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Improvements in use of python SharedMemory (#26)
* Improvements in use of python SharedMemory: - Remove previous patch and instead ship a backport of the changes which are in python 3.13. This allows the "track=False" option when creating SharedMemory segments. - In order to better handle cleanup, keep a registry of all memory segments allocated on every process. Register a cleanup handler for python atexit and also register a cleanup handler for signals such as SIGTERM. - Expand unit tests - Convert build to pyproject.toml with minimal setup.py backend. - Improve test and deployment workflows. * Fix test.yml branch * Remove some typing info in backport, for compatibility with 3.9 * Use mpich for running CI tests * Remove stale scripts * Add multinode test script for perlmutter. * Remove stale scripts and fix typo in readme
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,72 +1,105 @@ | ||
| # Use pre-built docker containers to run our unit tests on different python versions. | ||
| # In general, we try to run on: | ||
| # - The oldest supported python | ||
| # - The latest stable python that is the common default on most systems and conda | ||
| # - (During transitions) The newly released bleeding edge python | ||
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| name: Tests | ||
| name: Run Test Suite | ||
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| on: | ||
| push: | ||
| branches: [ master ] | ||
| branches: | ||
| - master | ||
| pull_request: | ||
| branches: [ master ] | ||
| branches: | ||
| - master | ||
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| concurrency: | ||
| group: ${{ github.workflow }}-${{ github.ref }} | ||
| cancel-in-progress: true | ||
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| jobs: | ||
| linux: | ||
| runs-on: ubuntu-latest | ||
| test: | ||
| name: Tests on ${{ matrix.arch }} with Conda Python-${{ matrix.python }} | ||
| runs-on: ${{ matrix.os }} | ||
| defaults: | ||
| run: | ||
| shell: bash -l {0} | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| python-version: ["3.8", "3.10", "3.11", "3.12"] | ||
| include: | ||
| - os: ubuntu-latest | ||
| python: "3.9" | ||
| arch: Linux-x86_64 | ||
| - os: ubuntu-latest | ||
| python: "3.11" | ||
| arch: Linux-x86_64 | ||
| - os: ubuntu-latest | ||
| python: "3.13" | ||
| arch: Linux-x86_64 | ||
| - os: macos-latest | ||
| python: "3.10" | ||
| arch: MacOSX-x86_64 | ||
| - os: macos-latest | ||
| python: "3.13" | ||
| arch: MacOSX-x86_64 | ||
| - os: macos-latest | ||
| python: "3.10" | ||
| arch: MacOSX-arm64 | ||
| - os: macos-latest | ||
| python: "3.13" | ||
| arch: MacOSX-arm64 | ||
| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
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| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
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| - name: Install Dependencies | ||
| run: ./test_scripts/install_deps_github_ubuntu.sh | ||
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| - name: Install Package | ||
| run: pip3 install . | ||
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| - name: Run Serial Test | ||
| run: MPI_DISABLE=1 python3 -c 'import pshmem.test; pshmem.test.run()' | ||
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| - name: Run MPI Test on 1 Process | ||
| run: mpirun -np 1 python3 -c 'import pshmem.test; pshmem.test.run()' | ||
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| - name: Run MPI Test on 2 Processes | ||
| run: mpirun -np 2 python3 -c 'import pshmem.test; pshmem.test.run()' | ||
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| macos: | ||
| runs-on: macos-latest | ||
| strategy: | ||
| matrix: | ||
| python-version: ["3.10", "3.11", "3.12"] | ||
| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
|
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||
| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
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| - name: Install Dependencies | ||
| run: ./test_scripts/install_deps_github_macos.sh | ||
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| - name: Install Package | ||
| run: pip3 install . | ||
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| - name: Run Serial Test | ||
| run: MPI_DISABLE=1 python3 -c 'import pshmem.test; pshmem.test.run()' | ||
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| - name: Run MPI Test on 1 Process | ||
| run: mpirun -np 1 python3 -c 'import pshmem.test; pshmem.test.run()' | ||
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||
| - name: Run MPI Test on 2 Processes | ||
| run: mpirun -np 2 python3 -c 'import pshmem.test; pshmem.test.run()' | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
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| - name: Setup Conda Base | ||
| run: | | ||
| sudo rm -rf /usr/share/miniconda \ | ||
| && sudo rm -rf /usr/local/miniconda \ | ||
| && curl -SL -o miniforge.sh https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-${{ matrix.arch }}.sh \ | ||
| && bash miniforge.sh -b -f -p ~/conda \ | ||
| && source ~/conda/etc/profile.d/conda.sh \ | ||
| && conda activate base \ | ||
| && conda update -n base --yes conda | ||
| - name: Check Conda Config | ||
| run: | | ||
| source ~/conda/etc/profile.d/conda.sh \ | ||
| && conda activate base \ | ||
| && conda info \ | ||
| && conda list \ | ||
| && conda config --show-sources \ | ||
| && conda config --show | ||
| - name: Install Dependencies | ||
| run: | | ||
| source ~/conda/etc/profile.d/conda.sh \ | ||
| && conda create --yes -n test python==${{ matrix.python }} \ | ||
| && conda activate test \ | ||
| && conda install --yes numpy mpich mpi4py | ||
| - name: Install | ||
| run: | | ||
| source ~/conda/etc/profile.d/conda.sh \ | ||
| && conda activate test \ | ||
| && pip install . | ||
| - name: Run Serial Tests | ||
| run: | | ||
| source ~/conda/etc/profile.d/conda.sh \ | ||
| && conda activate test \ | ||
| && mkdir -p test \ | ||
| && pushd test >/dev/null 2>&1 \ | ||
| && MPI_DISABLE=1 python3 -c 'import pshmem.test; pshmem.test.run()' \ | ||
| && popd >/dev/null 2>&1 | ||
| - name: Run MPI Tests | ||
| run: | | ||
| source ~/conda/etc/profile.d/conda.sh \ | ||
| && conda activate test \ | ||
| && mkdir -p test \ | ||
| && pushd test >/dev/null 2>&1 \ | ||
| && mpirun -np 1 python3 -c 'import pshmem.test; pshmem.test.run()' \ | ||
| && mpirun -np 2 python3 -c 'import pshmem.test; pshmem.test.run()' \ | ||
| && popd >/dev/null 2>&1 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,60 @@ | ||
| ## | ||
| # Copyright (c) 2017-2025, all rights reserved. Use of this source code | ||
| # is governed by a BSD license that can be found in the top-level | ||
| # LICENSE file. | ||
| ## | ||
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| import sys | ||
| import atexit | ||
| import signal | ||
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| class MPISharedRegistry: | ||
| """Registry of shared memory buffers. | ||
| This tracks all MPIShared memory buffers on the current process and | ||
| ensures they are cleaned up when the process is terminated. | ||
| """ | ||
| def __init__(self): | ||
| self.reg = dict() | ||
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| def register(self, name, buffer, noderank): | ||
| self.reg[name] = (buffer, noderank) | ||
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| def unregister(self, name): | ||
| del self.reg[name] | ||
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| def cleanup(self): | ||
| for name, (buf, noderank) in self.reg.items(): | ||
| buf.close() | ||
| if noderank == 0: | ||
| buf.unlink() | ||
| self.reg.clear() | ||
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| """Single instance of the registry""" | ||
| registry = MPISharedRegistry() | ||
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| def _signal_handler(sig, frame): | ||
| global registry | ||
| registry.cleanup() | ||
| sys.exit(0) | ||
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| @atexit.register | ||
| def _atexit_handler(): | ||
| global registry | ||
| registry.cleanup() | ||
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| def _register_signals(): | ||
| signal.signal(signal.SIGINT, _signal_handler) | ||
| signal.signal(signal.SIGTERM, _signal_handler) | ||
| signal.signal(signal.SIGQUIT, _signal_handler) | ||
| signal.signal(signal.SIGHUP, _signal_handler) | ||
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| # Register signal handlers on import | ||
| _register_signals() |
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