diff --git a/science/py-hoomd-blue/Makefile b/science/py-hoomd-blue/Makefile index 13a2b9fe990f..786efb6125e8 100644 --- a/science/py-hoomd-blue/Makefile +++ b/science/py-hoomd-blue/Makefile @@ -1,69 +1,71 @@ PORTNAME= hoomd-blue DISTVERSIONPREFIX= v -DISTVERSION= 4.9.1 +DISTVERSION= 5.0.0 CATEGORIES= science # physics PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Molecular dynamics and Monte Carlo soft matter simulation WWW= https://glotzerlab.engin.umich.edu/hoomd-blue/ \ https://github.com/glotzerlab/hoomd-blue LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= pybind11>0:devel/pybind11 USES= cmake:testing compiler:c++17-lang eigen:3 localbase:ldflags python shebangfix # see https://github.com/glotzerlab/hoomd-blue/issues/1204 USE_GITHUB= yes GH_ACCOUNT= glotzerlab -GH_TUPLE= glotzerlab:upp11:0c1fb8d:glotzerlab_upp11/hoomd/extern/upp11 \ - glotzerlab:nano-signal-slot:34223a4:glotzerlab_nano_signal_slot/hoomd/extern/nano-signal-slot \ - glotzerlab:quickhull:1ffbc6f:glotzerlab_quickhull/hoomd/extern/quickhull \ - glotzerlab:random123:a2c4f04:glotzerlab_random123/hoomd/extern/random123 \ - glotzerlab:HIP:d211f99:glotzerlab_HIP/hoomd/extern/HIP \ - glotzerlab:hipCUB:c70e193:glotzerlab_hipCUB/hoomd/extern/hipCUB \ - mphowardlab:neighbor:ba0f068:mphowardlab_neighbor/hoomd/extern/neighbor \ - mphowardlab:hipper:b6da049:mphowardlab_hipper/hoomd/extern/hipper +GH_TUPLE= glotzerlab:upp11:0c1fb8dfb4bcdc1c5c4eff9165539b15e70c4360:glotzerlab_upp11/hoomd/extern/upp11 \ + glotzerlab:nano-signal-slot:34223a4a7e97f8e114ef007e5360cf7a71265da3:glotzerlab_nano_signal_slot/hoomd/extern/nano-signal-slot \ + glotzerlab:quickhull:1ffbc6f884ea1da89e104a5996cf8a726db673d5:glotzerlab_quickhull/hoomd/extern/quickhull \ + glotzerlab:HIP:d211f99eebb3637b6840f310f8797abb25012c18:glotzerlab_HIP/hoomd/extern/HIP \ + glotzerlab:hipCUB:c70e19332a8402049b3359b409e50220a759c42d:glotzerlab_hipCUB/hoomd/extern/hipCUB \ + mphowardlab:neighbor:ba0f06869b766066a7068852fa3b8c5fa746f71f:mphowardlab_neighbor/hoomd/extern/neighbor \ + mphowardlab:hipper:b6da049a516ada03e4e1b66ca6b4c2c7c9668595:mphowardlab_hipper/hoomd/extern/hipper \ + glotzerlab:hoomd-examples:2710e2708877e375a56d2faa1df7d400b12d75a2:glotzerlab_hoomd_examples/sphinx-doc/tutorial \ + glotzerlab:OpenRAND:92dc12a23dff2d0aa3545f749d1c013677b9a87e:glotzerlab_OpenRAND/hoomd/extern/OpenRAND \ + mphowardlab:hipper:b6da049a516ada03e4e1b66ca6b4c2c7c9668595:mphowardlab_hipper/hoomd/extern/hipper SHEBANG_GLOB= *.sh CMAKE_OFF= BUILD_TESTING LDFLAGS+= -lexecinfo OPTIONS_DEFINE= TBB OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI OPTIONS_DEFAULT= MPICH TBB 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 MPICH_BUILD_DEPENDS= cereal>0:devel/cereal OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DENABLE_MPI=ON OPENMPI_BUILD_DEPENDS= cereal>0:devel/cereal OPENMPI_BROKEN= see https://github.com/glotzerlab/hoomd-blue/issues/1397 TBB_DESC= Enable support for Threading Building Blocks (TBB) TBB_CMAKE_BOOL= ENABLE_TBB TBB_LIB_DEPENDS= libtbb.so:devel/onetbb # the test mpi-test_communication requires excessive resources, see https://github.com/glotzerlab/hoomd-blue/issues/1396 .include post-patch: .if ${COMPILER_TYPE} == clang @${REINPLACE_CMD} -e 's|std::unary_function|std::__unary_function|' \ ${WRKSRC}/hoomd/ParticleData.cc .endif .include diff --git a/science/py-hoomd-blue/distinfo b/science/py-hoomd-blue/distinfo index 28fbbfa7b40e..abd6106c0cef 100644 --- a/science/py-hoomd-blue/distinfo +++ b/science/py-hoomd-blue/distinfo @@ -1,19 +1,21 @@ -TIMESTAMP = 1730613350 -SHA256 (glotzerlab-hoomd-blue-v4.9.1_GH0.tar.gz) = 80f474a209b621215ea005acac1340e123551b06fda1b678cceab97fc51ead50 -SIZE (glotzerlab-hoomd-blue-v4.9.1_GH0.tar.gz) = 2939390 -SHA256 (glotzerlab-upp11-0c1fb8d_GH0.tar.gz) = fe9db1b06fd504876e243c9031a594edbd0323e8337f908885f31cc980f642e9 -SIZE (glotzerlab-upp11-0c1fb8d_GH0.tar.gz) = 21024 -SHA256 (glotzerlab-nano-signal-slot-34223a4_GH0.tar.gz) = bfe51f7dd2cc097b70202f849c1a42a13ea5f53a1e902e053df155c3a157c30b -SIZE (glotzerlab-nano-signal-slot-34223a4_GH0.tar.gz) = 4747 -SHA256 (glotzerlab-quickhull-1ffbc6f_GH0.tar.gz) = b57bf720afd1c44741d7d7018501a9ce4f869897ea9530a0d2cc076873f96e11 -SIZE (glotzerlab-quickhull-1ffbc6f_GH0.tar.gz) = 16242 -SHA256 (glotzerlab-random123-a2c4f04_GH0.tar.gz) = 9d24475b2544cfe9cf9c1f2fc43e811d8861869b1ec0ee9b8bf7586c27e06007 -SIZE (glotzerlab-random123-a2c4f04_GH0.tar.gz) = 318755 -SHA256 (glotzerlab-HIP-d211f99_GH0.tar.gz) = 16913e77070effade693b326449bd4fd688cf6550d47b698a7e03affe215f206 -SIZE (glotzerlab-HIP-d211f99_GH0.tar.gz) = 897743 -SHA256 (glotzerlab-hipCUB-c70e193_GH0.tar.gz) = c9f132a8359e8ee3074f8f56b8070d9aa3c5d60eecea330529ed4020236d77fd -SIZE (glotzerlab-hipCUB-c70e193_GH0.tar.gz) = 110385 -SHA256 (mphowardlab-neighbor-ba0f068_GH0.tar.gz) = e21cef8dab85131d2cc5f2d1b49bd1030d27b9e24c2cde5f18fe57744faeb9a8 -SIZE (mphowardlab-neighbor-ba0f068_GH0.tar.gz) = 49050 -SHA256 (mphowardlab-hipper-b6da049_GH0.tar.gz) = b332ae31399ba972e1ac57428e92385291ba7f1100b2fb45ab2b7e77391d037f -SIZE (mphowardlab-hipper-b6da049_GH0.tar.gz) = 20201 +TIMESTAMP = 1733334979 +SHA256 (glotzerlab-hoomd-blue-v5.0.0_GH0.tar.gz) = 09a568d87eaa0af09a75512f8b5b2118d1f3f54dcbf89dbb9794b804a6193852 +SIZE (glotzerlab-hoomd-blue-v5.0.0_GH0.tar.gz) = 2768876 +SHA256 (glotzerlab-upp11-0c1fb8dfb4bcdc1c5c4eff9165539b15e70c4360_GH0.tar.gz) = 759695139bddae1d8a7cd52c967b856d6debf28fb37ea177f78c4434e2b210a8 +SIZE (glotzerlab-upp11-0c1fb8dfb4bcdc1c5c4eff9165539b15e70c4360_GH0.tar.gz) = 21058 +SHA256 (glotzerlab-nano-signal-slot-34223a4a7e97f8e114ef007e5360cf7a71265da3_GH0.tar.gz) = d15030482c82d9e4a99c2f67d8ef23b33cc318dd48ac0f8e804c6d4750f27ff4 +SIZE (glotzerlab-nano-signal-slot-34223a4a7e97f8e114ef007e5360cf7a71265da3_GH0.tar.gz) = 4748 +SHA256 (glotzerlab-quickhull-1ffbc6f884ea1da89e104a5996cf8a726db673d5_GH0.tar.gz) = 55c87e78bf990509ff35e3e039213ca6e3890ce988c2891647d65079696ae3a9 +SIZE (glotzerlab-quickhull-1ffbc6f884ea1da89e104a5996cf8a726db673d5_GH0.tar.gz) = 16242 +SHA256 (glotzerlab-HIP-d211f99eebb3637b6840f310f8797abb25012c18_GH0.tar.gz) = badcb27eb7d540a668877dd193aba529755d5f69c8e6411ee495668984640e5c +SIZE (glotzerlab-HIP-d211f99eebb3637b6840f310f8797abb25012c18_GH0.tar.gz) = 898870 +SHA256 (glotzerlab-hipCUB-c70e19332a8402049b3359b409e50220a759c42d_GH0.tar.gz) = f3dbd921ea8c5fe9068d6d9e6e9112c11c7e18488169ce48423d9fdb014536c6 +SIZE (glotzerlab-hipCUB-c70e19332a8402049b3359b409e50220a759c42d_GH0.tar.gz) = 110500 +SHA256 (mphowardlab-neighbor-ba0f06869b766066a7068852fa3b8c5fa746f71f_GH0.tar.gz) = 089129a1539d8e993f725017f1aadc60f9e40116e8a65dfbe70b0df9ac2d7cf3 +SIZE (mphowardlab-neighbor-ba0f06869b766066a7068852fa3b8c5fa746f71f_GH0.tar.gz) = 49039 +SHA256 (mphowardlab-hipper-b6da049a516ada03e4e1b66ca6b4c2c7c9668595_GH0.tar.gz) = c64a484884eaab3eb9fd8f7b27b144a7bfadfeab101e95d82bc2a6f7e4fb7cec +SIZE (mphowardlab-hipper-b6da049a516ada03e4e1b66ca6b4c2c7c9668595_GH0.tar.gz) = 20228 +SHA256 (glotzerlab-hoomd-examples-2710e2708877e375a56d2faa1df7d400b12d75a2_GH0.tar.gz) = 5d20f4b15cd785bc730a8b5ac10cb3f8632c5bbc088fc684223706576e31513c +SIZE (glotzerlab-hoomd-examples-2710e2708877e375a56d2faa1df7d400b12d75a2_GH0.tar.gz) = 5969219 +SHA256 (glotzerlab-OpenRAND-92dc12a23dff2d0aa3545f749d1c013677b9a87e_GH0.tar.gz) = a84657d9ac24083c1aef3d883927d5993270697af69a04f616227f9077eb8e19 +SIZE (glotzerlab-OpenRAND-92dc12a23dff2d0aa3545f749d1c013677b9a87e_GH0.tar.gz) = 298040 diff --git a/science/py-hoomd-blue/files/patch-hoomd_GPUFlags.h b/science/py-hoomd-blue/files/patch-hoomd_GPUFlags.h deleted file mode 100644 index 9b655f55b4af..000000000000 --- a/science/py-hoomd-blue/files/patch-hoomd_GPUFlags.h +++ /dev/null @@ -1,18 +0,0 @@ -Fix build with LLVM 19 - -/wrkdirs/usr/ports/science/py-hoomd-blue/work/hoomd-blue-4.9.0/hoomd/GPUFlags.h:160:27: -error: reference to non-static member function must be called - 160 | this->resetFlags(from.readFlags); - | ~~~~~^~~~~~~~~ - ---- hoomd/GPUFlags.h.orig 2024-10-31 16:09:15 UTC -+++ hoomd/GPUFlags.h -@@ -157,7 +157,7 @@ GPUFlags::GPUFlags(const GPUFlags& from) - memclear(); - - // copy over the data to the new GPUFlags -- this->resetFlags(from.readFlags); -+ this->resetFlags(from.readFlags()); - } - - template GPUFlags& GPUFlags::operator=(const GPUFlags& rhs) diff --git a/science/py-hoomd-blue/pkg-plist b/science/py-hoomd-blue/pkg-plist index 0aa294d0609f..422aef1db7a8 100644 --- a/science/py-hoomd-blue/pkg-plist +++ b/science/py-hoomd-blue/pkg-plist @@ -1,942 +1,867 @@ lib/cmake/hoomd/FindCUDALibs.cmake -lib/cmake/hoomd/FindTBB.cmake lib/cmake/hoomd/HOOMDHIPSetup.cmake lib/cmake/hoomd/hoomd-config-version.cmake lib/cmake/hoomd/hoomd-config.cmake lib/cmake/hoomd/hoomd-macros.cmake lib/cmake/hoomd/hoomd-targets-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/__init__.py -%%PYTHON_SITELIBDIR%%/hoomd/_compile.py %%PYTHON_SITELIBDIR%%/hoomd/_hoomd%%PYTHON_EXT_SUFFIX%%.so %%PYTHON_SITELIBDIR%%/hoomd/box.py %%PYTHON_SITELIBDIR%%/hoomd/communicator.py %%PYTHON_SITELIBDIR%%/hoomd/conftest.py %%PYTHON_SITELIBDIR%%/hoomd/custom/__init__.py %%PYTHON_SITELIBDIR%%/hoomd/custom/custom_action.py %%PYTHON_SITELIBDIR%%/hoomd/custom/custom_operation.py %%PYTHON_SITELIBDIR%%/hoomd/data/__init__.py %%PYTHON_SITELIBDIR%%/hoomd/data/array.py %%PYTHON_SITELIBDIR%%/hoomd/data/array_view.py %%PYTHON_SITELIBDIR%%/hoomd/data/collections.py %%PYTHON_SITELIBDIR%%/hoomd/data/local_access.py %%PYTHON_SITELIBDIR%%/hoomd/data/local_access_cpu.py %%PYTHON_SITELIBDIR%%/hoomd/data/local_access_gpu.py %%PYTHON_SITELIBDIR%%/hoomd/data/parameterdicts.py %%PYTHON_SITELIBDIR%%/hoomd/data/smart_default.py %%PYTHON_SITELIBDIR%%/hoomd/data/syncedlist.py %%PYTHON_SITELIBDIR%%/hoomd/data/typeconverter.py %%PYTHON_SITELIBDIR%%/hoomd/data/typeparam.py %%PYTHON_SITELIBDIR%%/hoomd/device.py %%PYTHON_SITELIBDIR%%/hoomd/error.py %%PYTHON_SITELIBDIR%%/hoomd/filter/__init__.py %%PYTHON_SITELIBDIR%%/hoomd/filter/all_.py %%PYTHON_SITELIBDIR%%/hoomd/filter/custom.py %%PYTHON_SITELIBDIR%%/hoomd/filter/filter_.py %%PYTHON_SITELIBDIR%%/hoomd/filter/null.py %%PYTHON_SITELIBDIR%%/hoomd/filter/rigid.py %%PYTHON_SITELIBDIR%%/hoomd/filter/set_.py %%PYTHON_SITELIBDIR%%/hoomd/filter/tags.py %%PYTHON_SITELIBDIR%%/hoomd/filter/type_.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/__init__.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/_hpmc%%PYTHON_EXT_SUFFIX%%.so %%PYTHON_SITELIBDIR%%/hoomd/hpmc/compute.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/external/__init__.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/external/external.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/external/field.py +%%PYTHON_SITELIBDIR%%/hoomd/hpmc/external/harmonic.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/external/linear.py -%%PYTHON_SITELIBDIR%%/hoomd/hpmc/external/user.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/external/wall.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/integrate.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/nec/__init__.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/nec/integrate.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/nec/tune.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/__init__.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/angular_step.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/expanded_gaussian.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/lennard_jones.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/lj_gauss.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/opp.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/pair.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/step.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/union.py -%%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/user.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/__init__.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/conftest.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_boxmc.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_boxmc_move_tuner.py -%%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_clusters.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_compute_free_volume.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_compute_sdf.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_external_field.py -%%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_external_user.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_external_wall.py +%%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_gca.py +%%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_kt.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_move_size_tuner.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_muvt.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_pair_angular_step.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_pair_expanded_gaussian.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_pair_lennard_jones.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_pair_lj_gauss.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_pair_opp.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_pair_step.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_pair_union.py -%%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_pair_union_user.py -%%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_pair_user.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_quick_compress.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_scale.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_shape.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_shape_updater.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_shape_utils.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_small_box_2d.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_small_box_3d.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/shape_move.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/tune/__init__.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/tune/boxmc_move_size.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/tune/mc_move_tune.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/tune/move_size.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/update.py %%PYTHON_SITELIBDIR%%/hoomd/include/HOOMDVersion.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/AABB.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/AABBTree.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/Action.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/Analyzer.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/ArrayView.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/Autotuned.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/Autotuner.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/BondedGroupData.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/BondedGroupData.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/BoxDim.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/BoxResizeUpdater.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/BoxResizeUpdaterGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/BoxResizeUpdaterGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/CachedAllocator.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/CellList.h 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