Tags: open-atmos/PyMPDATA-MPI
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Add 'None' courant field for ShallowWaterScenario tests, change plots… … in README.md to show MPI calculation in ShallowWaterScenario (#178) * change initial condition and output_steps size to give a more visible wireframe in plot * add None courant field option for ShallowWaterScenario * add temporary ssh interface to macos worker * remove the interface * add plotting of shallow water scenario * fix filename generation with None argument * fix typo leading to wrong calls for plotting * add new animations to README
Update package name to match package name format that is required on … …PyPi; pre-commit bump (incl. docstring updates) (#153) * Update package name to match binary distribution format that is required on PyPi * run pre-commit locally for black reformatting
remove setup.py; update pyproject.toml; switch from macos-12 to macos… …-13+macos-14 on CI; bump CI actions; add check for threading level in MPI; docstring formatting updates to match pre-commit update (#151) * remove setup.py and update pyproject.toml * fixed formmating and added PyMPDATA.impl package to pyproject.toml * updated workflows and __init__.py * bump h5py version in CI * changes to workflows to adress macos errors * changes cont. * added full hdf5 path * added different hdf5 path * added different hdf5 path * added bash line to find hdf5 lib * added arm architecture flag to brew install * add forced linking to hdf5 in homebrew * enable ssh access * resolve merge conflitcs * remove ssh access * readded ssh capability due to macos-13+python3.12 errors * fix yml formmating * change macos version to 14 to see arm behaviour * fix macos versions in workflows * bump actions versions * add ssh point during test failure * add ssh point during test failure * add ssh point after test_setup to check macos and numba-mpi comaptability * removed ssh entry points, added macos env variable to allow for numba-mpi initialization * moved path variable export * move path variable assignment agian * change macos to macos-15, add failure entry point * fix typo * readded ubuntu tests, activate mpich on macos-15, change DYLD_FALLBACK_LIBRARY_PATH to include default macos paths * remove mpich from macos test matrix * actually remove mpich from macos tests * add intel-based macos tests * fix yml formatting * fix formmating * exclude macos-13 and python 3.12 pair * change exclusion logic * change exclusion logic * add threads test, disable macos-13 inner * add test file * remove threading tests in favour of sanity check in PyMPDATA * bump numba-mpi and PyMPDATA * change macos-15 to macos-14 for testing * change macos-15 to macos-14 due to openmpi version issues * black formatting * reword xfail condition * temporarily remove xfail condition * temporarily remove xfail condition * add fixture with less broad xfail selection * linting fixes * fix typo * change xfail to check only results of first worker * fix rank check typo * change mpi rank check * make xfail condition narrower * move xfail condition to if-tree in class constructor * reword xfail to actually run test * broaden xfail condition * add pylint flags * change test checks * changed logic to single if clause * changed logic to single if clause * reverse jit disable flag check * change xfail logic * change exclusion logic to include mpi.size * add rank check * increase test time due to ubuntu timeout * add numba threading layer variable * add mpi multithreading assertion * added missing import * added missing import * fix call to mpi4py.MPI.Query_thread() * unbump numba, numpy, numba-mpi and PyMPDATA deps * go back to Python 3.10 only * disable P3.12 in one more place * disable xfail * precommit * add installation of GraphicsMagick on CI * shorten timeout * shorten one more timeout --------- Co-authored-by: Sylwester Arabas <sylwester.arabas@agh.edu.pl>
cache pip dependencies in CI; pin setuptool[_scm] dependencies to fix… … build; codecov action bump (#106) * cache pip dependencies in CI * h5py as fixed version * save cache * save at the end * print env * get path from purelib * use restore action: * show pytest * restore HDF5_LIBDIR variable * back with .[test] install * comment cache * comment restore cache * debug: restore cache after install * uncomment pip install * pytest without mpiexec * update path * debug: where does pytest binary is? * run with python -m * md5 as key, filter warning * cat build.log * proper warning message * setuptools < 69.2.0 * setup setuptools to 56 * rm build-backend * setuptools==69.1.0 * setuptools-scm==7.1.0 * remove hdf5 variables * codecov update and added badge
add support for threading and for user-specified MPI dimension. Closes … …#35 (#98) * mpi: outer, threads:2 * add TODO ids * add TODO label (3D support) * skipping multi-threading tests if JIT disabled * add pylint-disable comment * print number of cores on workers * log info about supported plotting options * debug: print num_threads per worker * debug: omit pylint * debug: omit pylint * hardcore threads * fix issue number * mpi_dim as scenarion ctor argument; new test for mpi_indices; more readable code around send/recv tags for threading * pylint fixes * pylint fixes ++ * pylint disable too-many-args for whole file * check thread number every time * increase workflow timeout * check if the 3rd-order-terms issue indeed is present? * indeed 3rd-order terms cause problems with mpi_dim=INNER :( * increase timeout to 120min * remove 4th worker from the test * increase timeout to 60min * updates to README to reflect threading support changes * removing debug leftover --------- Co-authored-by: Sylwester Arabas <sylwester.arabas@uj.edu.pl> Co-authored-by: Sylwester Arabas <sylwester.arabas@agh.edu.pl>
avoiding buffer allocations in each time step in MPI boundary conditi… …ons, closes #53 (#61) * initial changes * adapt to a new API * Update pyproject.toml * remove numpy * precommit * force older Numpy to avoid NaN-cast warnings in PyMPDATA fields ctors * disable kwargs * comment non-supported option * downgrade numba * try passing dtype to view() * code formatting fix * add missing dtype params * fix shape setting for Numba * add complex buffer support and uncomment back non-oscillatory tests * use chank assignement instead of reshape to ensure nojit tests fail if mem needs to be copied * silence pylint on numba.config access * make the code compilable --------- Co-authored-by: derlk <kacper.derlatka@pega.com> Co-authored-by: Sylwester Arabas <sylwester.arabas@uj.edu.pl>
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