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#5050false5010828SUCCESS1792262128215https://carson.math.uwm.edu/jenkins/view/clubb_branch_tests/job/clubb_branch_python/50/- run_scripts/run_scm_loss.pyutilities/time_clubb.pyclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pytests/pytests/auto_llm_generated_pytests/test_scm_jax_driver_test.pyutilities/timing_profiles.pyrun_scripts/run_tuner_job.pyutilities/pytests/test_create_case_namelist.pyutilities/pytests/test_time_clubb.pyca95e8ec8301f3e6088664879410da55291165b21792202474000https://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhuebler@uwm.eduComplete case-runner procedure descriptions
Describe the remaining changed CLI, test and profile routines under the current
documentation standards. Executable Python ASTs are unchanged from f66ccf2ff,
the revision running in Jenkins; existing validation still applies.
2026-10-16 21:01:14 -0500ca95e8ec8301f3e6088664879410da55291165b2Complete case-runner procedure descriptionseditrun_scripts/run_scm_loss.pyeditutilities/time_clubb.pyeditrun_scripts/run_tuner_job.pyeditutilities/pytests/test_create_case_namelist.pyeditutilities/pytests/test_time_clubb.pyedittests/pytests/auto_llm_generated_pytests/test_scm_jax_driver_test.pyeditutilities/timing_profiles.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.py
- clubb_jax/src/CLUBB_core/code_timer_module.pyclubb_jax/src/clubb_case_initalization.pyclubb_jax/src/clubb_standalone.pyutilities/README.mdutilities/time_clubb.pyclubb_jax/pytests/auto_llm_generated_pytests/test_code_timer_module.pyclubb_jax/src/advance_clubb_to_end.pyclubb_jax/README.md607c58bdb517fa6677567b5015cb1db2a55549151792207323000https://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhuebler@uwm.eduSeparate JAX timing from case runner changes
Keep runtime selection and process reuse independent so the case runner
can merge into master before JAX timing. Shared runner/CLI/timing
checks pass (445 tests, including provisional coverage).
2026-10-16 22:22:03 -0500607c58bdb517fa6677567b5015cb1db2a5554915Separate JAX timing from case runner changeseditutilities/time_clubb.pydeleteclubb_jax/src/CLUBB_core/code_timer_module.pyeditclubb_jax/README.mdeditclubb_jax/src/clubb_standalone.pyeditutilities/README.mdeditclubb_jax/src/advance_clubb_to_end.pyeditclubb_jax/src/clubb_case_initalization.pydeleteclubb_jax/pytests/auto_llm_generated_pytests/test_code_timer_module.py
- clubb_jax/src/clubb_standalone.pyutilities/README.mdutilities/pytests/auto_llm_generated_pytests/test_timing_workers.pyrun_scripts/README.mdutilities/pytests/auto_llm_generated_pytests/test_loss_cli.pyutilities/clubb_case_runner.pyrun_scripts/run_scm.pyclubb_python_driver/clubb_standalone.pysrc/clubb_standalone.F90run_scripts/run_scm_loss.pyutilities/tests/run_case_runner_test.pyutilities/time_clubb.pyclubb_jax/src/Microphys/microphys_init_cleanup.pyutilities/create_case_namelist.pyutilities/pytests/auto_llm_generated_pytests/test_clubb_case_runner.py2c4fa0aa2e5c816571ac586013f9ad27e80671a81792208789000https://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhuebler@uwm.eduDocument case runner lifecycle and timing
Clarify process reuse, model cleanup, runner status and timing boundaries.
Improve procedure descriptions and runnable examples without changing logic.
Shared checks pass (445); JAX reuse and native timing README examples pass.
2026-10-16 22:46:29 -05002c4fa0aa2e5c816571ac586013f9ad27e80671a8Document case runner lifecycle and timingeditutilities/pytests/auto_llm_generated_pytests/test_clubb_case_runner.pyeditclubb_python_driver/clubb_standalone.pyeditutilities/create_case_namelist.pyeditrun_scripts/run_scm_loss.pyeditclubb_jax/src/clubb_standalone.pyeditclubb_jax/src/Microphys/microphys_init_cleanup.pyeditrun_scripts/README.mdeditutilities/pytests/auto_llm_generated_pytests/test_loss_cli.pyeditsrc/clubb_standalone.F90editutilities/tests/run_case_runner_test.pyeditutilities/README.mdeditutilities/clubb_case_runner.pyeditutilities/time_clubb.pyeditrun_scripts/run_scm.pyeditutilities/pytests/auto_llm_generated_pytests/test_timing_workers.py
- src/Microphys/microphys_init_cleanup.F90d9e8b9588ff7b16679ca79b67fcf5382bcc723c41792209029000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comReset microphysics defaults when initializing another case (#1398)
Restore module and saved-local namelist defaults before reading a new case.
This prevents omitted settings from inheriting the previous case's values. This isn't an issue for any way that clubb is currently run in the codebase, but would potentially cause an issue for a future use case (this is foreshadowing).
2026-10-16 22:50:29 -0500d9e8b9588ff7b16679ca79b67fcf5382bcc723c4Reset microphysics defaults when initializing another case (#1398)editsrc/Microphys/microphys_init_cleanup.F90
- .agents/skills/clubb-fortran-format/SKILL.md.agents/skills/clubb-fortran-port/SKILL.md3baa924b39a5ad3627f7ba2b6bc34e509fb167731792211462000https://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhuebler@uwm.eduDocument Fortran whitespace conventions
Separate control flow and continued statements, and align small groups
of related one-liners. Prefer recently maintained examples and share
the guidance with the porting workflow. Both skills pass validation.
2026-10-16 23:31:02 -05003baa924b39a5ad3627f7ba2b6bc34e509fb16773Document Fortran whitespace conventionsedit.agents/skills/clubb-fortran-format/SKILL.mdedit.agents/skills/clubb-fortran-port/SKILL.md
- clubb_jax/src/CLUBB_core/sfc_varnce_module.pyclubb_jax/src/CLUBB_core/model_flags.pyclubb_jax/src/CLUBB_core/new_hybrid_pdf_main.pyclubb_jax/src/CLUBB_core/adg1_adg2_3d_luhar_pdf.pyclubb_jax/src/CLUBB_core/advance_wp2_wp3_module.pyclubb_jax/src/CLUBB_core/parameters_tunable.pyclubb_jax/src/CLUBB_core/interpolation.pyclubb_jax/src/CLUBB_core/precipitation_fraction.pyclubb_jax/src/CLUBB_core/setup_clubb_pdf_params.pyclubb_jax/src/CLUBB_core/advance_windm_edsclrm_module.pyclubb_jax/src/CLUBB_core/jax_stats.pyclubb_jax/src/CLUBB_core/file_functions.pyclubb_jax/src/CLUBB_core/advance_clubb_core_module.pyclubb_jax/src/CLUBB_core/grid_class.pyclubb_jax/src/CLUBB_core/advance_xm_wpxp_module.pyclubb_jax/src/CLUBB_core/advance_xp2_xpyp_module.pyclubb_jax/src/CLUBB_core/mono_flux_limiter.pyclubb_jax/src/CLUBB_core/fill_holes.pyclubb_jax/src/CLUBB_core/stats_netcdf.pyclubb_jax/src/CLUBB_core/clip_explicit.pyclubb_jax/src/CLUBB_core/mixing_length.pyclubb_jax/src/CLUBB_core/err_info.pyclubb_jax/pytests/auto_llm_generated_pytests/test_sfc_varnce_diagnostics.pyclubb_jax/src/CLUBB_core/pdf_params.pyclubb_jax/pytests/auto_llm_generated_pytests/test_core_diagnostics.pyclubb_jax/src/CLUBB_core/remapping_module.pyclubb_jax/src/CLUBB_core/sponge_layer_damping.pyclubb_jax/src/CLUBB_core/new_pdf.pyclubb_jax/src/CLUBB_core/matrix_operations.pyclubb_jax/src/CLUBB_core/pdf_closure_module.pyclubb_jax/src/CLUBB_core/pos_definite_module.pyclubb_jax/src/CLUBB_core/numerical_check.pyclubb_jax/src/CLUBB_core/matrix_solver_wrapper.pyclubb_jax/src/CLUBB_core/new_tsdadg_pdf.pyclubb_jax/src/CLUBB_core/corr_varnce_module.pyc47faf30cea562966e64eedc259a5074c6cf89b11792221315000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comRestore missing debug printouts in JAX core (#1390)
* Restore missing debug printouts in JAX core
The port kept many failure checks but omitted their Fortran messages, making
failed columns and solvers difficult to diagnose. Restore runtime messages,
column headers and available field dumps with the source debug gates. Record
diagnostics needing unported machinery in the skip report.
BFB is not established by the available comparisons. All 23 curated CPU
JAX/Fortran cases matched within default tolerances: absolute 1e-7 and
percentage 1e-7%, or 0.001% for the curated Morrison cases. Runs used four
columns, standard statistics and existing durations/caps. Separately, 24
starting-tree kernel comparisons found exactly equal result/state values.
The CPU JAX suite passed 787 tests, including compiled diagnostic checks;
the focused rerun passed 14. Source/diff review and git diff --check passed.
* Remove diagnostic restoration report
Remove the standalone report on intentionally skipped diagnostics. Observed
Fortran differences remain documented in the affected JAX modules.
This removes documentation only, so model/output BFB is not applicable.
Diff review, a tracked-file reference search and git diff --check passed.
Runtime tests were not rerun for this deletion.
* Identify scalar fields in solver diagnostics
The separate scalar solves all printed the same generic field label. Restore
the Fortran names sclrp2, sclrprtp and sclrpthlp so a failure identifies which
variance or covariance solve failed.
Source comparison confirms the three labels match their Fortran call sites.
Python syntax and whitespace checks passed. Jenkins validation will exercise
the published revision.
2026-10-17 02:15:15 -0500c47faf30cea562966e64eedc259a5074c6cf89b1Restore missing debug printouts in JAX core (#1390)editclubb_jax/src/CLUBB_core/err_info.pyeditclubb_jax/src/CLUBB_core/new_tsdadg_pdf.pyeditclubb_jax/src/CLUBB_core/clip_explicit.pyeditclubb_jax/src/CLUBB_core/corr_varnce_module.pyeditclubb_jax/src/CLUBB_core/advance_wp2_wp3_module.pyeditclubb_jax/src/CLUBB_core/file_functions.pyeditclubb_jax/src/CLUBB_core/numerical_check.pyeditclubb_jax/src/CLUBB_core/parameters_tunable.pyeditclubb_jax/src/CLUBB_core/mono_flux_limiter.pyeditclubb_jax/src/CLUBB_core/pdf_closure_module.pyeditclubb_jax/src/CLUBB_core/interpolation.pyeditclubb_jax/src/CLUBB_core/new_pdf.pyeditclubb_jax/src/CLUBB_core/matrix_operations.pyeditclubb_jax/src/CLUBB_core/sponge_layer_damping.pyeditclubb_jax/src/CLUBB_core/mixing_length.pyeditclubb_jax/src/CLUBB_core/pdf_params.pyeditclubb_jax/src/CLUBB_core/advance_xm_wpxp_module.pyeditclubb_jax/src/CLUBB_core/model_flags.pyeditclubb_jax/src/CLUBB_core/matrix_solver_wrapper.pyeditclubb_jax/src/CLUBB_core/precipitation_fraction.pyeditclubb_jax/src/CLUBB_core/pos_definite_module.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_sfc_varnce_diagnostics.pyeditclubb_jax/src/CLUBB_core/fill_holes.pyeditclubb_jax/src/CLUBB_core/sfc_varnce_module.pyeditclubb_jax/src/CLUBB_core/advance_clubb_core_module.pyeditclubb_jax/src/CLUBB_core/setup_clubb_pdf_params.pyeditclubb_jax/src/CLUBB_core/remapping_module.pyeditclubb_jax/src/CLUBB_core/advance_windm_edsclrm_module.pyeditclubb_jax/src/CLUBB_core/jax_stats.pyeditclubb_jax/src/CLUBB_core/adg1_adg2_3d_luhar_pdf.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_core_diagnostics.pyeditclubb_jax/src/CLUBB_core/advance_xp2_xpyp_module.pyeditclubb_jax/src/CLUBB_core/stats_netcdf.pyeditclubb_jax/src/CLUBB_core/grid_class.pyeditclubb_jax/src/CLUBB_core/new_hybrid_pdf_main.py
- clubb_jax/pytests/auto_llm_generated_pytests/test_windm_edsclrm_scalar_indices.pyclubb_jax/pytests/auto_llm_generated_pytests/test_radiation_error_diagnostics.pyclubb_jax/src/CLUBB_core/advance_windm_edsclrm_module.pyclubb_jax/pytests/auto_llm_generated_pytests/test_xp2_error_diagnostics.pyclubb_jax/src/CLUBB_core/err_info.pyclubb_jax/pytests/auto_llm_generated_pytests/test_jit_compile.pyclubb_jax/src/CLUBB_core/__init__.pyclubb_jax/src/advance_clubb_to_end.pyclubb_jax/src/CLUBB_core/numerical_check.pyclubb_jax/src/CLUBB_core/err_info_codes.pyclubb_python_api/JAX_INTEROPERABILITY_PROPOSAL.mdclubb_jax/src/CLUBB_core/advance_xp2_xpyp_module.pyclubb_jax/src/Radiation/radiation_module.pyaa8c2aa4037dda69d686ca97bcbbe1a8208401fd1792259885000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comRemove the JAX error-message code registry (#1401)
* Remove the JAX error-message code registry
Print failure details at the runtime checks that detect them. Remove the
extra reason_code field and its setters, decoder, initialization/reset
handling and exports; retain the normal per-column fatal-error status.
Update the scalar-guard assertions and add cached-call diagnostic checks.
Local CPU checks passed for the ErrInfo pytree, diagnostic output, driver
debug gates and state reset/batching behavior (65 cases across five modules).
* Correct the multiple-LHS diagnostic test's wp3 grid
Allocate synthetic wp3 on thermodynamic levels, as required by
calc_wp3_on_wp2, so the test reaches the multiple-LHS guard during tracing.
The 21 selected CPU diagnostic checks pass, covering cached-call output,
per-column fatal status and preservation of fields on the unsupported path.
* Restore the C2 explanation in the multiple-LHS diagnostic
Name C2rt, C2thl and C2rtthl when their unequal values prevent a single-LHS
solve. Keep the direct runtime print and existing fatal-status handling.
The focused CPU cached-call test passes, including the restored explanation,
quiet valid calls and preservation of incoming fields on failure.
* Revert "Restore the C2 explanation in the multiple-LHS diagnostic"
This reverts commit 170a13e2bc7af24e92d8d8bc9de9d9db601921ed.
* List single-LHS requirements in the JAX diagnostic
Print the approved static requirements after the unsupported multiple-LHS
message: explicit turbulent advection or ADG1, plus per-column equivalence
of C2thl and C2rtthl to C2rt within the relative epsilon tolerance.
The focused CPU cached-call test passes, checking the listed requirements,
quiet valid calls and preservation of incoming fields and fatal status.
2026-10-17 12:58:05 -0500aa8c2aa4037dda69d686ca97bcbbe1a8208401fdRemove the JAX error-message code registry (#1401)addclubb_jax/pytests/auto_llm_generated_pytests/test_radiation_error_diagnostics.pyeditclubb_jax/src/advance_clubb_to_end.pydeleteclubb_jax/src/CLUBB_core/err_info_codes.pyeditclubb_python_api/JAX_INTEROPERABILITY_PROPOSAL.mdeditclubb_jax/pytests/auto_llm_generated_pytests/test_jit_compile.pyeditclubb_jax/src/CLUBB_core/advance_xp2_xpyp_module.pyeditclubb_jax/src/CLUBB_core/advance_windm_edsclrm_module.pyeditclubb_jax/src/Radiation/radiation_module.pyeditclubb_jax/src/CLUBB_core/__init__.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_xp2_error_diagnostics.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_windm_edsclrm_scalar_indices.pyeditclubb_jax/src/CLUBB_core/numerical_check.pyeditclubb_jax/src/CLUBB_core/err_info.py
- .agents/skills/clubb-jax-port/SKILL.md.agents/skills/clubb-testing-and-reporting/SKILL.md.agents/skills/clubb-documentation/change-messages/SKILL.md6e48f97c2a96bc78fb498c82f1ed0bb6902353491792260807000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comRestrict BIT_CHANGING guidance to Fortran result changes (#1399)
Keep JAX numerical acceptance focused on agreement with the corresponding
Fortran implementation rather than preserving earlier JAX output. Clarify
the reporting rule and link it from the JAX porting workflow.
All 21 skill schemas, 112 local links and 7 heading anchors pass, along with
diff formatting. Only three skill Markdown files change.
2026-10-17 13:13:27 -05006e48f97c2a96bc78fb498c82f1ed0bb690235349Restrict BIT_CHANGING guidance to Fortran result changes (#1399)edit.agents/skills/clubb-testing-and-reporting/SKILL.mdedit.agents/skills/clubb-jax-port/SKILL.mdedit.agents/skills/clubb-documentation/change-messages/SKILL.md
- jenkins_tests/clubb_driver/Jenkinsfiletests/README.mdutilities/README.mdtests/case_runner_lifecycle_test.pyutilities/tests/run_case_runner_test.py167076807d2a8cfe95c58da710eaee8f53994d001792261464000https://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhuebler@uwm.eduRun case runner lifecycle checks in the driver pipeline
Move the workflow to tests/case_runner_lifecycle_test.py and run native,
Python and CPU JAX checks before the existing driver comparisons. Keep
the case sequence and exact comparison assertions unchanged.
Native/Python lifecycle checks and 445 shared checks pass. Jenkins
validates the pipeline syntax; branch execution follows the push.
2026-10-17 13:24:24 -0500167076807d2a8cfe95c58da710eaee8f53994d00Run case runner lifecycle checks in the driver pipelineedittests/README.mdeditjenkins_tests/clubb_driver/Jenkinsfiledeleteutilities/tests/run_case_runner_test.pyeditutilities/README.mdaddtests/case_runner_lifecycle_test.py
- src/clubb_standalone.F900c985605a47a651c813c6697e3c3c4e32365f9c71792262101000https://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhuebler@uwm.eduClarify standalone worker flow
2026-10-17 13:35:01 -05000c985605a47a651c813c6697e3c3c4e32365f9c7Clarify standalone worker floweditsrc/clubb_standalone.F90
githttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerfalse51https://carson.math.uwm.edu/jenkins/view/clubb_branch_tests/job/clubb_branch_python/51/49https://carson.math.uwm.edu/jenkins/view/clubb_branch_tests/job/clubb_branch_python/49/