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After an update to mpi4py v4.0 pyzoltan starts to fail with the following error (see also the original bug report):
creating build/temp.linux-aarch64-cpython-313/pyzoltan/core aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/trilinos -I/<<PKGBUILDDIR>>/pyzoltan/czoltan -I/usr/lib/python3/dist-packages/cyarray -I/usr/lib/python3/dist-packages/mpi4py/include -I/usr/include/python3.13 -c pyzoltan/core/zoltan.cpp -o build/temp.linux-aarch64-cpython-313/pyzoltan/core/zoltan.o -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from pyzoltan/core/zoltan.cpp:1291: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ pyzoltan/core/zoltan.cpp:2287:3: error: ‘MPI_Session’ does not name a type 2287 | MPI_Session ob_mpi; | ^~~~~~~~~~~ error: command '/usr/bin/aarch64-linux-gnu-g++' failed with exit code 1 E: pybuild pybuild:389: build: plugin distutils failed with: exit code=1: /usr/bin/python3.13 setup.py build I: pybuild base:311: /usr/bin/python3 setup.py build ---------------------------------------------------------------------- Using Zoltan from: /usr/include/trilinos /usr/lib ---------------------------------------------------------------------- /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'setup_requres' warnings.warn(msg) running build running build_py creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan copying pyzoltan/api.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan copying pyzoltan/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core copying pyzoltan/core/zoltan_utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core copying pyzoltan/core/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan copying pyzoltan/czoltan/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/tools copying pyzoltan/tools/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/tools copying pyzoltan/tools/run_parallel_script.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/tools creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core/tests copying pyzoltan/core/tests/zcomm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core/tests copying pyzoltan/core/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core/tests copying pyzoltan/core/tests/3d_partition.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core/tests copying pyzoltan/core/tests/test_zoltan.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core/tests copying pyzoltan/core/tests/geometric_partitioner.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core/tests running egg_info writing PyZoltan.egg-info/PKG-INFO writing dependency_links to PyZoltan.egg-info/dependency_links.txt writing requirements to PyZoltan.egg-info/requires.txt writing top-level names to PyZoltan.egg-info/top_level.txt reading manifest file 'PyZoltan.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'PyZoltan.egg-info/SOURCES.txt' copying pyzoltan/core/__init__.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core copying pyzoltan/core/msstdint.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core copying pyzoltan/core/zoltan.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core copying pyzoltan/core/zoltan_comm.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core copying pyzoltan/core/zoltan_dd.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core copying pyzoltan/czoltan/__init__.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan copying pyzoltan/czoltan/czoltan.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan copying pyzoltan/czoltan/czoltan_comm.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan copying pyzoltan/czoltan/czoltan_config.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan copying pyzoltan/czoltan/czoltan_dd.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan copying pyzoltan/czoltan/czoltan_types.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan copying pyzoltan/czoltan/mpi-compat.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan copying pyzoltan/core/tests/mesh.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core/tests running build_ext building 'pyzoltan.core.zoltan' extension creating build/temp.linux-aarch64-cpython-312 creating build/temp.linux-aarch64-cpython-312/pyzoltan creating build/temp.linux-aarch64-cpython-312/pyzoltan/core aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/trilinos -I/<<PKGBUILDDIR>>/pyzoltan/czoltan -I/usr/lib/python3/dist-packages/cyarray -I/usr/lib/python3/dist-packages/mpi4py/include -I/usr/include/python3.12 -c pyzoltan/core/zoltan.cpp -o build/temp.linux-aarch64-cpython-312/pyzoltan/core/zoltan.o -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from pyzoltan/core/zoltan.cpp:1291: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ pyzoltan/core/zoltan.cpp:2287:3: error: ‘MPI_Session’ does not name a type 2287 | MPI_Session ob_mpi; | ^~~~~~~~~~~ error: command '/usr/bin/aarch64-linux-gnu-g++' failed with exit code 1 E: pybuild pybuild:389: build: plugin distutils failed with: exit code=1: /usr/bin/python3 setup.py build dh_auto_build: error: pybuild --build -i python{version} -p "3.13 3.12" returned exit code 13 make: *** [debian/rules:14: binary-arch] Error 25 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2024-09-13T09:22:53Z
Looking at the generated zoltan.cpp line 2287 the problem seems to come form the following statement:
zoltan.cpp
/* "mpi4py/MPI.pxd":107 * cdef object __weakref__ * * ctypedef api class Session [ # <<<<<<<<<<<<<< * type PyMPISession_Type, * object PyMPISessionObject, */ struct PyMPISessionObject { PyObject_HEAD MPI_Session ob_mpi; // line 2278 unsigned int flags; PyObject *__weakref__; }; typedef struct PyMPISessionObject PyMPISessionObject;
Which is clearly linked to mpi4py, probably an API change.
The text was updated successfully, but these errors were encountered:
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After an update to mpi4py v4.0 pyzoltan starts to fail with the following error (see also the original bug report):
Looking at the generated
zoltan.cpp
line 2287 the problem seems to come form the following statement:Which is clearly linked to mpi4py, probably an API change.
The text was updated successfully, but these errors were encountered: