Date: Sat, 7 May 2022 19:23:30 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: b6aecffa15a2 - main - misc/adios2: Update 2.7.1 -> 2.8.0 Message-ID: <202205071923.247JNUZ5099576@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=b6aecffa15a20221cb45de272ba142e6c2eb03eb commit b6aecffa15a20221cb45de272ba142e6c2eb03eb Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2022-05-07 19:22:51 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2022-05-07 19:23:28 +0000 misc/adios2: Update 2.7.1 -> 2.8.0 Reported by: portscout --- misc/adios2/Makefile | 30 +++- misc/adios2/distinfo | 6 +- misc/adios2/files/patch-cmake_DetectOptions.cmake | 28 ++++ .../patch-source_adios2_helper_adiosNetwork.cpp | 12 -- ..._adios2_toolkit_profiling_taustubs_tautimer.cpp | 30 ---- misc/adios2/pkg-plist | 170 +++++++++++++++++++-- 6 files changed, 215 insertions(+), 61 deletions(-) diff --git a/misc/adios2/Makefile b/misc/adios2/Makefile index 3b1c658c9233..1f22047326c7 100644 --- a/misc/adios2/Makefile +++ b/misc/adios2/Makefile @@ -1,6 +1,6 @@ PORTNAME= adios2 DISTVERSIONPREFIX= v -DISTVERSION= 2.7.1 +DISTVERSION= 2.8.0 CATEGORIES= misc science MAINTAINER= yuri@FreeBSD.org @@ -12,29 +12,45 @@ LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_i386= constant expression evaluates to 18446744073709551613 which cannot be narrowed to type 'unsigned int': https://github.com/ornladios/ADIOS2/issues/2469 BROKEN_powerpc= constant expression evaluates to 18446744073709551613 which cannot be narrowed to type 'unsigned int': https://github.com/ornladios/ADIOS2/issues/2469 -BUILD_DEPENDS= bash:shells/bash +PY_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}mpi4py>=3.0.3:net/py-mpi4py@${PY_FLAVOR} +BUILD_DEPENDS= bash:shells/bash \ + pybind11>0:devel/pybind11 \ + ${PYTHON_PKGNAMEPREFIX}pybind11>=2.4:devel/py-pybind11@${PY_FLAVOR} \ + ${PY_DEPENDS} LIB_DEPENDS= libblosc.so:archivers/c-blosc \ libepoll-shim.so:devel/libepoll-shim \ libfabric.so:net/libfabric \ libffi.so:devel/libffi \ libhdf5.so:science/hdf5 \ - libmpi.so:net/openmpi \ + libmpi.so:net/mpich \ libpng.so:graphics/png \ + libsodium.so:security/libsodium \ libsz.so:science/szip \ libzmq.so:net/libzmq4 \ libzfp.so:devel/zfp -RUN_DEPENDS= bash:shells/bash +RUN_DEPENDS= bash:shells/bash \ + ${PY_DEPENDS} USES= bison cmake compiler:c++11-lang fortran localbase:ldflags pkgconfig \ perl5 python shebangfix -SHEBANG_FILES= cmake/install/post/adios2-config.pre.sh.in cmake/install/post/generate-adios2-config.sh.in source/utils/bp4dbg/bp4dbg.py \ - source/utils/adios_deactivate_bp.sh source/utils/adios_reorganize/adios2_reorganize_wrapper +USE_LDCONFIG= yes + +SHEBANG_FILES= cmake/install/post/adios2-config.pre.sh.in cmake/install/post/generate-adios2-config.sh.in \ + source/utils/adios_reorganize/adios2_reorganize_wrapper source/utils/adios2_deactivate_bp +SHEBANG_GLOB= *.sh *.py + USE_GITHUB= yes GH_ACCOUNT= ornladios GH_PROJECT= ADIOS2 -USE_LDCONFIG= yes +CMAKE_ARGS= -DFREEBSD_PYTHON_VERSION=${PYTHON_VER} CMAKE_OFF= BUILD_TESTING LDFLAGS+= -lepoll-shim +OPTIONS_DEFINE= DOCS + +DOCSDIR= ${PREFIX}/share/doc/ADIOS2 +PORTDOCS= * + .include <bsd.port.mk> diff --git a/misc/adios2/distinfo b/misc/adios2/distinfo index 19d1953c07fb..f8558d9c2652 100644 --- a/misc/adios2/distinfo +++ b/misc/adios2/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1612982157 -SHA256 (ornladios-ADIOS2-v2.7.1_GH0.tar.gz) = c8e237fd51f49d8a62a0660db12b72ea5067512aa7970f3fcf80b70e3f87ca3e -SIZE (ornladios-ADIOS2-v2.7.1_GH0.tar.gz) = 5462614 +TIMESTAMP = 1651945103 +SHA256 (ornladios-ADIOS2-v2.8.0_GH0.tar.gz) = 5af3d950e616989133955c2430bd09bcf6bad3a04cf62317b401eaf6e7c2d479 +SIZE (ornladios-ADIOS2-v2.8.0_GH0.tar.gz) = 5742811 diff --git a/misc/adios2/files/patch-cmake_DetectOptions.cmake b/misc/adios2/files/patch-cmake_DetectOptions.cmake new file mode 100644 index 000000000000..415ed96552c5 --- /dev/null +++ b/misc/adios2/files/patch-cmake_DetectOptions.cmake @@ -0,0 +1,28 @@ +- fix the python version + +--- cmake/DetectOptions.cmake.orig 2022-03-29 11:54:45 UTC ++++ cmake/DetectOptions.cmake +@@ -312,12 +312,12 @@ if(NOT SHARED_LIBS_SUPPORTED) + endif() + + if(ADIOS2_USE_Python STREQUAL AUTO) +- find_package(Python 3 COMPONENTS Interpreter Development NumPy) ++ find_package(Python ${FREEBSD_PYTHON_VERSION} EXACT COMPONENTS Interpreter Development NumPy) + if(Python_FOUND AND ADIOS2_HAVE_MPI) + find_package(PythonModule COMPONENTS mpi4py mpi4py/mpi4py.h) + endif() + elseif(ADIOS2_USE_Python) +- find_package(Python 3 REQUIRED COMPONENTS Interpreter Development NumPy) ++ find_package(Python ${FREEBSD_PYTHON_VERSION} EXACT REQUIRED COMPONENTS Interpreter Development NumPy) + if(ADIOS2_HAVE_MPI) + find_package(PythonModule REQUIRED COMPONENTS mpi4py mpi4py/mpi4py.h) + endif() +@@ -334,7 +334,7 @@ endif() + + # Even if no python support, we still want the interpreter for tests + if(BUILD_TESTING AND NOT Python_Interpreter_FOUND) +- find_package(Python REQUIRED COMPONENTS Interpreter) ++ find_package(Python ${FREEBSD_PYTHON_VERSION} EXACT REQUIRED COMPONENTS Interpreter) + endif() + + if(Python_Interpreter_FOUND) diff --git a/misc/adios2/files/patch-source_adios2_helper_adiosNetwork.cpp b/misc/adios2/files/patch-source_adios2_helper_adiosNetwork.cpp deleted file mode 100644 index 329bfa1aa320..000000000000 --- a/misc/adios2/files/patch-source_adios2_helper_adiosNetwork.cpp +++ /dev/null @@ -1,12 +0,0 @@ -- workaround for https://github.com/ornladios/ADIOS2/issues/2615 - ---- source/adios2/helper/adiosNetwork.cpp.orig 2021-02-10 18:38:17 UTC -+++ source/adios2/helper/adiosNetwork.cpp -@@ -23,6 +23,7 @@ - #include <string.h> //AvailableIpAddresses() strncp - #include <sys/ioctl.h> //AvailableIpAddresses() ioctl - #include <unistd.h> //AvailableIpAddresses() close -+#include <netinet/in.h> - - #include <nlohmann/json.hpp> - diff --git a/misc/adios2/files/patch-source_adios2_toolkit_profiling_taustubs_tautimer.cpp b/misc/adios2/files/patch-source_adios2_toolkit_profiling_taustubs_tautimer.cpp deleted file mode 100644 index e1a83f26c3c0..000000000000 --- a/misc/adios2/files/patch-source_adios2_toolkit_profiling_taustubs_tautimer.cpp +++ /dev/null @@ -1,30 +0,0 @@ ---- source/adios2/toolkit/profiling/taustubs/tautimer.cpp.orig 2019-07-28 09:15:02 UTC -+++ source/adios2/toolkit/profiling/taustubs/tautimer.cpp -@@ -21,6 +21,9 @@ - #include <sys/syscall.h> - #include <sys/types.h> - #include <thread> -+#if defined(__FreeBSD__) || defined(__DragonFly__) -+#include <pthread_np.h> -+#endif - - /* Clean assertion handling */ - inline void _tautimer_assert(const char *expression, const char *file, int line) -@@ -204,6 +207,8 @@ TauTimer::TauTimer(void) : initialized(false) - #if defined(__APPLE__) && defined(__MACH__) - // why should Apple support gettid? BE DIFFERENT, BABY! - pthread_threadid_np(NULL, &mytid); -+#elif defined(__FreeBSD__) || defined(__DragonFly__) -+ mytid = pthread_getthreadid_np(); - #else - mytid = (uint64_t)syscall(__NR_gettid); - #endif -@@ -232,6 +237,8 @@ inline void TauTimer::_RegisterThread(void) - #if defined(__APPLE__) && defined(__MACH__) - // why should Apple support gettid? BE DIFFERENT, BABY! - pthread_threadid_np(NULL, &mytid); -+#elif defined(__FreeBSD__) || defined(__DragonFly__) -+ mytid = pthread_getthreadid_np(); - #else - mytid = (uint64_t)syscall(__NR_gettid); - #endif diff --git a/misc/adios2/pkg-plist b/misc/adios2/pkg-plist index ff26360172c8..ce9c998c03ba 100644 --- a/misc/adios2/pkg-plist +++ b/misc/adios2/pkg-plist @@ -1,11 +1,13 @@ bin/adios2-config bin/adios2_deactivate_bp bin/adios2_iotest +bin/adios2_json_pp bin/adios2_reorganize bin/adios2_reorganize_mpi bin/bp2h5 bin/bp2h5_mpi bin/bp4dbg +bin/bp5dbg bin/bpls bin/sst_conn_tool include/adios2.h @@ -20,6 +22,18 @@ include/adios2/common/ADIOSConfig.h include/adios2/common/ADIOSMacros.h include/adios2/common/ADIOSTypes.h include/adios2/common/ADIOSTypes.inl +include/adios2/core/ADIOS.h +include/adios2/core/Attribute.h +include/adios2/core/AttributeBase.h +include/adios2/core/CoreTypes.h +include/adios2/core/Engine.h +include/adios2/core/Group.h +include/adios2/core/IO.h +include/adios2/core/Operator.h +include/adios2/core/Stream.h +include/adios2/core/Variable.h +include/adios2/core/VariableBase.h +include/adios2/core/VariableCompound.h include/adios2/cxx11/ADIOS.h include/adios2/cxx11/ADIOS.inl include/adios2/cxx11/Attribute.h @@ -31,6 +45,36 @@ include/adios2/cxx11/Query.h include/adios2/cxx11/Types.h include/adios2/cxx11/Variable.h include/adios2/cxx11/fstream/ADIOS2fstream.h +include/adios2/engine/bp3/BP3Reader.h +include/adios2/engine/bp3/BP3Writer.h +include/adios2/engine/bp4/BP4Reader.h +include/adios2/engine/bp4/BP4Writer.h +include/adios2/engine/bp5/BP5Engine.h +include/adios2/engine/bp5/BP5Reader.h +include/adios2/engine/bp5/BP5Writer.h +include/adios2/engine/dataman/DataManMonitor.h +include/adios2/engine/dataman/DataManReader.h +include/adios2/engine/dataman/DataManWriter.h +include/adios2/engine/dataspaces/DataSpacesReader.h +include/adios2/engine/dataspaces/DataSpacesWriter.h +include/adios2/engine/hdf5/HDF5ReaderP.h +include/adios2/engine/hdf5/HDF5WriterP.h +include/adios2/engine/inline/InlineReader.h +include/adios2/engine/inline/InlineWriter.h +include/adios2/engine/mhs/MhsReader.h +include/adios2/engine/mhs/MhsWriter.h +include/adios2/engine/null/NullReader.h +include/adios2/engine/null/NullWriter.h +include/adios2/engine/plugin/PluginEngine.h +include/adios2/engine/plugin/PluginEngineInterface.h +include/adios2/engine/skeleton/SkeletonReader.h +include/adios2/engine/skeleton/SkeletonWriter.h +include/adios2/engine/ssc/SscHelper.h +include/adios2/engine/ssc/SscReader.h +include/adios2/engine/ssc/SscWriter.h +include/adios2/engine/sst/SstParamParser.h +include/adios2/engine/sst/SstReader.h +include/adios2/engine/sst/SstWriter.h include/adios2/fortran/adios2.mod include/adios2/fortran/adios2.smod include/adios2/fortran/adios2_adios_init_mod.mod @@ -60,12 +104,109 @@ include/adios2/fortran/adios2_parameters_mod.mod include/adios2/fortran/adios2_variable_max_mod.mod include/adios2/fortran/adios2_variable_min_mod.mod include/adios2/fortran/adios2_variable_mod.mod +include/adios2/helper/adiosCUDA.h +include/adios2/helper/adiosComm.h +include/adios2/helper/adiosComm.inl +include/adios2/helper/adiosCommDummy.h +include/adios2/helper/adiosCommMPI.h +include/adios2/helper/adiosDynamicBinder.h +include/adios2/helper/adiosFunctions.h +include/adios2/helper/adiosJSONcomplex.h +include/adios2/helper/adiosLog.h +include/adios2/helper/adiosMath.h +include/adios2/helper/adiosMath.inl +include/adios2/helper/adiosMemory.h +include/adios2/helper/adiosMemory.inl +include/adios2/helper/adiosMpiHandshake.h +include/adios2/helper/adiosNetwork.h +include/adios2/helper/adiosPluginManager.h +include/adios2/helper/adiosRangeFilter.h +include/adios2/helper/adiosString.h +include/adios2/helper/adiosSystem.h +include/adios2/helper/adiosType.h +include/adios2/helper/adiosType.inl +include/adios2/helper/adiosXML.h +include/adios2/helper/adiosXMLUtil.h +include/adios2/helper/adiosYAML.h +include/adios2/operator/OperatorFactory.h +include/adios2/operator/callback/Signature1.h +include/adios2/operator/callback/Signature2.h +include/adios2/operator/compress/CompressBZIP2.h +include/adios2/operator/compress/CompressBlosc.h +include/adios2/operator/compress/CompressLibPressio.h +include/adios2/operator/compress/CompressMGARD.h +include/adios2/operator/compress/CompressMGARDPlus.h +include/adios2/operator/compress/CompressNull.h +include/adios2/operator/compress/CompressPNG.h +include/adios2/operator/compress/CompressSZ.h +include/adios2/operator/compress/CompressSirius.h +include/adios2/operator/compress/CompressZFP.h +include/adios2/operator/plugin/PluginOperator.h +include/adios2/operator/plugin/PluginOperatorInterface.h +include/adios2/toolkit/aggregator/mpi/MPIAggregator.h +include/adios2/toolkit/aggregator/mpi/MPIChain.h +include/adios2/toolkit/aggregator/mpi/MPIShmChain.h +include/adios2/toolkit/burstbuffer/FileDrainer.h +include/adios2/toolkit/burstbuffer/FileDrainerSingleThread.h +include/adios2/toolkit/dataspaces/ds.h +include/adios2/toolkit/dataspaces/ds_data.h +include/adios2/toolkit/format/bp/BPBase.h +include/adios2/toolkit/format/bp/BPBase.inl +include/adios2/toolkit/format/bp/BPSerializer.h +include/adios2/toolkit/format/bp/BPSerializer.inl +include/adios2/toolkit/format/bp/bp3/BP3Base.h +include/adios2/toolkit/format/bp/bp3/BP3Deserializer.h +include/adios2/toolkit/format/bp/bp3/BP3Serializer.h +include/adios2/toolkit/format/bp/bp4/BP4Base.h +include/adios2/toolkit/format/bp/bp4/BP4Deserializer.h +include/adios2/toolkit/format/bp/bp4/BP4Serializer.h +include/adios2/toolkit/format/bp5/BP5Base.h +include/adios2/toolkit/format/bp5/BP5Deserializer.h +include/adios2/toolkit/format/bp5/BP5Serializer.h +include/adios2/toolkit/format/buffer/Buffer.h +include/adios2/toolkit/format/buffer/BufferV.h +include/adios2/toolkit/format/buffer/chunk/ChunkV.h +include/adios2/toolkit/format/buffer/ffs/BufferFFS.h +include/adios2/toolkit/format/buffer/heap/BufferSTL.h +include/adios2/toolkit/format/buffer/ipc/BufferSystemV.h +include/adios2/toolkit/format/buffer/malloc/MallocV.h +include/adios2/toolkit/format/dataman/DataManSerializer.h +include/adios2/toolkit/interop/hdf5/HDF5Common.h +include/adios2/toolkit/profiling/iochrono/IOChrono.h +include/adios2/toolkit/profiling/iochrono/Timer.h +include/adios2/toolkit/query/BlockIndex.h +include/adios2/toolkit/query/Index.h +include/adios2/toolkit/query/Query.h +include/adios2/toolkit/query/Util.h +include/adios2/toolkit/query/Worker.h +include/adios2/toolkit/shm/SerializeProcesses.h +include/adios2/toolkit/shm/Spinlock.h +include/adios2/toolkit/shm/TokenChain.h include/adios2/toolkit/sst/SSTConfig.h +include/adios2/toolkit/sst/cp/cp_internal.h +include/adios2/toolkit/sst/cp/ffs_marshal.h +include/adios2/toolkit/sst/dp_interface.h +include/adios2/toolkit/sst/sst.h +include/adios2/toolkit/sst/sst_comm.h +include/adios2/toolkit/sst/sst_comm_fwd.h +include/adios2/toolkit/sst/sst_data.h +include/adios2/toolkit/transport/Transport.h +include/adios2/toolkit/transport/file/FileDaos.h +include/adios2/toolkit/transport/file/FileFStream.h +include/adios2/toolkit/transport/file/FileIME.h +include/adios2/toolkit/transport/file/FilePOSIX.h +include/adios2/toolkit/transport/file/FileStdio.h +include/adios2/toolkit/transport/null/NullTransport.h +include/adios2/toolkit/transport/shm/ShmSystemV.h +include/adios2/toolkit/transportman/TransportMan.h +include/adios2/toolkit/zmq/zmqpubsub/ZmqPubSub.h +include/adios2/toolkit/zmq/zmqreqrep/ZmqReqRep.h include/adios2_c.h lib/cmake/adios2/CMakeFindDependencyMacro.cmake lib/cmake/adios2/FindBZip2.cmake lib/cmake/adios2/FindBlosc.cmake lib/cmake/adios2/FindCrayDRC.cmake +lib/cmake/adios2/FindDAOS.cmake lib/cmake/adios2/FindDataSpaces.cmake lib/cmake/adios2/FindHDF5.cmake lib/cmake/adios2/FindIME.cmake @@ -76,6 +217,7 @@ lib/cmake/adios2/FindPkgConfig.cmake lib/cmake/adios2/FindPython.cmake lib/cmake/adios2/FindPythonModule.cmake lib/cmake/adios2/FindSZ.cmake +lib/cmake/adios2/FindSodium.cmake lib/cmake/adios2/FindZeroMQ.cmake lib/cmake/adios2/Findpugixml.cmake lib/cmake/adios2/adios2-c-targets-%%CMAKE_BUILD_TYPE%%.cmake @@ -134,15 +276,16 @@ lib/cmake/adios2/upstream/FindPkgConfig.cmake lib/cmake/adios2/upstream/FindPython.cmake lib/cmake/adios2/upstream/FindPython/Support.cmake lib/cmake/adios2/upstream/GoogleTest.cmake +lib/libEncryptionOperator.so lib/libadios2_atl.so lib/libadios2_atl.so.2 lib/libadios2_atl.so.2.2.1 lib/libadios2_c.so lib/libadios2_c.so.2 -lib/libadios2_c.so.2.7.1 +lib/libadios2_c.so.2.8.0 lib/libadios2_c_mpi.so lib/libadios2_c_mpi.so.2 -lib/libadios2_c_mpi.so.2.7.1 +lib/libadios2_c_mpi.so.2.8.0 lib/libadios2_cmenet.so lib/libadios2_cmfabric.so lib/libadios2_cmmulticast.so @@ -152,16 +295,16 @@ lib/libadios2_cmudp.so lib/libadios2_cmzplenet.so lib/libadios2_core.so lib/libadios2_core.so.2 -lib/libadios2_core.so.2.7.1 +lib/libadios2_core.so.2.8.0 lib/libadios2_core_mpi.so lib/libadios2_core_mpi.so.2 -lib/libadios2_core_mpi.so.2.7.1 +lib/libadios2_core_mpi.so.2.8.0 lib/libadios2_cxx11.so lib/libadios2_cxx11.so.2 -lib/libadios2_cxx11.so.2.7.1 +lib/libadios2_cxx11.so.2.8.0 lib/libadios2_cxx11_mpi.so lib/libadios2_cxx11_mpi.so.2 -lib/libadios2_cxx11_mpi.so.2.7.1 +lib/libadios2_cxx11_mpi.so.2.8.0 lib/libadios2_dill.so lib/libadios2_dill.so.2 lib/libadios2_dill.so.2.4.1 @@ -174,16 +317,23 @@ lib/libadios2_ffs.so.1 lib/libadios2_ffs.so.1.6.0 lib/libadios2_fortran.so lib/libadios2_fortran.so.2 -lib/libadios2_fortran.so.2.7.1 +lib/libadios2_fortran.so.2.8.0 lib/libadios2_fortran_mpi.so lib/libadios2_fortran_mpi.so.2 -lib/libadios2_fortran_mpi.so.2.7.1 -lib/libadios2_taustubs.so +lib/libadios2_fortran_mpi.so.2.8.0 +lib/libadios2_perfstubs.so +%%PYTHON_SITELIBDIR%%/adios2/__init__.py +%%PYTHON_SITELIBDIR%%/adios2/adios2%%PYTHON_EXT_SUFFIX%%.so %%PYTHON_SITELIBDIR%%/adios2/bp4dbg/__init__.py %%PYTHON_SITELIBDIR%%/adios2/bp4dbg/data.py %%PYTHON_SITELIBDIR%%/adios2/bp4dbg/idxtable.py %%PYTHON_SITELIBDIR%%/adios2/bp4dbg/metadata.py %%PYTHON_SITELIBDIR%%/adios2/bp4dbg/utils.py +%%PYTHON_SITELIBDIR%%/adios2/bp5dbg/__init__.py +%%PYTHON_SITELIBDIR%%/adios2/bp5dbg/data.py +%%PYTHON_SITELIBDIR%%/adios2/bp5dbg/idxtable.py +%%PYTHON_SITELIBDIR%%/adios2/bp5dbg/metadata.py +%%PYTHON_SITELIBDIR%%/adios2/bp5dbg/utils.py share/iotest-config/coupling2.xml share/iotest-config/coupling2_blocking_01_simple.txt share/iotest-config/coupling2_blocking_02_dump_result.txt @@ -197,3 +347,5 @@ share/iotest-config/pipe2_05_add_variables.txt share/iotest-config/pipe2_06_busy.txt share/iotest-config/wf_2_to_1.txt share/iotest-config/wf_2_to_1.xml +@dir include/adios2/toolkit/sst/dp +@dir include/adios2/toolkit/sst/util
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