fix mpi4py version#51
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* Benchmark changes * Added benchmark configurations * Removed benchmark configs from configs to be tested in unit tests * Changed dace submodule to point to Florian fix * Dace submodule points to gcc_dies_on_dacecpu branch * Set 'rf_fast' to true in baroclinic_c384_cpu/gpu.yaml * fix mpi4py version (#51) * [Feature] Better translate test (#39) (#47) Translate test: small improvements - Parametrize perturbation upon failure - Refactor error folder to be `pwd` based - Fix GPU translate unable to dump error `nc` - Fix mixmatch precision on translate test - Update README.md Test fix: - Orchestrate YPPM for translate purposes Misc: - Fix bad logger formatting on DaCeProgress * [NASA] [Feature] Guarding against unimplemented configuration (#40) (#48) * [Feature] Guarding against unimplemented configuration (#40) Guarding against unimplemented namelists options: - a2b_ord4 - d_sw - fv_dynamics - fv_subgridz - neg_adj3 - divergence damping - xppm - yppm Misc: - Fix `netcdf_monitor` not mkdir the directory - Add `as_dict` to the dycore state to dump the dycore more easily * Unused assert * Update fv3core/pace/fv3core/stencils/yppm.py Co-authored-by: Oliver Elbert <oliver.elbert36@gmail.com> * Update fv3core/pace/fv3core/stencils/xppm.py Co-authored-by: Oliver Elbert <oliver.elbert36@gmail.com> * Change NotImplemented to ValueError for n_sponge<3 * lint --------- Co-authored-by: Oliver Elbert <oliver.elbert36@gmail.com> * Re-try of updating dace submodule to track Florian fix branch * Reverted gt4py submodule to match main checkout * Added benchmark README file * Read in ak, bk coefficients (#36) * initial changes to read in ak bk * read ak/bk * add xfail * remove input dir * further changes to unit tests * finish up test * add history * commit uncommited files * fix test comment * add input to top * read in data * read in netcdf file in eta mod * remove txt file * test * modify test and fix generate.py * remove emacs backup file * driver tests pass * fix helper.py * fix fv3core tests * fix physics test * fix grid tests * nullcommconfig * cleanup input * remove driver input * remove top level input * fix circular import problems * modify eta_file readin for test_restart_serial * comment out 91 test * rm safety checks * revert diagnostics.py * restore driver.py * revert initialization.py * restore state.py * restore analytic_init.py * restore init_utils.py and analytic_init.py * restore c_sw.py * d2a2c_vect.py * restore fv3core/stensils * restore translate_fvdynamics * restore physics/stencils * restore stencils * remove circular dependency * use pytest parametrize * cleanup generation.py * fstrinngs * add eta_file to MetricTerm init * remove eta_file argument in new_from_metric_terms and geos_wrapper * use pytest parametrize for the xfail tests * use pytest parametrize for the xfail tests * fix geos_wrapper and grid * fix tests * fstring * add test comments * fix util/HISTORY.md * fix comments * remove __init__.py from tests/main/grid * add jupyter notebooks to generate eta files * generate ak,bk,ptop on metricterm init * fix tests * exploit np.all in eta mod * remove tests/main/grid/input * update ci * test * remove input * edit ci yaml * remove push --------- Co-authored-by: mlee03 <Mikyung.Lee@lscamd50-d.gfdl.noaa.gov> * Move Active Physics Schemes to Config (#44) * initial commit, need to adapt and run tests * revising scheme name * tests pass * update history * linting * changing typehints for physics schemes to enum instead of str * driver now works with physics config enum, tests pass * fixed tests * missed one * D-grid data input method (#42) * Testing changes reflected across branches * Undoing changes made in build_gaea_c5.sh * Testing vscode functionality, by adding a change to external_grid branch * Testing vscode functionality, by adding a change to external_grid branch * Addition of from_generated method and calc_flag to util/pace/util/grid/generation.py * Added get_grid method for external grid data to driver/pace/driver/grid.py * Preliminary xarray netcdf read in method added to driver/pace/driver/grid.py * Updating util/pace/util/grid/generation.py from_generated method * Addition of external grid data read in methods for initialization of grid. Current method uses xarray to interact with netcdf tile files. Values for longitutde, latitude, number of points in x an y, grid edge distances read in. * driver/examples/configs/test_external_C12_1x1.yaml * Preliminary unit test for external grid data read in * Current state of unit tests as of 27 Nov 2023 * External grid method and unit tests added * Re-excluding external grid data yamls from test_example_configs.py * Update driver/pace/driver/grid.py Co-authored-by: Florian Deconinck <deconinck.florian@gmail.com> * Changed name of grid initializer function to match NetCDF dependency and class descriptor * Update util/pace/util/grid/generation.py Moved position of doc string for "from_external" MetricTerms class method Co-authored-by: Oliver Elbert <oliver.elbert36@gmail.com> * Fixed indentation error in generation.py from suggestion in PR 42 * Removal of TODO comment in grid.py, changes to method of file accessing in test_analytic_init, test_external_grid_* * Changed grid data read-in unit tests to compare data directly from file to driver grid data generated from yaml * Change to reading in lon and lat, other metric terms calculated as needed * Removed read-in of dx, dy, and area. Changed unit tests to compare calculated area to 'ideal' surface area as given by selected constants type. * Update tests/mpi_54rank/test_external_grid_1x1.py Incorrect name of test in test_external_grid_1x1.py changed to match file name Co-authored-by: Oliver Elbert <oliver.elbert36@gmail.com> * Added comparisons for read-in vs generated by driver lon, lat, dx, dy, and area data to unit tests * Added relative error calculations to unit tests for external grid data read-in * External grid data read in tests changed: relative errors printed by each rank and get_tile_number replacing get_tile_index * Removing commented out sections in test_external_grid_2x2.py Co-authored-by: Oliver Elbert <oliver.elbert36@gmail.com> * Updated external grid data read-in to take configuration and input data locations from command line, updated test description, and added documentation on grid construction to external grid data configuration selection dataclass. * Updated documentation in grid.py * Updated external grid data read in unit test to use parametrize functionality of pytest * Ammended files to reference changes to PR 36 --------- Co-authored-by: Frank Malatino <Frank.Malatino@ldt-4788481.gfdl.noaa.gov> Co-authored-by: Florian Deconinck <deconinck.florian@gmail.com> Co-authored-by: Oliver Elbert <oliver.elbert36@gmail.com> --------- Co-authored-by: Oliver Elbert <Oliver.Elbert@noaa.gov> Co-authored-by: Florian Deconinck <deconinck.florian@gmail.com> Co-authored-by: Oliver Elbert <oliver.elbert36@gmail.com> Co-authored-by: MiKyung Lee <58964324+mlee03@users.noreply.github.com> Co-authored-by: mlee03 <Mikyung.Lee@lscamd50-d.gfdl.noaa.gov> Co-authored-by: Frank Malatino <Frank.Malatino@ldt-4788481.gfdl.noaa.gov>
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Purpose
This PR fixes the version of mpi4py installed in the examples docker image so that we can run notebooks successfully
Code changes:
Checklist
Before submitting this PR, please make sure:
pace-util, HISTORY has been updated