINE= LUA MFEM OPENMP OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI OPTIONS_DEFAULT= LUA MFEM MPICH #OPENMP LUA,MFEM,MPI are required for LLNL/serac OPTIONS_SUB= yes LUA_USES= lua:54 LUA_CMAKE_ON= -DLUA_DIR=${LUA_BASE} \ -DFREEBSD_LUA_VER_STR=${LUA_VER_STR} \ -DFREEBSD_LUA_VER=${LUA_VER} MFEM_DESC= Use mfem - library for finite element methods MFEM_CMAKE_ON= -DMFEM_DIR=${LOCALBASE} MFEM_LIB_DEPENDS= libmfem.so:math/mfem NOMPI_DESC= Build without parallel processing support NOMPI_BROKEN= https://github.com/LLNL/axom/issues/913 MPICH_USES= mpi:mpich MPICH_CMAKE_ON= -DENABLE_MPI=ON OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DENABLE_MPI=ON OPENMP_CMAKE_BOOL= ENABLE_OPENMP OPENMP_BROKEN= https://github.com/LLNL/axom/issues/911 post-install: # installs headers of a third party library sparsehash: https://github.com/LLNL/axom/issues/365 @${RM} -r ${STAGEDIR}${PREFIX}/include/sparsehash # 2 tests are known to fail, see https://github.com/LLNL/axom/issues/912 # tests don't run in newer revisions, see https://github.com/LLNL/axom/issues/1492 .include diff --git a/science/conduit/Makefile b/science/conduit/Makefile index fe04ba696b7a..5f2c3994456b 100644 --- a/science/conduit/Makefile +++ b/science/conduit/Makefile @@ -1,50 +1,51 @@ PORTNAME= conduit DISTVERSIONPREFIX= v DISTVERSION= 0.9.5 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Simplified data exchange for HPC simulations WWW= https://github.com/LLNL/conduit LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/../LICENSE LIB_DEPENDS= libhdf5.so:science/hdf5 \ libsiloh5.so:science/silo USES= cmake:testing compiler:c++11-lang fortran USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= LLNL GH_TUPLE= LLNL:blt:058b312:blt/blt \ Alpine-DAV:spack_configs:26a5d10:spack_configs/../scripts/uberenv_configs/spack_configs \ LLNL:uberenv:5430066:LLNL_uberenv/../scripts/uberenv WRKSRC_SUBDIR= src CMAKE_ON= ENABLE_FORTRAN CMAKE_OFF= CONDUIT_ENABLE_TESTS ENABLE_DOCS ENABLE_EXAMPLES ENABLE_GIT ENABLE_TESTS ENABLE_VALGRIND CMAKE_ARGS= -DHDF5_DIR=${LOCALBASE} \ -DSILO_DIR=${LOCALBASE} \ -DFREEBSD_EXAMPLESDIR=${EXAMPLESDIR} # complete list of optional dependencies (enabled with *_DIR): https://llnl-conduit.readthedocs.io/en/latest/building.html #CMAKE_ARGS+= -DADIOS_DIR=${LOCALBASE} # broken, see https://github.com/LLNL/conduit/issues/841 CMAKE_TESTING_ON= ENABLE_TESTS OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI OPTIONS_DEFAULT= MPICH OPTIONS_SUB= yes NOMPI_DESC= Build without parallel processing support MPICH_USES= mpi:mpich MPICH_CMAKE_ON= -DENABLE_MPI=ON OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DENABLE_MPI=ON # tests as of 0.9.5: 100% tests passed, 0 tests failed out of 3 .include diff --git a/science/parthenon/Makefile b/science/parthenon/Makefile index 98f08b45d7b7..b09ecf9ad2ee 100644 --- a/science/parthenon/Makefile +++ b/science/parthenon/Makefile @@ -1,54 +1,54 @@ PORTNAME= parthenon DISTVERSIONPREFIX= v DISTVERSION= 24.08 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Portable block-structured Adaptive Mesh Refinement (AMR) framework WWW= https://parthenon-hpc-lab.github.io/parthenon/develop/index.html LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_armv7= compilation fails, see https://github.com/parthenon-hpc-lab/parthenon/issues/1226 BROKEN_i386= compilation fails, see https://github.com/parthenon-hpc-lab/parthenon/issues/1226 RUN_DEPENDS= bash:shells/bash LIB_DEPENDS= libkokkoscore.so:devel/kokkos USES= cmake:testing compiler:c++17-lang mpi:mpich python:test USE_GITHUB= yes GH_ACCOUNT= parthenon-hpc-lab GH_TUPLE= catchorg:Catch2:216713a:catch2/external/Catch2 CMAKE_ON= BUILD_SHARED_LIBS \ PARTHENON_IMPORT_KOKKOS \ PARTHENON_DISABLE_EXAMPLES CMAKE_OFF= PARTHENON_ENABLE_TESTING CMAKE_TESTING_ON= PARTHENON_ENABLE_TESTING \ PARTHENON_ENABLE_UNIT_TESTS \ PARTHENON_ENABLE_INTEGRATION_TESTS \ PARTHENON_ENABLE_REGRESSION_TESTS LDFLAGS+= -lexecinfo TEST_ENV= ${MAKE_ENV} PYTHONPATH=${WRKSRC}/scripts/python/packages/parthenon_tools/parthenon_tools OPTIONS_DEFINE= ASCENT HDF5 OPTIONS_DEFAULT= ASCENT ASCENT_DESC= Enable Ascent for in situ visualization and analysis ASCENT_CMAKE_BOOL= PARTHENON_ENABLE_ASCENT ASCENT_LIB_DEPENDS= libascent_mpi.so:science/ascent \ libconduit.so:science/conduit \ libhdf5.so:science/hdf5 \ libsiloh5.so:science/silo HDF5_CMAKE_OFF= -DPARTHENON_DISABLE_HDF5=ON HDF5_BROKEN= configure fails: Both MPI and HDF5 are enabled but only a serial version of HDF5 was found. # few tests don't find some test files .include diff --git a/science/polytope/Makefile b/science/polytope/Makefile index cd2985964500..51d29d283c38 100644 --- a/science/polytope/Makefile +++ b/science/polytope/Makefile @@ -1,36 +1,37 @@ PORTNAME= polytope DISTVERSION= 0.7.4 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Library for generating Voronoi and Voronoi-like tessellations WWW= https://github.com/LLNL/polytope LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${LOCALBASE}/include/boost/geometry.hpp:devel/boost-libs LIB_DEPENDS= libsz.so:science/libaec USES= cmake:testing USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= LLNL CXXFLAGS+= -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_NONE # prevent hardening issues with libc++, see https://github.com/LLNL/polytope/issues/24 CMAKE_ON= BUILD_SHARED_LIBS CMAKE_OFF= TESTING CMAKE_TESTING_ON= TESTING OPTIONS_DEFINE= SILO OPTIONS_DEFAULT= SILO SILO_DESC= Use SILO reader/writer SILO_CMAKE_BOOL= USE_SILO SILO_LIB_DEPENDS= libsiloh5.so:science/silo # tests as of 0.7.4: 96% tests passed, 1 tests failed out of 28 .include diff --git a/science/serac/Makefile b/science/serac/Makefile index 79535619d3e5..9ced914a7e86 100644 --- a/science/serac/Makefile +++ b/science/serac/Makefile @@ -1,56 +1,56 @@ PORTNAME= serac PORTVERSION= g20220823 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= High order nonlinear thermomechanical simulation code WWW= https://github.com/LLNL/serac LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN= fails to build with axom-0.10.1, see https://github.com/LLNL/serac/issues/1313 LIB_DEPENDS= libaxom.so:science/axom \ libconduit.so:science/conduit \ libhdf5.so:science/hdf5 \ libHYPRE.so:science/hypre \ libmfem.so:math/mfem \ libsiloh5.so:science/silo USES= cmake:testing compiler:c++17-lang USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= LLNL GH_TAGNAME= 07b8ef1 GH_TUPLE= LLNL:blt:49971b88e631aba76a9990c7702ceee47a7c3216:LLNL_blt/cmake/blt \ LLNL:uberenv:2cd030dd8fa9ff381900bfbe12fe1eea44a57bb5:LLNL_uberenv/scripts/uberenv \ LLNL:serac_tests:2fee9739eadeb218e99f7f5549e0800df81ca757:LLNL_serac_tests/tests CMAKE_TESTING_ON= ENABLE_TESTS # tests fail to compile, see https://github.com/LLNL/serac/issues/786 CMAKE_ON= BUILD_SHARED_LIBS CMAKE_OFF= ENABLE_TESTS CMAKE_ARGS= -DAXOM_DIR=${LOCALBASE} \ -DCONDUIT_DIR=${LOCALBASE} \ -DMFEM_DIR=${LOCALBASE} OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_DEFAULT= MPICH OPTIONS_SUB= yes MPICH_USES= mpi:mpich MPICH_CMAKE_ON= -DENABLE_MPI=ON \ -DMPI_C_COMPILER=${MPICC} \ -DMPI_CXX_COMPILER=${MPICXX} OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DENABLE_MPI=ON \ -DMPI_C_COMPILER=${MPICC} \ -DMPI_CXX_COMPILER=${MPICXX} OPENMPI_BROKEN= mixes OpenMPI and MPICH when both are installed, see https://github.com/LLNL/serac/issues/787 .include diff --git a/science/silo/Makefile b/science/silo/Makefile index 9759d1b7565c..dac1c6649952 100644 --- a/science/silo/Makefile +++ b/science/silo/Makefile @@ -1,51 +1,50 @@ PORTNAME= silo -DISTVERSION= 4.11-68 -PORTREVISION= 1 -DISTVERSIONSUFFIX= -g819658e +DISTVERSION= 4.12.0 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Mesh and field I/O library and scientific database WWW= https://wci.llnl.gov/simulation/computer-codes/silo LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/COPYRIGHT USES= cmake:testing perl5 readline USE_PERL5= build USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= LLNL GH_PROJECT= Silo +CMAKE_ON= SILO_ENABLE_INSTALL_LITE_HEADERS CMAKE_TESTING_ON= SILO_ENABLE_TESTS # 3 tests fail, see https://github.com/LLNL/Silo/issues/289 CMAKE_TESTING_TARGET= check FFLAGS+= -fallow-argument-mismatch # needed only for tests CONFLICTS_INSTALL= deforaos-browser # bin/browser OPTIONS_DEFINE= BROWSER FORTRAN HDF5 PYTHON SILOCK OPTIONS_DEFAULT= BROWSER FORTRAN HDF5 PYTHON SILOCK OPTIONS_SUB= yes BROWSER_DESC= Enable building of browser BROWSER_CMAKE_BOOL= SILO_ENABLE_BROWSER FORTRAN_CMAKE_BOOL= SILO_ENABLE_FORTRAN FORTRAN_USES= fortran HDF5_CMAKE_BOOL= SILO_ENABLE_HDF5 HDF5_CFLAGS= -DH5_USE_110_API=1 HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 HDF5_PLIST_SUB= SUFX_HDF5="h5" HDF5_PLIST_SUB_OFF= SUFX_HDF5="" PYTHON_CMAKE_BOOL= SILO_ENABLE_PYTHON_MODULE PYTHON_USES= python SILOCK_DESC= Enable building of silock SILOCK_CMAKE_BOOL= SILO_ENABLE_SILOCK .include diff --git a/science/silo/distinfo b/science/silo/distinfo index a3cf26715bd2..2fe4efe79810 100644 --- a/science/silo/distinfo +++ b/science/silo/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1670041617 -SHA256 (LLNL-Silo-4.11-68-g819658e_GH0.tar.gz) = 3a7a75e196c9e39922998054378efa02b2d24dc57ab126ab15a631e2645bd0ce -SIZE (LLNL-Silo-4.11-68-g819658e_GH0.tar.gz) = 14028123 +TIMESTAMP = 1763923185 +SHA256 (LLNL-Silo-4.12.0_GH0.tar.gz) = 5251816e43b08c19c925480b2daf85cc9b75e494b91df37df0eacc092279cfd0 +SIZE (LLNL-Silo-4.12.0_GH0.tar.gz) = 99198889 diff --git a/science/silo/files/patch-CMakeLists.txt b/science/silo/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..1d76b4832b67 --- /dev/null +++ b/science/silo/files/patch-CMakeLists.txt @@ -0,0 +1,13 @@ +- workaround for https://github.com/LLNL/Silo/issues/501 + +--- CMakeLists.txt.orig 2025-11-23 19:03:43 UTC ++++ CMakeLists.txt +@@ -700,7 +700,7 @@ install(FILES ${silo_public_headers} DESTINATION ${CMA + WORLD_READ) + + # Symlink old style silo_f77.inc +-if(SILO_ENABLE_FORTRAN AND CMAKE_Fortran_COMPILER) ++if(FALSE AND SILO_ENABLE_FORTRAN AND CMAKE_Fortran_COMPILER) + install(CODE "execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink silo.inc silo_f77.inc + WORKING_DIRECTORY ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR})") + endif() diff --git a/science/silo/files/patch-git-commit-be29ddf b/science/silo/files/patch-git-commit-be29ddf deleted file mode 100644 index fba494b0b956..000000000000 --- a/science/silo/files/patch-git-commit-be29ddf +++ /dev/null @@ -1,44 +0,0 @@ -commit be29ddf0352bc8e5a7eecc8772a3acb64dfde18c -Author: miller86 -Date: Fri Dec 2 19:00:20 2022 -0800 - - fix obj-case-macro - -diff --git src/hdf5_drv/silo_hdf5.c src/hdf5_drv/silo_hdf5.c -index 17af250..c45d689 100644 ---- src/hdf5_drv/silo_hdf5.c -+++ src/hdf5_drv/silo_hdf5.c -@@ -1809,7 +1809,7 @@ db_hdf5_cwg(DBfile *_dbfile) - *dscount = m.MEMCNT; \ - *dsnames = (char **) calloc(*dscount, sizeof(char**)); \ - for (i = 0; i < *dscount; i++) \ -- (*dsnames)[i] = strdup(m.MEMNAME[i]); \ -+ (*dsnames)[i] = strdup(m.MEMNAME); \ - break; \ - } - -@@ -1857,15 +1857,15 @@ db_hdf5_get_obj_dsnames(DBfile *_dbfile, char const *name, int *dscount, char ** - - switch(_objtype) - { -- DB_OBJ_CASE(DB_QUADVAR, DBquadvar_mt, nvals, value) -- /*DB_OBJ_CASE(DB_QUAD_RECT, DBquadmesh_mt, nspace, coord) wont work for rect case */ -- DB_OBJ_CASE(DB_QUAD_CURV, DBquadmesh_mt, nspace, coord) -- DB_OBJ_CASE(DB_QUADMESH, DBquadmesh_mt, nspace, coord) -- DB_OBJ_CASE(DB_UCDVAR, DBucdvar_mt, nvals, value) -- DB_OBJ_CASE(DB_UCDMESH, DBucdmesh_mt, ndims, coord) -- DB_OBJ_CASE(DB_POINTVAR, DBpointvar_mt, nvals, data) -- DB_OBJ_CASE(DB_POINTMESH, DBpointmesh_mt, ndims, coord) -- DB_OBJ_CASE(DB_CSGVAR, DBcsgvar_mt, nvals, vals) -+ DB_OBJ_CASE(DB_QUADVAR, DBquadvar_mt, nvals, value[i]) -+ /*DB_OBJ_CASE(DB_QUAD_RECT, DBquadmesh_mt, nspace, coord[i]) wont work for rect case */ -+ DB_OBJ_CASE(DB_QUAD_CURV, DBquadmesh_mt, nspace, coord[i]) -+ DB_OBJ_CASE(DB_QUADMESH, DBquadmesh_mt, nspace, coord[i]) -+ DB_OBJ_CASE(DB_UCDVAR, DBucdvar_mt, nvals, value[i]) -+ DB_OBJ_CASE(DB_UCDMESH, DBucdmesh_mt, ndims, coord[i]) -+ DB_OBJ_CASE(DB_POINTVAR, DBpointvar_mt, nvals, data[i]) -+ DB_OBJ_CASE(DB_POINTMESH, DBpointmesh_mt, ndims, coord[i]) -+ DB_OBJ_CASE(DB_CSGVAR, DBcsgvar_mt, nvals, vals[i]) - DB_OBJ_CASE(DB_CURVE, DBcurve_mt, npts?1:1, yvarname) - } - H5Tclose(o); diff --git a/science/silo/files/patch-src_silo_silo.c b/science/silo/files/patch-src_silo_silo.c deleted file mode 100644 index d20855c5ca9b..000000000000 --- a/science/silo/files/patch-src_silo_silo.c +++ /dev/null @@ -1,39 +0,0 @@ ---- src/silo/silo.c.orig 2022-12-03 02:30:10 UTC -+++ src/silo/silo.c -@@ -238,12 +238,8 @@ typedef struct db_silo_stat_t { - #ifndef SIZEOF_OFF64_T - #error missing definition for SIZEOF_OFF64_T in silo_private.h - #else --#if SIZEOF_OFF64_T > 4 -- struct stat64 s; --#else - struct stat s; - #endif --#endif - #ifdef _WIN32 - DWORD fileindexlo; - DWORD fileindexhi; -@@ -2121,11 +2117,7 @@ db_silo_stat_one_file(const char *name, db_silo_stat_t - errno = 0; - memset(&(statbuf->s), 0, sizeof(statbuf->s)); - --#if SIZEOF_OFF64_T > 4 -- retval = stat64(name, &(statbuf->s)); --#else - retval = stat(name, &(statbuf->s)); --#endif /* #if SIZEOF_OFF64_T > 4 */ - - #ifdef _WIN32 - if (retval == 0) -@@ -4136,11 +4128,7 @@ DBOpenReal(const char *name, int type, int mode) - /********************************/ - /* System level error occured. */ - /********************************/ --#if SIZEOF_OFF64_T > 4 -- printf("stat64() failed with error: "); --#else - printf("stat() failed with error: "); --#endif - switch (errno) - { - case EACCES: printf("EACCES\n"); break; diff --git a/science/silo/files/patch-src_silo_silo__json.c b/science/silo/files/patch-src_silo_silo__json.c index 576f7eea757f..331a87c8890e 100644 --- a/science/silo/files/patch-src_silo_silo__json.c +++ b/science/silo/files/patch-src_silo_silo__json.c @@ -1,14 +1,14 @@ ---- src/silo/silo_json.c.orig 2022-12-03 02:30:10 UTC +--- src/silo/silo_json.c.orig 2025-11-21 05:30:59 UTC +++ src/silo/silo_json.c -@@ -441,11 +441,7 @@ json_object_from_binary_file(char const *filename) +@@ -446,11 +446,7 @@ json_object_from_binary_file(char const *filename) #ifndef SIZEOF_OFF64_T #error missing definition for SIZEOF_OFF64_T in silo_private.h #else -#if SIZEOF_OFF64_T > 4 - struct stat64 s; -#else struct stat s; -#endif #endif errno = 0; diff --git a/science/silo/files/patch-tests_CMake_SiloMakeCheckRunner.cmake b/science/silo/files/patch-tests_CMake_SiloMakeCheckRunner.cmake deleted file mode 100644 index c25272a9a103..000000000000 --- a/science/silo/files/patch-tests_CMake_SiloMakeCheckRunner.cmake +++ /dev/null @@ -1,13 +0,0 @@ -- workaround for https://github.com/LLNL/Silo/issues/288 - ---- tests/CMake/SiloMakeCheckRunner.cmake.orig 2022-12-03 06:53:38 UTC -+++ tests/CMake/SiloMakeCheckRunner.cmake -@@ -72,7 +72,7 @@ function(silo_add_make_check_runner) - message(WARNING "silo_add_make_check_runner: NAME argument is required.") - return() - endif() -- set(test_cmd ${samcr_NAME}) -+ set(test_cmd "./${samcr_NAME}") - if("ARGS" IN_LIST samcr_KEYWORDS_MISSING_VALUES) - message(WARNING "silo_add_make_check_runner: ARGS argument provided without a value.") - return() diff --git a/science/silo/pkg-plist b/science/silo/pkg-plist index c55c7a873580..fc056e66313d 100644 --- a/science/silo/pkg-plist +++ b/science/silo/pkg-plist @@ -1,20 +1,21 @@ %%BROWSER%%bin/browser %%PYTHON%%bin/s2ex.py %%SILOCK%%bin/silock %%BROWSER%%bin/silodiff %%BROWSER%%bin/silofile -cmake/SiloConfig.cmake -cmake/SiloConfigVersion.cmake -cmake/SiloTargets-%%CMAKE_BUILD_TYPE%%.cmake -cmake/SiloTargets.cmake include/lite_pdb.h include/lite_score.h -include/pdform.h include/pmpio.h include/silo.h -include/silo.inc +%%FORTRAN%%include/silo.inc %%FORTRAN%%include/silo_FC.h include/silo_exports.h include/silo_f9x.inc %%PYTHON%%lib/Silo.so +lib/cmake/Silo/SiloConfig.cmake +lib/cmake/Silo/SiloConfigVersion.cmake +lib/cmake/Silo/SiloTargets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/Silo/SiloTargets.cmake lib/libsilo%%SUFX_HDF5%%.so +lib/libsilo%%SUFX_HDF5%%.so.4.12.0 +lib/libsilo%%SUFX_HDF5%%.so.412 diff --git a/science/spheral/Makefile b/science/spheral/Makefile index 1f6d29f4af1c..d35d06393bf2 100644 --- a/science/spheral/Makefile +++ b/science/spheral/Makefile @@ -1,81 +1,81 @@ PORTNAME= spheral DISTVERSIONPREFIX= v DISTVERSION= 2025.06.1 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org COMMENT= Environment for hydrodynamical & gravitational numerical simulations WWW= https://github.com/LLNL/spheral LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${LOCALBASE}/include/polyclipper2d.hh:math/polyclipper LIB_DEPENDS= libadiak.so:misc/adiak \ libaxom_core.so:science/axom \ libboost_filesystem.so:devel/boost-libs \ libcamp.so:devel/camp \ libchai.so:devel/chai \ libconduit.so:science/conduit \ libfmt.so:devel/libfmt \ libhdf5.so:science/hdf5 \ libmfem.so:math/mfem \ libosdCPU.so:graphics/opensubdiv \ libpolytope.so:science/polytope \ libqhull_r.so:math/qhull \ libRAJA.so:misc/raja \ libsiloh5.so:science/silo \ libsz.so:science/libaec \ libsundials_core.so:math/sundials \ libumpire.so:devel/umpire USES= cmake:testing compiler:c++14-lang eigen:3 fortran localbase:ldflags lua mpi:mpich python USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= LLNL GH_TUPLE= LLNL:PolyClipper:e1fe47c:PolyClipper/extern/PolyClipper \ LLNL:PYB11Generator:7160812:PYB11Generator/extern/PYB11Generator \ llnl:blt:29eecef:blt/cmake/blt \ llnl:uberenv:126f8de:uberenv/scripts/devtools/uberenv CMAKE_ARGS= -Daneos_DIR=${LOCALBASE} \ -Daxom_DIR=${LOCALBASE} \ -Dboost_DIR=${LOCALBASE} \ -Dconduit_DIR=${LOCALBASE} \ -Deigen_DIR=${LOCALBASE} \ -Dhdf5_DIR=${LOCALBASE} \ -Dopensubdiv_DIR=${LOCALBASE} \ -Dpython_DIR=${LOCALBASE} \ -Dpolyclipper_DIR=${LOCALBASE} \ -Dpolytope_DIR=${LOCALBASE} \ -Dpybind11_DIR=${LOCALBASE} \ -Dqhull_DIR=${LOCALBASE} \ -Dsilo_DIR=${LOCALBASE} \ -Dzlib_DIR=/usr CMAKE_ARGS+= -DPYTHON_EXECUTABLE=${PYTHON_CMD} \ -DPython_EXECUTABLE=${PYTHON_CMD} \ -DPython3_EXECUTABLE=${PYTHON_CMD} CMAKE_OFF= ENABLE_TESTS ENABLE_DOCS \ ENABLE_ANEOS \ ENABLE_CUDA CMAKE_ON= ENABLE_CXXONLY # disable Python support which is still for Python-2.7, see https://github.com/LLNL/spheral/issues/183 CMAKE_ON+= ENABLE_OPENMP \ USE_EXTERNAL_CHAI \ ENABLE_SUNDIALS CMAKE_TESTING_ON= ENABLE_TESTS # tests fail to build, see https://github.com/LLNL/spheral/issues/230 CXXFLAGS+= -I${LOCALBASE}/include/eigen3 BINARY_ALIAS= git=false python=${PYTHON_CMD} python3=${PYTHON_CMD} post-patch: @${REINPLACE_CMD} -e 's|\.a|.so|; s|qhullstatic|qhull_r|; s|python2\.7|python${PYTHON_VER}|g' ${WRKSRC}/cmake/tpl/*.cmake @${CHMOD} +x ${WRKSRC}/src/helpers/InstantiationGenerator.py post-install: # remove the stray file Spheral/mpi.py @${RM} -r ${STAGEDIR}${PREFIX}/Spheral .include