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@@ -14,15 +14,21 @@
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}
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# Best to start with the serial version when debugging build failures
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- %bcond_without mpich
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- %bcond_without openmpi
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+ %bcond mpich 1
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+ %bcond openmpi 1
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- %bcond_without tests
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+ %bcond tests 1
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+
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+ # Python unit tests in MPI environment fail in a non-deterministic way.
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+ # Using pytest _as is_ doesn't work either and `-m unittest` does not
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+ # allow filtering tests as `pytest -k` does.
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+ # For now we don't run the Python MPI tests.
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+ %bcond mpi_py_unittest 0
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%global forgeurl https://github.com/arbor-sim/arbor
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Name: arbor
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- Version: 0.7
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+ Version: 0.9.0
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Release: %autorelease
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Summary: Multi-compartment neural network simulation library
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@@ -36,13 +42,6 @@
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License: BSD-3-Clause
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Patch: 0001-Quote-various-cmake-var-values.patch
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- # Add some missing #include directives
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- # Fixes failure to compile with GCC 13.
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- # https://github.com/arbor-sim/arbor/pull/2080
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- Patch: %{forgeurl}/pull/2080.patch
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- # Replace use of LooseVersion from distutils.version (removed in Python3.12)
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- # https://github.com/arbor-sim/arbor/pull/2157
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- Patch: looseversion.patch
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# Random123 does not support:
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# mips64r2 mips32r2 s390
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@@ -90,11 +89,13 @@
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%package doc
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# Does not require the main package, since it may be installed by people using
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# the MPI builds
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- Summary: Documentation for arbor
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+ Summary: Documentation for arbor
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BuildRequires: python3-sphinx
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BuildRequires: python3-sphinx_rtd_theme
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BuildRequires: python3-svgwrite
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+ BuildArch: noarch
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+
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%description doc %{_description}
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%if %{with mpich}
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@@ -172,6 +173,9 @@
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# Correct Python shebangs in all files
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find . -type f -name "*" -exec sed -i 's|^#![ ]*/usr/bin/env.*python.*$|#!/usr/bin/python3|' {} 2>/dev/null ';'
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+ # Fix shebang (special case)
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+ sed -i 's|^#![ ]*/usr/env/bin.*python.*$|#!/usr/bin/python3|' example/lfp/neuron_lfp_example.py
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+
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# test scripts
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cp %{SOURCE1} scripts/
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cp %{SOURCE2} scripts/
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@@ -216,6 +220,7 @@
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-DARB_WITH_MPI:BOOL=$MPI_YES \\\
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-DARB_WITH_GPU:BOOL=OFF \\\
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-DARB_ARCH:STRING="none" \\\
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+ -DARB_CXX_FLAGS_TARGET:STRING="-ffat-lto-objects" \\\
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-DCMAKE_INSTALL_LIBDIR=%{_lib} \\\
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-DARB_WITH_PYTHON:BOOL=ON \\\
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-DARB_PYTHON_LIB_PATH:STRING=$MPI_PYTHON3_SITEARCH \\\
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@@ -348,51 +353,51 @@
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%endif
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- # https://github.com/arbor-sim/arbor/blob/master/.github/workflows/test-everything.yml
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+ # https://github.com/arbor-sim/arbor/blob/master/.github/workflows/test-matrix.yml
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%if %{with tests}
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%check
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- # General tests
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- export PYTHONPATH="%{buildroot}%{python3_sitearch}:%{buildroot}%{python3_sitelib}"
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- # for arbor-build-catalogue
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- export PATH="$PATH:%{buildroot}/%{_bindir}"
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+
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+ # Taken from upstream's GitHub workflow
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+ %global mpirun mpirun -n %{_smp_build_ncpus}
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# these tests segfault, filter out
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+ gtest_filter="${gtest_filter--}${gtest_filter+:}*diffusion*"
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+
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pushd build-serial
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- %{python3} -m unittest discover -v -s ../python
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- ./bin/unit --gtest_filter=-*task_system.test_copy*:*notification_queue.test_copy*
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+ %{py3_test_envvars} %{python3} -m unittest discover -v -s ../python
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+ ./bin/unit ${gtest_filter+--gtest_filter=}${gtest_filter-}
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./bin/unit-modcc
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cp ../scripts/run_cpp_examples.sh .
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./run_cpp_examples.sh
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popd
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- ./scripts/run_python_examples.sh
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# MPICH
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%if %{with mpich}
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%{_mpich_load}
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- export PYTHONPATH="%{buildroot}/$MPI_PYTHON3_SITEARCH"
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- export PATH="$PATH:."
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pushd build-mpich
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- mpirun -n %{_smp_build_ncpus} %{python3} -m unittest discover -v -s ../python
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- mpirun -n %{_smp_build_ncpus} ./bin/unit-mpi
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+ %if %{with mpi_py_unittest}
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+ %{py3_test_envvars} %{mpirun} %{python3} -m unittest discover -v -s ../python
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+ %endif
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+ %{mpirun} ./bin/unit-mpi
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cp ../scripts/run_cpp_examples.sh .
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- ./run_cpp_examples.sh "mpirun -n %{_smp_build_ncpus}"
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+ ./run_cpp_examples.sh "%{mpirun}"
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popd
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- ./scripts/run_python_examples.sh "mpirun -n %{_smp_build_ncpus}"
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+ %{py3_test_envvars} ./scripts/run_python_examples.sh "%{mpirun}"
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%{_mpich_unload}
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%endif
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# OpenMPI
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%if %{with openmpi}
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%{_openmpi_load}
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- export PYTHONPATH="%{buildroot}/$MPI_PYTHON3_SITEARCH"
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- export PATH="$PATH:."
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pushd build-openmpi
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- mpirun -n %{_smp_build_ncpus} %{python3} -m unittest discover -v -s ../python
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- mpirun -n %{_smp_build_ncpus} ./bin/unit-mpi
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+ %if %{with mpi_py_unittest}
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+ %{py3_test_envvars} %{mpirun} %{python3} -m unittest discover -v -s ../python
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+ %endif
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+ %{mpirun} ./bin/unit-mpi
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cp ../scripts/run_cpp_examples.sh .
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- ./run_cpp_examples.sh "mpirun -n %{_smp_build_ncpus}"
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+ ./run_cpp_examples.sh "%{mpirun}"
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popd
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- ./scripts/run_python_examples.sh "mpirun -n %{_smp_build_ncpus}"
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+ %{py3_test_envvars} ./scripts/run_python_examples.sh "%{mpirun}"
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%{_openmpi_unload}
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%endif
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%endif
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gui1ty
commented 4 months ago
Python unit tests are failing. I disabled them for now. Use
--with mpi_py_unittestto enable them for further inspection. For the serial build all tests succeed, if that is any consolation. Upstream has stopped runningrun_python_examples.shin their workflow. Maybe we can drop that script as well. Although, it still runs fine without issues.I also fixed some rpmlint errors. I haven't checked if these were present before. One error (
static-library-without-debuginfo) remains, though. If my understanding of the error is correct, the static libraries need to be added tofind-debuginfo. Yet, I couldn't find any information on how to achieve that. It seemsfind-debuginfois baked in to rpm at the end of the%installstage and doesn't take static libraries into consideration.More info is in the commit messages.