https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/Tests CLUBB's vertical grid generalization by calling advance_clubb_core_api twice -- once in with an ascending grid and once with a descending grid -- and then comparing that the output results are bit-for-bit when run with -O0 optimization. The test is run for all cases and for a large number of flag sets that vary some of CLUBB's configurable model flags.clubb_generalized_gridclubb_generalized_gridclubb_generalized_gridclubb_generalized_gridhttps://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/trueStarted by an SCM change000605985043285871.0379987998168369512fcc6487603491e12ac13376de2aec2a0b8369512fcc6487603491e12ac13376de2aec2a0brefs/remotes/origin/master8369512fcc6487603491e12ac13376de2aec2a0b8369512fcc6487603491e12ac13376de2aec2a0brefs/remotes/origin/master8369512fcc6487603491e12ac13376de2aec2a0b8369512fcc6487603491e12ac13376de2aec2a0brefs/remotes/origin/masterhttps://github.com/larson-group/clubb.gittrue#16013433486clubb_generalized_grid #1616false16111331792484769900https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/16/src/generalized_grid_test.F90src/CLUBB_core/setup_clubb_pdf_params.F90clubb_python_api/clubb_f2py.pyfsrc/CLUBB_core/fill_holes.F90clubb_python_api/f2py_fortran_wrappers/precipitation_fraction_wrapper.F90clubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_precipitation_fraction.pysrc/G_unit_test_types/mu_sigma_hm_tests.F90src/Microphys/pdf_hydromet_microphys_wrapper.F90clubb_python_api/clubb_python/CLUBB_core/precipitation_fraction.pysrc/CLUBB_core/precipitation_fraction.F908369512fcc6487603491e12ac13376de2aec2a0b1792463005000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comClubb params 1d to 2d fix (#1392) * Fix: clubb params is a shape (ngrdcol,nparams) that is passed into subroutines that expect a 1d array Also fixed dependent other places in code and changed the python api. This is BIT_CHANGING for multicol. If a 2d array is passed into a function that expects the arr to be 1d fortran just passes the first col of the arr. Therefore the changes dont affect single col runs. For multicol runs other indexing is needed * fill_holes_vertical_api expects the passed gr%dzt to have shape(ngrdcol,nz) but the code passes the whole gr%dzt array although each column is traversed one by one. So ngrdcol=1 is passed each time. No effect on single col, as with ngrdcol = 1, gr%dzt and gr%dzt(1:1,:) are the same. Affects multicol if l_hole_fill = .true. and the hydrometeor is a mixing ratio (name starts with r) and some value is actually negative Therefore BIT_CHANGING 2026-10-19 21:23:25 -05008369512fcc6487603491e12ac13376de2aec2a0bClubb params 1d to 2d fix (#1392)editclubb_python_api/clubb_f2py.pyfeditsrc/CLUBB_core/fill_holes.F90editsrc/generalized_grid_test.F90editsrc/CLUBB_core/setup_clubb_pdf_params.F90editclubb_python_api/f2py_fortran_wrappers/precipitation_fraction_wrapper.F90editclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_precipitation_fraction.pyeditsrc/Microphys/pdf_hydromet_microphys_wrapper.F90editclubb_python_api/clubb_python/CLUBB_core/precipitation_fraction.pyeditsrc/CLUBB_core/precipitation_fraction.F90editsrc/G_unit_test_types/mu_sigma_hm_tests.F90githttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblertrue15https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/15/Started by an SCM change000012914478173309961.3445636563615ec5e8070d3173282a6317b067f8673a657a1eb6fec5e8070d3173282a6317b067f8673a657a1eb6frefs/remotes/origin/masterec5e8070d3173282a6317b067f8673a657a1eb6fec5e8070d3173282a6317b067f8673a657a1eb6frefs/remotes/origin/masterec5e8070d3173282a6317b067f8673a657a1eb6fec5e8070d3173282a6317b067f8673a657a1eb6frefs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#151291447813433486clubb_generalized_grid #1515false1511023FAILURE1792398368289https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/15/.agents/skills/clubb-bit-changing/SKILL.md.agents/skills/clubb-jax-port/SKILL.md.agents/skills/clubb-finalization/SKILL.mdAGENTS.md.agents/skills/clubb-documentation/change-messages/SKILL.md.agents/skills/clubb-testing-and-reporting/SKILL.mdccafe4f166f956eed26b91f7fdacd5600f60f5b21792344464000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comDefine when to declare bit-changing commits (#1403) * Define conservative bit-change declarations Centralize the policy around intentional Fortran numerical answer changes, with named affected BFB tests or precise untested conditions. Preserve standalone coverage and the current JAX parity boundary, keep declarations sparse, and separate answer-changing edits from preserving cleanup. Route message writing, validation and branch finalization to one owner. Skill schemas, local links, heading anchors, parser examples and manual decision scenarios were checked; no model or CI code changes. * Define the optimization level for bitwise preservation Use -O0 as the normal preservation standard. Differences confined to optimized builds do not require an answer-change declaration when -O0 is verified BFB; report known optimized-only differences and their configuration in the PR. The changed skill schema and whitespace checks pass. Inspected current debug compile flags and manually reviewed the optimized-only decision scenario; documentation only, no numerical rerun. 2026-10-18 12:27:44 -0500ccafe4f166f956eed26b91f7fdacd5600f60f5b2Define when to declare bit-changing commits (#1403)edit.agents/skills/clubb-documentation/change-messages/SKILL.mdedit.agents/skills/clubb-finalization/SKILL.mdedit.agents/skills/clubb-testing-and-reporting/SKILL.mdedit.agents/skills/clubb-jax-port/SKILL.mdeditAGENTS.mdadd.agents/skills/clubb-bit-changing/SKILL.mdclubb_jax/src/clubb_standalone.pyclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyrun_scripts/README.mdutilities/clubb_case_runner.pyutilities/pytests/test_time_clubb.pytests/run_timestep_sweep.pyclubb_jax/pytests/auto_llm_generated_pytests/test_case_cache_reuse.pyclubb_python_driver/clubb_standalone.pysrc/clubb_standalone.F90tests/README.mdrun_scripts/run_scm_loss.pyutilities/time_clubb.py.agents/skills/clubb-testing-and-reporting/SKILL.mdutilities/create_case_namelist.pyutilities/pytests/test_create_case_namelist.pytests/run_stats_output_consistency.pytests/run_jax_vs_fortran_cases.py.agents/skills/clubb-fortran-port/SKILL.mdclubb_jax/src/clubb_case_initalization.pytests/case_runner_lifecycle_test.pyutilities/README.mdutilities/pytests/auto_llm_generated_pytests/test_timing_workers.pyclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.py.agents/skills/clubb-numerical-diagnosis/SKILL.mdutilities/pytests/auto_llm_generated_pytests/test_loss_cli.pytests/pytests/auto_llm_generated_pytests/test_scm_jax_driver_test.pyrun_scripts/run_scm.py.agents/skills/clubb-fortran-format/SKILL.md.agents/skills/clubb-finalization/SKILL.mdAGENTS.mdclubb_jax/src/Microphys/microphys_init_cleanup.pyjenkins_tests/clubb_driver/Jenkinsfileutilities/timing_profiles.pyclubb_jax/README.mdrun_scripts/run_tuner_job.pyutilities/pytests/auto_llm_generated_pytests/test_clubb_case_runner.pytests/run_restart_test.pyutilities/pytests/timing_test_inputs.pyclubb_jax/src/CLUBB_core/calc_pressure.pytests/run_loss_output_consistency.py4f8368a377989b649fc0ed53c26957e193d210671792350419000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd reusable case runners for timing (#1400) We have multiple entry points now for clubb standalone (fortran,python,jax), and there's additional logic that chooses which fortran installation to use (gfortran,ifort,nvhpc,etc). All of this has historically (~1 year) been done by run_scm.py, but we have a number of other scripts that need this same kind of logic, so instead of making run_scm.py more complicated and letting other scripts import it's pieces, we've made a `clubb_case_runner`. `clubb_case_runner` is a python object that abstracts the backend decisions. The "flow" is roughly: - high level script wants to run a clubb case some how - generates one or more case namelists (arm.in, bomex.in, etc) - creates a `clubb_case_runner` by passing it whatever runtime options (-jax/-python/-exe) the user requested - runs a case by passing this `clubb_case_runner` whatever namelists it wants to run. In addition to deduplicating runtime setting logic, this allows python scripts to create these high level `clubb_case_runner` objects and use those to do things that usually requires duplicate multiprocessesing and error code parsing logic. 2026-10-18 14:06:59 -05004f8368a377989b649fc0ed53c26957e193d21067Add reusable case runners for timing (#1400)edittests/run_jax_vs_fortran_cases.pyeditrun_scripts/run_scm.pyaddutilities/pytests/timing_test_inputs.pyeditrun_scripts/README.mdeditutilities/create_case_namelist.pyeditutilities/time_clubb.pyeditclubb_jax/src/clubb_standalone.pyeditsrc/clubb_standalone.F90addtests/case_runner_lifecycle_test.pyedit.agents/skills/clubb-finalization/SKILL.mdaddclubb_jax/pytests/auto_llm_generated_pytests/test_case_cache_reuse.pyeditjenkins_tests/clubb_driver/Jenkinsfileeditutilities/pytests/auto_llm_generated_pytests/test_loss_cli.pyeditutilities/timing_profiles.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyedit.agents/skills/clubb-testing-and-reporting/SKILL.mdeditclubb_python_driver/clubb_standalone.pyedit.agents/skills/clubb-numerical-diagnosis/SKILL.mdeditAGENTS.mdedit.agents/skills/clubb-fortran-port/SKILL.mdeditclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyeditrun_scripts/run_tuner_job.pyaddutilities/clubb_case_runner.pyedit.agents/skills/clubb-fortran-format/SKILL.mdedittests/pytests/auto_llm_generated_pytests/test_scm_jax_driver_test.pyeditutilities/pytests/test_time_clubb.pyeditclubb_jax/src/Microphys/microphys_init_cleanup.pyedittests/run_stats_output_consistency.pyeditrun_scripts/run_scm_loss.pyaddutilities/pytests/auto_llm_generated_pytests/test_clubb_case_runner.pyeditclubb_jax/src/CLUBB_core/calc_pressure.pyedittests/README.mdeditutilities/README.mdeditclubb_jax/src/clubb_case_initalization.pyedittests/run_loss_output_consistency.pyedittests/run_restart_test.pyeditclubb_jax/README.mdaddutilities/pytests/auto_llm_generated_pytests/test_timing_workers.pyeditutilities/pytests/test_create_case_namelist.pyedittests/run_timestep_sweep.pyclubb_jax/src/clubb_case_initalization.pyclubb_jax/src/clubb_standalone.pyutilities/README.mdclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyclubb_jax/pytests/auto_llm_generated_pytests/test_code_timer_module.pyclubb_jax/src/clubb_loss_driver.pyrun_scripts/README.mdclubb_jax/view_profile.pyclubb_jax/run_jax.pyclubb_jax/pytests/auto_llm_generated_pytests/test_profile_cli.pyclubb_jax/src/CLUBB_core/code_timer_module.pyutilities/time_clubb.pyclubb_jax/src/advance_clubb_to_end.pyclubb_jax/src/clubb_driver_test.pyclubb_jax/README.mdec5e8070d3173282a6317b067f8673a657a1eb6f1792362852000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd JAX timing and profiling (#1393) * Add JAX timing and persistent benchmark workers Write Fortran-format CPU timing summaries and optional XProf/Perfetto traces from JAX driver phases. Use synchronized persistent workers for full-case warmups and repetitions across Fortran, Python and JAX. Retain compiled JAX programs when initialization settings are unchanged. Validation: 243 focused checks and CPU case workflows passed. Repeated five-step BOMEX/RICO_SILHS numeric outputs matched fresh controls exactly. The two-column BOMEX JAX/Fortran comparison passed 1e-7 absolute and percent thresholds. BFB against the parent is not established by these comparisons. GPU and GPTL execution remain untested. * Making jax timer use wall clock time instead of cpu/process time * Keep JAX timing separate from reusable runners Move process persistence, cache reuse and Python timing adapters to the case-runner branch. Keep JAX wall-clock summaries, optional deep profiles, driver instrumentation and the parser change that reads their clock label. The timing-only shared suite and a three-step CPU BOMEX run pass. BFB against master is not established; physics expressions are unchanged. * Add reusable case runners for timing and tuning Share runtime selection and persistent standalone sessions between SCM, timing and tuning. Support namelist replacement and empty model reruns, plus parameter matrices for loss sessions. Synchronize timing cohorts and record retained-model initialization separately. Use executable loss workers for native tuning instead of requiring F2PY. Restore microphysics defaults between cases (BIT_CHANGING for sessions that previously inherited settings). Short native/CPU JAX sessions match fresh same-backend stats values exactly; broader BFB is not established. Native build, focused suites and repeated loss/tuner/timing workflows pass. * Use F2PY for reusable Fortran loss runs Run persistent Fortran loss sessions through the existing Python API. Restore the native loss standalone and remove its parameter namelist reader and result writers. Python workers pass arrays directly into F2PY; ordinary standalone persistence and JAX execution remain available. Fifteen native loss metric arrays match saved results exactly. Native and CPU JAX repeated loss/tuning workflows, tuner shutdown, the native build, 454 shared checks and four API checks pass. Broader BFB is not established. * Keep case runners persistent without retaining model state Run each ordinary request through full initialization, advancement and cleanup while keeping the process alive for in-memory JIT reuse. Remove retained-model commands, transport, timing/UI options and extra bindings. Restore tuning and loss frontends to their existing allocation-reusing APIs. The native build, 445 shared checks, 121 focused JAX checks and 85 Dash checks pass. Short native/JAX/Python reused-process stats match fresh controls exactly; tuning and synchronized timing sweeps pass. Two full 16-column JAX repeats log no new compilations. These comparisons do not establish blanket BFB. * Separate microphysics initialization fixes from case runners Move native default resets to their own branch/PR and keep the runner focused on shared runtime selection and full-case process reuse. Record the mixed-case native test's dependency on that fix. Refresh the timing base and master, and clarify runner, driver and test documentation under the current skills. The shared checks pass, including output drainage, cancellation, synchronized warmup/repetition barriers and CLI forwarding. Python AST checks confirm the remaining audit edits change only documentation. Jenkins validation follows this published checkpoint. * Complete 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. * Separate 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). * Add JAX timing after the case runner Restore the audited wall-clock summaries and optional execution tracing on top of the independent case runner. Keep the existing implementation and review history while reversing the PR merge order. * Add a JAX profiling option and viewer commands Enable captures with -jax=profile and print commands after cleanup. Keep capture export in the timer and viewing in view_profile.py. 181 focused checks pass. CPU BOMEX captures preserve numeric stats; both viewers were verified in-browser. Large full-Python Perfetto exports can truncate; XProf retained all five tested timesteps. * Clarify JAX timing usage and cleanup Document the timer lifecycle, failure handling and Dash wall-time comparison metric. Executable Python AST is unchanged. 2026-10-18 17:34:12 -0500ec5e8070d3173282a6317b067f8673a657a1eb6fAdd JAX timing and profiling (#1393)addclubb_jax/src/CLUBB_core/code_timer_module.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_profile_cli.pyeditclubb_jax/src/clubb_case_initalization.pyeditutilities/README.mdeditclubb_jax/src/advance_clubb_to_end.pyaddclubb_jax/view_profile.pyeditclubb_jax/src/clubb_driver_test.pyeditutilities/time_clubb.pyeditclubb_jax/README.mdaddclubb_jax/pytests/auto_llm_generated_pytests/test_code_timer_module.pyeditclubb_jax/src/clubb_standalone.pyeditrun_scripts/README.mdeditclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyeditclubb_jax/run_jax.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyeditclubb_jax/src/clubb_loss_driver.pygithttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerfalse16https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/16/14https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/14/Started by an SCM change000014383273185868701.29452665266146e48f97c2a96bc78fb498c82f1ed0bb6902353496e48f97c2a96bc78fb498c82f1ed0bb690235349refs/remotes/origin/master6e48f97c2a96bc78fb498c82f1ed0bb6902353496e48f97c2a96bc78fb498c82f1ed0bb690235349refs/remotes/origin/master6e48f97c2a96bc78fb498c82f1ed0bb6902353496e48f97c2a96bc78fb498c82f1ed0bb690235349refs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#141438327313433486clubb_generalized_grid #1414false1410902FAILURE1792311967636https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/14/clubb_jax/pytests/auto_llm_generated_pytests/test_windm_edsclrm_scalar_indices.pyclubb_jax/src/CLUBB_core/err_info.pyclubb_jax/src/CLUBB_core/advance_windm_edsclrm_module.pyclubb_jax/pytests/auto_llm_generated_pytests/test_radiation_error_diagnostics.pyclubb_jax/pytests/auto_llm_generated_pytests/test_xp2_error_diagnostics.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_python_api/JAX_INTEROPERABILITY_PROPOSAL.mdclubb_jax/src/CLUBB_core/advance_xp2_xpyp_module.pyclubb_jax/src/CLUBB_core/err_info_codes.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)editclubb_python_api/JAX_INTEROPERABILITY_PROPOSAL.mdeditclubb_jax/pytests/auto_llm_generated_pytests/test_windm_edsclrm_scalar_indices.pyeditclubb_jax/src/CLUBB_core/err_info.pyeditclubb_jax/src/CLUBB_core/__init__.pyeditclubb_jax/src/CLUBB_core/advance_xp2_xpyp_module.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_jit_compile.pyeditclubb_jax/src/advance_clubb_to_end.pydeleteclubb_jax/src/CLUBB_core/err_info_codes.pyeditclubb_jax/src/CLUBB_core/advance_windm_edsclrm_module.pyeditclubb_jax/src/CLUBB_core/numerical_check.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_radiation_error_diagnostics.pyeditclubb_jax/src/Radiation/radiation_module.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_xp2_error_diagnostics.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-documentation/change-messages/SKILL.mdedit.agents/skills/clubb-jax-port/SKILL.mdgithttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerfalse15https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/15/13https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/13/Started by an SCM change000013002707203280741.5646534653413c47faf30cea562966e64eedc259a5074c6cf89b1c47faf30cea562966e64eedc259a5074c6cf89b1refs/remotes/origin/masterc47faf30cea562966e64eedc259a5074c6cf89b1c47faf30cea562966e64eedc259a5074c6cf89b1refs/remotes/origin/masterc47faf30cea562966e64eedc259a5074c6cf89b1c47faf30cea562966e64eedc259a5074c6cf89b1refs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#131300270713433486clubb_generalized_grid #1313false1310757FAILURE1792225569040https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/13/.agents/skills/clubb-doc-language/SKILL.md.agents/skills/clubb-file-descriptions/SKILL.md.agents/skills/clubb-documentation/SKILL.mdAGENTS.md.agents/skills/clubb-change-messages/SKILL.md.agents/skills/clubb-readmes/SKILL.md.agents/skills/clubb-code-comments/SKILL.mdc179bae7435e6e90a0f796cb621d9de4690429b81792177736000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd CLUBB documentation skills (#1397) * Add CLUBB documentation skills Add focused guidance for READMEs, file descriptions, routine/code comments, and plain language, with a documentation entry skill selected by AGENTS.md. This gives agents one route to the writing rules for the current task. Shorten the existing PR/commit guide and require BFB discussion only when a change could plausibly affect model results or scientific output. All 18 skill definitions and 45 local guidance links validate; git diff --check passes. * Require code reading and checks before finishing documentation Route small documentation edits through the writing skills. Require agents to inspect the implementation before drafting and check facts, coverage, links, and comment syntax before finishing. Clarify that weak file headers need complete descriptions in the appropriate language form. Validation: all 18 skill schemas, 46 local guidance links, and whitespace checks pass. The fresh-agent study uses these exact frozen guidance files. * Clarify documentation wording and optional usage examples Explain meaning before usage and make important ordering clear. Read the applicable language or porting standards for documentation conventions. Describe file interfaces independently of current callers, using callers as optional examples. Recommend examples in file headers when useful, or beside individual routines for collections of independent helpers. Validation: all 18 skill schemas, 49 local guidance links, and whitespace checks pass. These refinements have not had a new fresh-agent trial. 2026-10-16 14:08:56 -0500c179bae7435e6e90a0f796cb621d9de4690429b8Add CLUBB documentation skills (#1397)add.agents/skills/clubb-code-comments/SKILL.mdadd.agents/skills/clubb-doc-language/SKILL.mdadd.agents/skills/clubb-file-descriptions/SKILL.mdadd.agents/skills/clubb-documentation/SKILL.mdadd.agents/skills/clubb-readmes/SKILL.mdedit.agents/skills/clubb-change-messages/SKILL.mdeditAGENTS.md.agents/skills/clubb-column-refactor/SKILL.mdjenkins_tests/README.md.agents/skills/clubb-jenkins/test-authoring/SKILL.md.agents/skills/clubb-jenkins/SKILL.md.agents/skills/clubb-documentation/code-comments/SKILL.md.agents/skills/clubb-testing-and-reporting/SKILL.md.agents/skills/clubb-documentation/file-descriptions/SKILL.md.agents/skills/clubb-script-cli/SKILL.md.agents/skills/clubb-fortran-port/SKILL.md.agents/skills/clubb-python-api/SKILL.md.agents/skills/clubb-documentation/readmes/SKILL.md.agents/skills/clubb-numerical-diagnosis/SKILL.md.agents/skills/clubb-documentation/language/SKILL.md.agents/skills/clubb-readmes/SKILL.md.agents/skills/clubb-code-comments/SKILL.mdjenkins_tests/jenkins_api_login.py.agents/skills/clubb-jax-port/SKILL.md.agents/skills/clubb-doc-language/SKILL.md.agents/skills/clubb-file-descriptions/SKILL.md.agents/skills/clubb-host-compatibility/SKILL.md.agents/skills/clubb-documentation/SKILL.mdAGENTS.md.agents/skills/clubb-finalization/SKILL.md.agents/skills/clubb-documentation/change-messages/SKILL.md.agents/skills/clubb-pytests/SKILL.md.agents/skills/clubb-change-messages/SKILL.mdeb23a4c1b51706cad0060c28d8c5ead8da595e1c1792199605000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd Jenkins workflows and branch finalization guidance (#1396) * Set up Jenkins API login over HTTPS Add an interactive token login script and teach the Jenkins skill to reuse its private local credential file or direct users through setup. This lets each developer use their own Jenkins account without SSH access. Ten focused regression checks and a live HTTPS login/save check passed. BFB is not applicable: login tooling and guidance do not affect model execution or output. * Explain Jenkins login setup and agent use Describe why agents use the saved login, how developers set it up, and what the public routines and failure paths do. Apply the new documentation guidance to the script, test comments and usage documentation. Executable Python statements are unchanged. Ten focused login checks pass. * Remove Jenkins login pytests Remove the provisional test file from the Jenkins login change at the user’s request. Keep the login script and workflow guidance unchanged. * Document Jenkins access and test authoring Add a Jenkins README and a separate authoring skill for simple, reproducible pipelines and coordinated live-job changes. Keep API access in its existing skill and route both workflows from AGENTS.md. Place the login script with the Jenkins files and update its references. Runtime statements and the credential location are unchanged. Login help, import, live HTTPS identity, skill validation and local links pass. * Prefer relevant Jenkins evidence in test reports Add shared guidance for choosing checks and explaining what their results establish. Lead PR reports with relevant Jenkins build links, include local checks when they add evidence, and keep unexpected failures visible. Connect validation and change-message workflows to the shared skill. Skill metadata and local guidance links validate; only Markdown changes. * Keep README verification notes in change reports Remove the authoring-history sentence from the Jenkins README and clarify where the README skill should record example verification. Review the PR documentation for similar notes while retaining reader-relevant setup. Skill metadata, local links and diff formatting checks pass. * Group related skills under their entry points Nest documentation guides and Jenkins test authoring while preserving skill names and workflow text. Rebase links, make shared parent guidance explicit, and use recursive skill discovery for validation. The Codex skill loader discovers every nested child. Recursive schema, link and preservation checks pass. * Clarify Jenkins test authoring scope and when to wait Require a user request before changing Jenkins test definitions, while allowing relevant existing branch builds during normal validation. Align pytest integration guidance with that boundary. Guide intermediate work toward fast meaningful checks and later review of slow builds; weigh longer waits at final validation and report pending results. All 20 skill schemas and 99 local guidance links validate; diff formatting passes. No pipeline or runtime changes, or live Jenkins actions. * Explain Jenkins permissions before promising site changes Describe the permissions needed to read, run, create or edit jobs without assuming a particular account. Link the guidance from authoring and setup, and explain how to use assigned tokens or switch saved accounts. All 20 skill schemas and 101 local guidance links pass, including the new section anchors. Diff formatting passes; this commit changes Markdown only. Prior live HTTPS checks confirmed creation, build and cancellation access, read-only configuration access, and denied configuration writes. * Add branch finalization workflow and agent PR conventions Define merge preparation as a full branch audit followed by current validation and a commit, push and draft-PR handoff. Pause for substantive unintended issues the user has not accepted; allow minor cleanup without interruption. Route finalization from AGENTS and shared testing guidance. Keep agent PRs as drafts and sign PR comments posted through a user account with the agent name. Codex discovers all 21 repo skills. All 21 schemas and 110 local guidance links validate; diff formatting passes. Only agent guidance changes. * Clarify which builds an agent may cancel Limit cancellation to builds and queue items launched for the current task unless the user authorizes stopping others. A shared Jenkins username does not establish ownership. Wrap the nearby setup and authoring text. Final branch audit found no substantive blockers. Login smoke checks passed for live HTTPS authentication, private credential replacement and failure preservation without changing the user credential file. All 21 skill schemas, 110 local links and 5 heading anchors pass; Codex discovers all 21 skills. 2026-10-16 20:13:25 -0500eb23a4c1b51706cad0060c28d8c5ead8da595e1cAdd Jenkins workflows and branch finalization guidance (#1396)add.agents/skills/clubb-jenkins/test-authoring/SKILL.mdedit.agents/skills/clubb-column-refactor/SKILL.mdedit.agents/skills/clubb-pytests/SKILL.mdeditAGENTS.mdedit.agents/skills/clubb-script-cli/SKILL.mdadd.agents/skills/clubb-documentation/language/SKILL.mddelete.agents/skills/clubb-code-comments/SKILL.mddelete.agents/skills/clubb-file-descriptions/SKILL.mdedit.agents/skills/clubb-host-compatibility/SKILL.mdadd.agents/skills/clubb-finalization/SKILL.mdedit.agents/skills/clubb-numerical-diagnosis/SKILL.mddelete.agents/skills/clubb-doc-language/SKILL.mdedit.agents/skills/clubb-jax-port/SKILL.mdadd.agents/skills/clubb-testing-and-reporting/SKILL.mdadd.agents/skills/clubb-documentation/change-messages/SKILL.mdedit.agents/skills/clubb-fortran-port/SKILL.mdadd.agents/skills/clubb-documentation/code-comments/SKILL.mdedit.agents/skills/clubb-python-api/SKILL.mddelete.agents/skills/clubb-readmes/SKILL.mdaddjenkins_tests/README.mdaddjenkins_tests/jenkins_api_login.pyedit.agents/skills/clubb-documentation/SKILL.mdadd.agents/skills/clubb-documentation/file-descriptions/SKILL.mdedit.agents/skills/clubb-jenkins/SKILL.mddelete.agents/skills/clubb-change-messages/SKILL.mdadd.agents/skills/clubb-documentation/readmes/SKILL.mdsrc/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.F90clubb_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/interpolation.pyclubb_jax/src/CLUBB_core/advance_wp2_wp3_module.pyclubb_jax/src/CLUBB_core/precipitation_fraction.pyclubb_jax/src/CLUBB_core/parameters_tunable.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/corr_varnce_module.pyclubb_jax/src/CLUBB_core/new_tsdadg_pdf.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/sfc_varnce_module.pyeditclubb_jax/src/CLUBB_core/model_flags.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_core_diagnostics.pyeditclubb_jax/src/CLUBB_core/file_functions.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_sfc_varnce_diagnostics.pyeditclubb_jax/src/CLUBB_core/new_hybrid_pdf_main.pyeditclubb_jax/src/CLUBB_core/sponge_layer_damping.pyeditclubb_jax/src/CLUBB_core/interpolation.pyeditclubb_jax/src/CLUBB_core/advance_wp2_wp3_module.pyeditclubb_jax/src/CLUBB_core/setup_clubb_pdf_params.pyeditclubb_jax/src/CLUBB_core/adg1_adg2_3d_luhar_pdf.pyeditclubb_jax/src/CLUBB_core/mono_flux_limiter.pyeditclubb_jax/src/CLUBB_core/corr_varnce_module.pyeditclubb_jax/src/CLUBB_core/fill_holes.pyeditclubb_jax/src/CLUBB_core/mixing_length.pyeditclubb_jax/src/CLUBB_core/precipitation_fraction.pyeditclubb_jax/src/CLUBB_core/numerical_check.pyeditclubb_jax/src/CLUBB_core/new_pdf.pyeditclubb_jax/src/CLUBB_core/remapping_module.pyeditclubb_jax/src/CLUBB_core/advance_windm_edsclrm_module.pyeditclubb_jax/src/CLUBB_core/stats_netcdf.pyeditclubb_jax/src/CLUBB_core/advance_clubb_core_module.pyeditclubb_jax/src/CLUBB_core/advance_xp2_xpyp_module.pyeditclubb_jax/src/CLUBB_core/pdf_params.pyeditclubb_jax/src/CLUBB_core/pdf_closure_module.pyeditclubb_jax/src/CLUBB_core/clip_explicit.pyeditclubb_jax/src/CLUBB_core/grid_class.pyeditclubb_jax/src/CLUBB_core/jax_stats.pyeditclubb_jax/src/CLUBB_core/advance_xm_wpxp_module.pyeditclubb_jax/src/CLUBB_core/parameters_tunable.pyeditclubb_jax/src/CLUBB_core/new_tsdadg_pdf.pyeditclubb_jax/src/CLUBB_core/matrix_operations.pyeditclubb_jax/src/CLUBB_core/matrix_solver_wrapper.pyeditclubb_jax/src/CLUBB_core/pos_definite_module.pygithttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerfalse14https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/14/12https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/12/Started by an SCM change000012648217161186751.274846084601209499c45d0ef25810f48bbd43c8f92afa1497caa09499c45d0ef25810f48bbd43c8f92afa1497caarefs/remotes/origin/master09499c45d0ef25810f48bbd43c8f92afa1497caa09499c45d0ef25810f48bbd43c8f92afa1497caarefs/remotes/origin/master09499c45d0ef25810f48bbd43c8f92afa1497caa09499c45d0ef25810f48bbd43c8f92afa1497caarefs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#121264821713433486clubb_generalized_grid #1212false1210648FAILURE1792139170962https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/12/clubb_jax/AGENTS.md.agents/skills/clubb-column-refactor/SKILL.md.agents/skills/clubb-jenkins/SKILL.mdtests/README.mdLLM_prompts/port_underlying_fortran_to_other_languages.mdLLM_prompts/README.md.agents/skills/clubb-session-retrospective/references/guidance_maintenance.mdtuner/pytests/auto_llm_generated_pytests/README.md.agents/skills/clubb-script-cli/SKILL.mdLLM_prompts/SHORTCUTS.mdtests/pytests/auto_llm_generated_pytests/README.mdLLM_prompts/update_host_models_after_clubb_changes.mdLLM_prompts/pytest_workflow.mdclubb_jax/JAX_CONVERSION_PLAN.mdLLM_prompts/fortran_routine_formatting.md.agents/skills/clubb-fortran-port/SKILL.md.agents/skills/clubb-python-api/SKILL.md.agents/skills/clubb-dash/SKILL.mdLLM_prompts/script_cli_conventions.mdutilities/pytests/auto_llm_generated_pytests/README.md.agents/skills/clubb-numerical-diagnosis/SKILL.mdLLM_prompts/update_python_api_and_drivers.mddash_app/pytests/auto_llm_generated_pytests/README.md.agents/skills/clubb-session-retrospective/SKILL.mdLLM_prompts/jenkins_workflow.mdLLM_prompts/change_messages.mdLLM_prompts/dash_app_workflow.md.agents/skills/clubb-jax-port/SKILL.mdLLM_prompts/numerical_regression_workflow.md.agents/skills/clubb-fortran-format/SKILL.md.agents/skills/clubb-host-compatibility/SKILL.mdAGENTS.md.agents/skills/clubb-pytests/SKILL.mdLLM_prompts/session_retrospective.mdLLM_prompts/fortran_column_refactor.md.agents/skills/clubb-change-messages/SKILL.mdLLM_prompts/jax_porting_workflow.md09499c45d0ef25810f48bbd43c8f92afa1497caa1792123599000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comConsolidate CLUBB workflows into skills (#1394) * Consolidate CLUBB workflows into skills Move the 13 workflows into repo skills and route to them from AGENTS.md, removing the legacy shortcut index and prompt directory. Keep the existing five skill identities and workflow instructions, including the scope rules previously stored in the index. Update only paths and obsolete routing text. Preservation checks passed for all workflow bodies, existing skill metadata, scope rules and task selectors. All 13 skills validate, all 55 local links resolve, and git diff --check passed. BFB is not applicable to this documentation-only migration. * Clarify skill selection and local guidance Allow multiple relevant skills in the task instructions, name user-facing documentation clearly, and explain that the ignored worklog is local to each checkout and should be created when absent. Add verified private host-repository links near the top of the compatibility skill so readers can identify the models and their access requirements. BFB is not applicable to these documentation-only clarifications. All 13 skill schemas, local guidance links, and git diff --check pass. Existing host workflow instructions are preserved. 2026-10-15 23:06:39 -050009499c45d0ef25810f48bbd43c8f92afa1497caaConsolidate CLUBB workflows into skills (#1394)add.agents/skills/clubb-python-api/SKILL.mddeleteLLM_prompts/update_python_api_and_drivers.mdedittests/README.mddeleteLLM_prompts/change_messages.mdeditclubb_jax/AGENTS.mdedit.agents/skills/clubb-jax-port/SKILL.mdadd.agents/skills/clubb-jenkins/SKILL.mdadd.agents/skills/clubb-column-refactor/SKILL.mdeditutilities/pytests/auto_llm_generated_pytests/README.mddeleteLLM_prompts/session_retrospective.mddeleteLLM_prompts/fortran_routine_formatting.mddeleteLLM_prompts/SHORTCUTS.mdeditclubb_jax/JAX_CONVERSION_PLAN.mdedit.agents/skills/clubb-pytests/SKILL.mddeleteLLM_prompts/update_host_models_after_clubb_changes.mddeleteLLM_prompts/jenkins_workflow.mdadd.agents/skills/clubb-dash/SKILL.mddeleteLLM_prompts/script_cli_conventions.mddeleteLLM_prompts/dash_app_workflow.mddeleteLLM_prompts/port_underlying_fortran_to_other_languages.mddeleteLLM_prompts/README.mdadd.agents/skills/clubb-fortran-format/SKILL.mdeditdash_app/pytests/auto_llm_generated_pytests/README.mdedittests/pytests/auto_llm_generated_pytests/README.mddeleteLLM_prompts/numerical_regression_workflow.mdadd.agents/skills/clubb-numerical-diagnosis/SKILL.mdedit.agents/skills/clubb-script-cli/SKILL.mddeleteLLM_prompts/fortran_column_refactor.mdadd.agents/skills/clubb-session-retrospective/references/guidance_maintenance.mdedit.agents/skills/clubb-change-messages/SKILL.mdeditAGENTS.mdadd.agents/skills/clubb-host-compatibility/SKILL.mdedit.agents/skills/clubb-session-retrospective/SKILL.mdedittuner/pytests/auto_llm_generated_pytests/README.mddeleteLLM_prompts/jax_porting_workflow.mddeleteLLM_prompts/pytest_workflow.mdadd.agents/skills/clubb-fortran-port/SKILL.mdgithttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerfalse13https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/13/11https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/11/Started by an SCM change000112846846172211441.3446500650111a8c952996409f8c94d6a28714171145ed7d2c2aea8c952996409f8c94d6a28714171145ed7d2c2aerefs/remotes/origin/mastera8c952996409f8c94d6a28714171145ed7d2c2aea8c952996409f8c94d6a28714171145ed7d2c2aerefs/remotes/origin/mastera8c952996409f8c94d6a28714171145ed7d2c2aea8c952996409f8c94d6a28714171145ed7d2c2aerefs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#111284684613433486clubb_generalized_grid #1111false1110519FAILURE1791966369019https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/11/READMEaf934ad3986d77e381919822755fc51a0168849f1791907259000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd blank line to trigger Jenkins tests 2026-10-13 11:00:59 -0500af934ad3986d77e381919822755fc51a0168849fAdd blank line to trigger Jenkins testseditREADMEsrc/G_unit_tests.F90src/G_unit_test_types/CMakeLists.txtsrc/CLUBB_core/calc_roots.F90tests/run_G_unit_tests.pysrc/G_unit_test_types/cubic_solve_tests.F90input_misc/G_unit_tests.ina8c952996409f8c94d6a28714171145ed7d2c2ae1791911400000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comFixed bug in cubic equation solve function. Only relevant if pdf is L… (#1387) * Fixed bug in cubic equation solve function. Only relevant if pdf is Luhar or iiPDF_type=4 Therefore technically BIT_CHANGING... The bug existed because the old code used the principal cube root which has an imaginary part for negative bases. The fix is to simply calc: -|w|**(1/3) for negative real numbers. * Replaced determinant with discriminant Verified via a new Fortran unit test and also manually checked with wolfram alpha. There is no way to actually run this code :/ would only work for iiPDF_types: iiPDF_3D_Luhar = 3 and iiPDF_3D_Luhar = 3 (and those are currently (Oct 2026) broken ) 2026-10-13 12:10:00 -0500a8c952996409f8c94d6a28714171145ed7d2c2aeFixed bug in cubic equation solve function. Only relevant if pdf is L… (#1387)editsrc/CLUBB_core/calc_roots.F90editsrc/G_unit_test_types/CMakeLists.txtedittests/run_G_unit_tests.pyaddsrc/G_unit_test_types/cubic_solve_tests.F90editinput_misc/G_unit_tests.ineditsrc/G_unit_tests.F90githttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerfalse12https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/12/10https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/10/Started by an SCM change000817113341124176814961.33490789078104292a70f53a6b6c4eab864fe27b8fd9af5d869094292a70f53a6b6c4eab864fe27b8fd9af5d86909refs/remotes/origin/master4292a70f53a6b6c4eab864fe27b8fd9af5d869094292a70f53a6b6c4eab864fe27b8fd9af5d86909refs/remotes/origin/master4292a70f53a6b6c4eab864fe27b8fd9af5d869094292a70f53a6b6c4eab864fe27b8fd9af5d86909refs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#101334112413433486clubb_generalized_grid #1010false1010404FAILURE1791879971556https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/10/LLM_prompts/SHORTCUTS.md.agents/skills/clubb-change-messages/SKILL.mdAGENTS.mdLLM_prompts/change_messages.mdfc9087d1a7a4a8f71c74f5763ece34f18328d2001791830025000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd CLUBB commit and PR writing guidance (#1391) * Add CLUBB commit and PR writing guidance Add a canonical workflow and historical examples for writing specific titles and explaining purpose, motivation, results and testing. Scope BFB claims to their comparisons and distinguish tolerance matches from bitwise equality. A thin repo skill, shortcut and AGENTS link make the workflow discoverable. This addresses generated messages that bury the reason for a change or overstate what testing establishes. Six historical PR/commit drafting pairs passed independent review. Skill format, 20 local links, canonical-text consistency and git diff --check passed. BFB is not applicable to these documentation-only changes. * Keep only the final commit and PR writing workflow Remove the worked historical examples and their references. The repository should contain the final reusable guidance; the research and evaluation artifacts stay outside it. The shortcut and repo skill still point to one canonical workflow. Skill-format validation, all 19 local guidance links and git diff --check passed. BFB is not applicable to these documentation-only changes. 2026-10-12 13:33:45 -0500fc9087d1a7a4a8f71c74f5763ece34f18328d200Add CLUBB commit and PR writing guidance (#1391)editLLM_prompts/SHORTCUTS.mdadd.agents/skills/clubb-change-messages/SKILL.mdeditAGENTS.mdaddLLM_prompts/change_messages.mdclubb_python_api/pytests/auto_llm_generated_pytests/test_advance_core_subs.pyclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_advance_xp2_xpyp.pyclubb_jax/src/Benchmark_cases/cobra.pyclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_advance_wp2_wp3.pyclubb_python_api/clubb_python/prescribe_forcings.pyclubb_jax/src/CLUBB_core/advance_windm_edsclrm_module.pysrc/Benchmark_cases/time_dependent_input.F90clubb_python_api/clubb_python/CLUBB_core/parameters_tunable.pyclubb_python_api/clubb_python/CLUBB_core/numerical_check.pysrc/CLUBB_core/advance_windm_edsclrm_module.F90clubb_jax/pytests/auto_llm_generated_pytests/test_driver_lifecycle.pyclubb_python_driver/advance_clubb_core.pyclubb_jax/src/Benchmark_cases/time_dependent_input.pyutilities/pytests/auto_llm_generated_pytests/test_expldiff_settings_rules.pyclubb_python_api/f2py_fortran_wrappers/advance_windm_edsclrm_module_wrapper.F90clubb_jax/src/CLUBB_core/advance_clubb_core_module.pyclubb_jax/pytests/auto_llm_generated_pytests/test_expldiff_edsclrm_forcing.pyclubb_jax/pytests/auto_llm_generated_pytests/test_pressure_coord_forcing.pyclubb_python_api/clubb_python/CLUBB_core/advance_windm_edsclrm.pyclubb_python_api/pytests/auto_llm_generated_pytests/test_init_sequence.pyclubb_jax/src/clubb_case_initalization.pyclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_advance_windm_edsclrm.pyclubb_jax/pytests/auto_llm_generated_pytests/test_windm_edsclrm_scalar_indices.pyexperimental/experimental_pdfs/python/dash_additions/misc_labs/sam_lscale.pyclubb_python_api/clubb_python/derived_types/nu_vert_res_dep.pysrc/CLUBB_core/numerical_check.F90clubb_python_driver/advance_clubb_to_end.pysrc/CLUBB_core/advance_clubb_core_module.F90clubb_python_driver/clubb_case_initalization.pyclubb_jax/pytests/auto_llm_generated_pytests/test_cobra_sfclyr.pyclubb_jax/src/Benchmark_cases/prescribe_forcings.pyclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_advance_core.pysrc/clubb_driver.F90utilities/clubb_settings_validation.pytests/run_clubb_settings_validation_test.pysrc/Benchmark_cases/prescribe_forcings.F90clubb_jax/src/CLUBB_core/numerical_check.pyclubb_jax/src/advance_clubb_to_end.pyclubb_python_api/clubb_f2py.pyfsrc/Benchmark_cases/cobra.F90clubb_python_api/f2py_fortran_wrappers/numerical_check_wrapper.F90clubb_jax/pytests/auto_llm_generated_pytests/test_forcing_port_structure.pyclubb_python_api/f2py_fortran_wrappers/prescribe_forcings_module_wrapper.F90clubb_jax/src/CLUBB_core/err_info_codes.pyclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_advance_xm_wpxp.py4292a70f53a6b6c4eab864fe27b8fd9af5d869091791843053000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comFix arm97+l do expldiff rtm thlm+set edsclrm f early (#1386) * Do not force the thlm/rtm copies in the expldiff eddy-scalar solve With l_do_expldiff_rtm_thlm, advance_windm_edsclrm copies thlm into edsclrm(:,:,edsclr_dim-1) and rtm into edsclrm(:,:,edsclr_dim), advances all eddy scalars, and copies those two slots back into thlm and rtm. The solve added edsclrm_forcing of each slot to the copies, but thlm and rtm are already advanced with thlm_forcing and rtm_forcing in advance_xm_wpxp. In the standalone driver the slots are filled by iiedsclr_thl/iiedsclr_rt: - arm_97 (iiedsclr_rt = 1, iiedsclr_thl = 2) put thlm_forcing [K/s] on rtm, so rtm < 0 at ~5.5-8.8 km within the first steps (flag11 / expldiff). - With the slots in expldiff order, rtm_forcing was applied twice and arm_97 still hit rtm < 0 near 12 km after 1379 of 5580 steps. The copies now get no forcing. Mirrored in the JAX port. Only changes runs with l_do_expldiff_rtm_thlm = .true. and non-zero edsclrm_forcing in the last two eddy scalars, therefore BIT_CHANGING for those. Default runs are bit-for-bit identical (arm_97, 1076 variables). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * not hardwire the thlm and rtm edsclrm variables to be the last two; instead use sclr_idx%iiedsclr_thlm and sclr_idx%iiedsclr_rtm Previously l_do_expldiff_rtm_thlm = true forced the last slot to be rtm and the one before that to be thlm. If in the ..._model.in file iiedsclr_rt = 1 ! Location in the edsclrm array to place total water and iiedsclr_thl = 2 ! Location in the edsclrm array to place a scalar like thetal a switcheroo happens. But if we use a not hardcoded indexing we need to check for out of bounds and distinctness of the 2 indices. * Zero edsclrm_forcings early in apply_time_dependent_forcings_from_array Check edsclrm_forcings != 0 instead of zeroing in advance_windm_edsclrm BIT_CHANGING for l_do_expldiff_rtm_thlm = .true. for arm_97 and for cobra. Python changes include: clubb_jax, clubb_python (+f2py) + tests * Check l_do_expldiff_rtm_thlm eddy scalars in check_clubb_settings_api 1. Move the eddy-scalar checks into check_clubb_settings_api check_clubb_settings_api now takes edsclr_dim and sclr_idx. With l_do_expldiff_rtm_thlm = .true. it stops the run if - edsclr_dim <= 1, since the copies of thlm and rtm need two eddy scalars, or - iiedsclr_thl and iiedsclr_rt are not distinct indices in 1:edsclr_dim. The index check moved to check_clubb_settings_api from advance_windm_edsclrm. The check that edsclrm_forcing is zero for the thlm/rtm copies stays in advance_windm_edsclrm, because prescribe_forcings sets edsclrm_forcing every time step, after the settings check has run. Callers in Fortran and mirrors (clubb-jax, python api) are updated Behavior change: l_do_expldiff_rtm_thlm = .true. with fewer than two eddy scalars used to skip explicit diffusion silently and now stops at setup. This affects flag sets that turn the flag on for every case, e.g. flag11 in input/flag_sets/run_bindiff_w_flags_config_core_flags.json. Host models must pass the new arguments; CAM must also set sclr_idx%iiedsclr_thl/iiedsclr_rt when clubb_l_do_expldiff_rtm_thlm is on, since it leaves them at -1. 2. Fix the Python API - calc_derived_params now requires nu_vert_res_dep and always pushes it to the F2PY storage (new helper NuVertResDep.zeros(ngrdcol)). Before, nu_vert_res_dep=None kept the previous call's stored arrays, and calc_derived_params only allocates them when unallocated. So a call with more columns than an earlier one in the same process wrote out of bounds. This crashed the in-process Python API pytest suite once the windm tests used two columns. - clubb_f2py.pyf was missing l_do_expldiff_rtm_thlm for f2py_prescribe_forcings, so the Python driver failed on every case. 3. Gate the JAX rerun settings check at debug level 0 set_case_initial_conditions in the JAX driver now runs check_clubb_settings at debug level >= 0, matching clubb_driver.F90 since 9429ba2f1. Also: put l_do_expldiff_rtm_thlm on its own line in the time_dependent_input/prescribe_forcings argument lists. Bit-for-bit: default-flag output is unchanged, and arm_97 with l_do_expldiff_rtm_thlm = .true. matches the previous commit exactly. Tested: debug + Python build and source checks; settings parity test; Python API pytests (237 passed in one process); JAX pytests (791 passed); utilities settings-rule pytests; python-vs-fortran and jax-vs-fortran bomex/atex; bomex and cobra with the flag stop at setup in the Fortran, Python and JAX drivers. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * Do not apply surface fluxes to the expldiff thlm/rtm eddy-scalar copies With l_do_expldiff_rtm_thlm, advance_windm_edsclrm copies thlm and rtm into the iiedsclr_thl and iiedsclr_rt eddy scalars, solves all eddy scalars with their surface flux wpedsclrp(:,gr%k_lb_zm,:) (from wpedsclrp_sfc) and copies the two slots back. thlm and rtm already get wpthlp_sfc and wprtp_sfc in advance_xm_wpxp, so a non-zero surface flux on the copies applies it twice. Same approach as the edsclrm_forcing fix: 1. cobra_sfclyr (the only case that sets these fluxes) takes l_do_expldiff_rtm_thlm and sets wpedsclrp_sfc of the thlm/rtm copies to zero when it is on. set_sclr_sfc_rtm_thlm already zeroes all eddy-scalar surface fluxes. 2. advance_windm_edsclrm stops with a fatal error if the surface flux of either copy is non-zero, after the edsclrm_forcing check. Mirrored in the JAX port (new reason code ERR_WINDM_EDSCLRM_SFC_FLUX_EXPLDIFF_COPY; marks the columns fatal without returning early, like the forcing check). No Python API wrapper changes. CAM zeroes all eddy-scalar surface fluxes, so it is unaffected. Default cobra output is unchanged. But technically BIT_CHANGING for cobra + l_use_expldiff_rtm_thlm * Compute cobra's CO2 surface flux per column cobra_sfclyr converted the CO2 surface flux with each column's surface density inside the column loop, but stored it in the scalar CO2_flx2, and the later loops gave every column that one value: - CPU: every column got the last column's CO2 flux. Standalone columns currently share one density profile, so results were unaffected. - OpenACC: the scalar was private to the device loop, and the later loops copied the never-set host value (implicit firstprivate). In the GPU build cobra's CO2 surface flux was 0 at every step. CO2_flx2 is now a per-column array (enter/exit data create/delete like other case routines). The JAX port already computes it per column. Bit-for-bit: CPU cobra output is unchanged (1 and 2 columns, standard stats incl. the CO2 scalars). GPU cobra output changes: before, the CO2 surface flux was 0 and CO2 differed from the CPU run by up to 10%; now the CO2 scalars match the CPU run to ~1e-11 relative, like the other fields. Tested: gfortran debug build and source checks; standalone check of cobra_sfclyr with two columns of different density (before: column 1 got column 2's flux); nvhpc 24.3 OpenACC build and cobra on a Quadro P4000. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * removed the idiot proofing * fully removed idiot proofing for l_do_expldiff_rtm_thlm+esclrdim --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com> 2026-10-12 17:10:53 -05004292a70f53a6b6c4eab864fe27b8fd9af5d86909Fix arm97+l do expldiff rtm thlm+set edsclrm f early (#1386)editclubb_python_driver/advance_clubb_core.pyaddutilities/pytests/auto_llm_generated_pytests/test_expldiff_settings_rules.pyeditclubb_jax/src/CLUBB_core/numerical_check.pyeditsrc/CLUBB_core/advance_clubb_core_module.F90editclubb_jax/src/CLUBB_core/advance_clubb_core_module.pyeditclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_advance_xp2_xpyp.pyeditsrc/Benchmark_cases/cobra.F90editclubb_jax/src/Benchmark_cases/cobra.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_cobra_sfclyr.pyeditclubb_python_api/clubb_python/derived_types/nu_vert_res_dep.pyeditclubb_python_api/clubb_python/prescribe_forcings.pyeditsrc/CLUBB_core/numerical_check.F90editclubb_jax/pytests/auto_llm_generated_pytests/test_driver_lifecycle.pyeditclubb_python_driver/clubb_case_initalization.pyeditclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_advance_xm_wpxp.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_forcing_port_structure.pyeditsrc/clubb_driver.F90editclubb_python_api/f2py_fortran_wrappers/prescribe_forcings_module_wrapper.F90editclubb_jax/src/Benchmark_cases/prescribe_forcings.pyeditclubb_jax/src/clubb_case_initalization.pyeditclubb_python_api/clubb_python/CLUBB_core/parameters_tunable.pyeditexperimental/experimental_pdfs/python/dash_additions/misc_labs/sam_lscale.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_expldiff_edsclrm_forcing.pyeditclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_advance_wp2_wp3.pyeditutilities/clubb_settings_validation.pyeditclubb_jax/src/Benchmark_cases/time_dependent_input.pyeditclubb_jax/src/advance_clubb_to_end.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_windm_edsclrm_scalar_indices.pyeditclubb_jax/src/CLUBB_core/advance_windm_edsclrm_module.pyeditclubb_python_api/clubb_f2py.pyfeditclubb_jax/pytests/auto_llm_generated_pytests/test_pressure_coord_forcing.pyeditclubb_python_api/clubb_python/CLUBB_core/advance_windm_edsclrm.pyeditclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_advance_windm_edsclrm.pyedittests/run_clubb_settings_validation_test.pyeditclubb_jax/src/CLUBB_core/err_info_codes.pyeditsrc/Benchmark_cases/time_dependent_input.F90editclubb_python_api/f2py_fortran_wrappers/numerical_check_wrapper.F90editclubb_python_api/pytests/auto_llm_generated_pytests/test_advance_core_subs.pyeditclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_advance_core.pyeditclubb_python_api/pytests/auto_llm_generated_pytests/test_init_sequence.pyeditsrc/Benchmark_cases/prescribe_forcings.F90editclubb_python_api/f2py_fortran_wrappers/advance_windm_edsclrm_module_wrapper.F90editsrc/CLUBB_core/advance_windm_edsclrm_module.F90editclubb_python_driver/advance_clubb_to_end.pyeditclubb_python_api/clubb_python/CLUBB_core/numerical_check.pygithttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerfalse11https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/11/9https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/9/Started by an SCM change000012855720170227701.3248386838699429ba2f18a79e7b17ef53bccc8f17af6649c3fd9429ba2f18a79e7b17ef53bccc8f17af6649c3fdrefs/remotes/origin/master9429ba2f18a79e7b17ef53bccc8f17af6649c3fd9429ba2f18a79e7b17ef53bccc8f17af6649c3fdrefs/remotes/origin/master9429ba2f18a79e7b17ef53bccc8f17af6649c3fd9429ba2f18a79e7b17ef53bccc8f17af6649c3fdrefs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#91285572013433486clubb_generalized_grid #99false910303FAILURE1791534370861https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/9/src/clubb_driver.F909429ba2f18a79e7b17ef53bccc8f17af6649c3fd1791488049000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAlways do idiot-proofing of flags in check_clubb_settings_api Changed debug level check from 1 to 0 for parameter sanity checks. 2026-10-08 14:34:09 -05009429ba2f18a79e7b17ef53bccc8f17af6649c3fdAlways do idiot-proofing of flags in check_clubb_settings_apieditsrc/clubb_driver.F90githttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerfalse10https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/10/8https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/8/Started by an SCM change000714082526174195781.244779577978e92c2f24486a32610935ff4eede3512c67e313eae92c2f24486a32610935ff4eede3512c67e313earefs/remotes/origin/mastere92c2f24486a32610935ff4eede3512c67e313eae92c2f24486a32610935ff4eede3512c67e313earefs/remotes/origin/mastere92c2f24486a32610935ff4eede3512c67e313eae92c2f24486a32610935ff4eede3512c67e313earefs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#81408252613433486clubb_generalized_grid #88false810223FAILURE1791447970649https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/8/tuner/loss_backend.pytuner/job_runtime.pytuner/pytests/auto_llm_generated_pytests/test_tuner_top_overrides.pyclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyjenkins_tests/clubb_tuner/Jenkinsfilerun_scripts/README.mddash_app/pytests/auto_llm_generated_pytests/test_tune_replay_completion.pydash_app/pytests/test_jax_device.pydash_app/shared/activity.pyclubb_jax/run_jax.pydash_app/README.mdtuner/pytests/auto_llm_generated_pytests/test_jax_launch_errors.pytuner/request.pydash_app/compile_tab/callbacks.pydash_app/shared/actions.pydash_app/shared/jax_device.pyutilities/create_case_namelist.pydash_app/profile_tab/runtime.pydash_app/tune_tab/runtime.pytuner/tune_clubb.pytuner/pytests/auto_llm_generated_pytests/test_runtime_device_settings.pytuner/tuning_worker.pyclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pydash_app/run_tab/runtime.pytuner/status.pyclubb_jax/backends/cuda.pydash_app/services/models.pydash_app/pytests/test_agent_services.pydash_app/pytests/auto_llm_generated_pytests/test_jax_tuning_runtime.pydash_app/tune_tab/callbacks_runs.pytuner/tuning_scheduler.pydash_app/DEVELOPMENT.mddash_app/pytests/test_run_broker_simplification.pydash_app/compile_tab/build_selector.pytuner/README.mdtuner/pytests/auto_llm_generated_pytests/test_jax_backend.pyclubb_jax/README.mdrun_scripts/run_tuner_job.py9a1b8b23408d3a5abe78ebae7dd1390755fa4fec1791407526000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comUse JAX in tuner (#1383) This makes the JAX work through the new tuner, same sort of way the fortran does. Probably needs a little more testing but seems to be working properly now. * Support reusable JAX driver state and runtime batches * Add standalone JAX loss evaluation and consistency coverage * Keep standalone loss CLI coverage separate from tuning * Integrate JAX with managed tuner jobs and add bounded Jenkins coverage * Remove trailing whitespace from extracted loss CLI tests * Run JAX loss help checks in the JAX pytest suite * Keep JAX lifecycle coverage with native driver tests and document its origins * Document loss test scenarios, native counterparts and JAX extensions * Keep the native loss executable path intact in the test description * Explain managed tuning test ownership and native backend contracts * Mirror the native driver lifecycle test and compare complete JAX statistics * Run JAX driver extensions as an independent step in the lifecycle stage * Update the C8 comparison mutation for indexed parameter loading * Refresh JAX tuner integration for merged loss frontends Use the relocated standalone loss entry point and retain CLI checks only in their shared owner. Give each Jenkins tuning run a separate job directory so repeated builds can succeed. * Record invalid direct tuner requests as terminal errors Let the existing request and launcher error handlers report malformed JSON and non-string JAX options instead of crashing during bootstrap before writing job results. * Preserve winning parameter columns in tuner reruns Retain request physics overrides while excluding initialized values for tuned parameters. Window and full-case reruns now use the winning candidate values, including multiple columns and grouped override names. * Use the selected JAX runtime throughout Dash tuning Persist backend and per-job device settings through native and typed broker requests, saved revisions, continuation and result reruns. Reuse the launcher, shared device controls and rerun override resolver; supervise browser replay processes in the broker. * Allow run IDs in broker replay completion metadata Avoid a selector argument collision that killed the replay watcher before recording terminal state. Preserve run IDs and cancellation metadata while reporting completed jobs accurately. * Keep JAX device setup inside the launcher and backends Expose a standard-library selection interface and forward per-job device and preallocation settings through the SCM and tuner launch paths. Use the same backend configuration for discovery, provenance, and execution; remove GPU environment handling from Dash and the tuner. Validate with Dash/shared suites, focused launcher checks, a CPU tuning and replay workflow, and synthetic two-GPU discovery. * Forward device settings through the existing JAX selection option Extend the launcher-owned -options grammar with device=UUID and prealloc_gpu_mem=true|false, while retaining xla_prealloc compatibility. Remove the transient device-specific options from SCM and tuner scripts so they forward one opaque -jax value. Validate saved settings, discovery and replays through the same public interface; verify CPU tuning metrics remain identical. 2026-10-07 16:12:06 -05009a1b8b23408d3a5abe78ebae7dd1390755fa4fecUse JAX in tuner (#1383)editdash_app/pytests/test_run_broker_simplification.pyaddtuner/pytests/auto_llm_generated_pytests/test_runtime_device_settings.pyeditclubb_jax/backends/cuda.pyedittuner/status.pyaddtuner/loss_backend.pyeditdash_app/pytests/test_jax_device.pyedittuner/job_runtime.pyeditdash_app/shared/actions.pyeditclubb_jax/run_jax.pyadddash_app/pytests/auto_llm_generated_pytests/test_jax_tuning_runtime.pyeditrun_scripts/run_tuner_job.pyedittuner/README.mdeditclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyeditrun_scripts/README.mdeditdash_app/pytests/test_agent_services.pyeditclubb_jax/README.mddeletedash_app/shared/jax_device.pyeditdash_app/tune_tab/runtime.pyeditjenkins_tests/clubb_tuner/Jenkinsfileedittuner/tuning_worker.pyeditdash_app/services/models.pyeditdash_app/shared/activity.pyaddtuner/pytests/auto_llm_generated_pytests/test_jax_launch_errors.pyeditdash_app/compile_tab/callbacks.pyeditdash_app/compile_tab/build_selector.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyedittuner/tuning_scheduler.pyedittuner/request.pyeditdash_app/README.mdeditdash_app/run_tab/runtime.pyeditutilities/create_case_namelist.pyaddtuner/pytests/auto_llm_generated_pytests/test_jax_backend.pyadddash_app/pytests/auto_llm_generated_pytests/test_tune_replay_completion.pyeditdash_app/profile_tab/runtime.pyeditdash_app/tune_tab/callbacks_runs.pyedittuner/tune_clubb.pyeditdash_app/DEVELOPMENT.mdaddtuner/pytests/auto_llm_generated_pytests/test_tuner_top_overrides.pyrun_scripts/run_tuner.pydash_app/run_tab/tab.pyutilities/README.md.gitignoredash_app/persistence.pydash_app/run_tab/callbacks_selection.pydash_app/run_tab/layout.pyutilities/case_json_to_namelist.pydash_app/pytests/auto_llm_generated_pytests/test_case_editor.pydash_app/README.mdinput/case_setups/case_definitions.jsondash_app/assets/34_case_editor.jsutilities/pytests/auto_llm_generated_pytests/test_case_json_to_namelist.pydash_app/shared/actions.pyrun_scripts/run_scm_loss.pydash_app/run_tab/discovery.pydash_app/assets/11_tab_run_theme.cssdash_app/assets/12_case_editor.cssutilities/create_case_namelist.pytuner/case_defaults.pydash_app/profile_tab/runtime.pyinput/case_setups/READMEdash_app/run_tab/cases.py5f8b57f69c01c59fc3c4457178ae85d57894c1d91791415324000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd JSON case definitions and Dash case editor (#1389) This is mainly a dash update right now, but it adds json versions of our model files. Basically just 2 new files for that - each json stores default values then one entry for each case with overrides it is not default yet and the current system of defining cases is unchanged. * Add JSON case definitions and Dash case editor * Simplify named case lookup and remove queued snapshots * Remove model validation from JSON case conversion 2026-10-07 18:22:04 -05005f8b57f69c01c59fc3c4457178ae85d57894c1d9Add JSON case definitions and Dash case editor (#1389)edittuner/case_defaults.pyeditdash_app/run_tab/callbacks_selection.pyaddutilities/pytests/auto_llm_generated_pytests/test_case_json_to_namelist.pyeditutilities/README.mdeditdash_app/profile_tab/runtime.pyeditdash_app/README.mdeditdash_app/run_tab/layout.pyedit.gitignoreaddinput/case_setups/case_definitions.jsoneditdash_app/shared/actions.pyaddutilities/case_json_to_namelist.pyeditdash_app/run_tab/tab.pyeditutilities/create_case_namelist.pyadddash_app/assets/34_case_editor.jseditinput/case_setups/READMEeditdash_app/assets/11_tab_run_theme.cssadddash_app/run_tab/cases.pyeditdash_app/run_tab/discovery.pyeditrun_scripts/run_scm_loss.pyeditrun_scripts/run_tuner.pyeditdash_app/persistence.pyadddash_app/pytests/auto_llm_generated_pytests/test_case_editor.pyadddash_app/assets/12_case_editor.csstests/README.mdtests/pytests/auto_llm_generated_pytests/test_run_stats_output_consistency.pyjenkins_tests/clubb_stats_output_consistency/Jenkinsfiletests/run_stats_output_consistency.py166ec211468128c37d8bb4b917ffac337bf802471791416548000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comRun JAX statistics consistency with an explicit rounding tolerance (#1385) This adds a jax jenkins stage for the statistics consistency test. This is the test that runs clubb with different batches sizes and averaging methods, e.g - start by: run once with 60s output intervals all the way through - test: running with 300s output intervals should give the same stats as manually averaging 5 steps of 60s output - test: outputing only a "window" of stats data (like from timesteps 100-200 instead of whole run), should produce a window idendical to the 60s full output run - test: running 16 columns at once should produce the same as running 16 columns in batches of 4 at a time In fortran these comparisons should be BFB (other than the manually averaging one, which is only close), but in jax, changing things like the batch size can cause optimizations to happen differently, which breaks BFBness and seems to cause differences larger than expected by fortran. For example, the threshold for the manual averaging test in fortran is 1e-12, but for the jax we need 1e-9 even for the batch test. I added a tolerance, `jax_tolerance`, that I left named after jax for now since that is the only current reason that flag exists. This difficulty with jax wasn't unexpected - we also have to compile the fortran with `-O0` to get this test working, also to disable optimizations. There just seems to be less control over how jax does that, so I went with a "relax the tolerance for this specific instance" approach. * Support reusable JAX driver state and runtime batches * Expose JAX in the strict statistics consistency workflow * Keep JAX lifecycle coverage with native driver tests and document its origins * Reference native driver and statistics owners in the JAX test workflow * Keep full Fortran statistics source paths in the test description * Mirror the native driver lifecycle test and compare complete JAX statistics * Run JAX driver extensions as an independent step in the lifecycle stage * Update the C8 comparison mutation for indexed parameter loading * Keep statistics windows within the capped native case duration * Allow explicit JAX statistics tolerance for JIT rounding differences 2026-10-07 18:42:28 -0500166ec211468128c37d8bb4b917ffac337bf80247Run JAX statistics consistency with an explicit rounding tolerance (#1385)addtests/pytests/auto_llm_generated_pytests/test_run_stats_output_consistency.pyeditjenkins_tests/clubb_stats_output_consistency/Jenkinsfileedittests/run_stats_output_consistency.pyedittests/README.mdtests/run_timestep_tests.pytests/README.mdjenkins_tests/clubb_timestep/Jenkinsfileclubb_jax/README.mdclubb_jax/run_jax.pyclubb_jax/pytests/auto_llm_generated_pytests/test_compilation_cache.pytests/run_timestep_sweep.pytests/pytests/auto_llm_generated_pytests/test_run_timestep_sweep.py341cac040a0d352fd5a4da6a5938a86d7d06e3321791417082000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comRun timestep sweep tests with JAX (#1384) Adding a jax run to the timestep test (now renamed timestep sweep because it's more descriptive). This was really slow on JAX at first - one trick was to add a compilation cache, so that different runs that only use different timesteps didn't need to be recompiled. From my undestanding this is super easy with jax, basically just set `JAX_COMPILATION_CACHE_DIR` to a directory the process can save compiled parts is all it takes, then the compiled parts can live there even after the processes dies, and future ones can reuse it. * Run existing timestep sweeps with the JAX runner * Explain the shared native and JAX timestep sweep behavior * Keep timestep checks aligned with current launcher and CLI conventions Select CPU explicitly in the bounded JAX stage and resolve optional output roots through the shared owner. Support standard single-dash help, reject ambiguous option abbreviations, and cover opaque runtime forwarding while preserving native defaults and exploratory status. Validate with 373 shared checks and four eight-step BOMEX/ATEX runs per backend at 60 and 600 seconds. * Rename the timestep sweep and run shared JAX cases at native defaults Select the 18 cases shared by the native sweep and JAX/Fortran comparison list. Remove Jenkins timestep and iteration overrides, update stage names and documentation, and preserve the sweep's stability-reporting behavior. Validate the selection and rename with 374 shared checks before live branch testing. * Reuse JAX compilations and parallelize case timestep sweeps Keep a backend-specific persistent cache outside the checkout and preserve explicit cache overrides. Run four isolated case sweeps, prioritize measured expensive cases, and print each completed report as a block while preserving timestep order and first-failure semantics. Validate cache reuse across fresh processes and cache clearing, scheduling/overlap/interruption contracts, 379 shared checks, and full 90-run cold-cache JAX/native matrices. 2026-10-07 18:51:22 -0500341cac040a0d352fd5a4da6a5938a86d7d06e332Run timestep sweep tests with JAX (#1384)editjenkins_tests/clubb_timestep/Jenkinsfileaddtests/run_timestep_sweep.pyeditclubb_jax/README.mdaddclubb_jax/pytests/auto_llm_generated_pytests/test_compilation_cache.pyaddtests/pytests/auto_llm_generated_pytests/test_run_timestep_sweep.pyeditclubb_jax/run_jax.pydeletetests/run_timestep_tests.pyedittests/README.mdjenkins_tests/clubb_plots/JenkinsfileLLM_prompts/jenkins_workflow.mde92c2f24486a32610935ff4eede3512c67e313ea1791427833000https://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhuebler@uwm.eduAdd JAX comparison plots 2026-10-07 21:50:33 -0500e92c2f24486a32610935ff4eede3512c67e313eaAdd JAX comparison plotseditjenkins_tests/clubb_plots/JenkinsfileeditLLM_prompts/jenkins_workflow.mdgithttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerfalse9https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/9/7https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/7/Started by an SCM change000012576504163527741.3480208020704ff5df702bc2ad372325353ee19dde5a2fc3fc104ff5df702bc2ad372325353ee19dde5a2fc3fc1refs/remotes/origin/master04ff5df702bc2ad372325353ee19dde5a2fc3fc104ff5df702bc2ad372325353ee19dde5a2fc3fc1refs/remotes/origin/master04ff5df702bc2ad372325353ee19dde5a2fc3fc104ff5df702bc2ad372325353ee19dde5a2fc3fc1refs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#71257650413433486clubb_generalized_grid #77false710116FAILURE1791361570940https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/7/clubb_jax/src/clubb_case_initalization.pyclubb_jax/src/clubb_standalone.pyclubb_jax/src/CLUBB_core/parameters_tunable.pytests/pytests/auto_llm_generated_pytests/test_scm_jax_driver_test.pyclubb_jax/src/Input_fields/namelist.pyclubb_jax/pytests/auto_llm_generated_pytests/test_driver_test_frontend.pyclubb_jax/run_jax.pytests/run_jax_comparison_mutation_test.pyclubb_jax/tests/run_driver_extensions_test.pyLLM_prompts/jenkins_workflow.mdrun_scripts/run_scm.pyclubb_jax/pytests/auto_llm_generated_pytests/test_driver_lifecycle.pyclubb_jax/pytests/auto_llm_generated_pytests/test_driver_error_window.pyclubb_jax/src/advance_clubb_to_end.pyjenkins_tests/clubb_driver/Jenkinsfileclubb_jax/src/clubb_driver_test.pyclubb_jax/README.mdLLM_prompts/pytest_workflow.md56e1502fbdd1be881a4c3ae1a2a9570dfc8615ab1791322777000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comSupport reusable JAX driver initialization and runtime batches (#1380) This is just getting the jax driver to be more in line with fortran. It was lacking features like being able to start/stop at a certain timestep. Certain driver tests were also missing, which got added and included in the driver jenkins test. * Support reusable JAX driver state and runtime batches * Keep JAX lifecycle coverage with native driver tests and document its origins * Mirror the native driver lifecycle test and compare complete JAX statistics * Run JAX driver extensions as an independent step in the lifecycle stage * Update the C8 comparison mutation for indexed parameter loading 2026-10-06 16:39:37 -050056e1502fbdd1be881a4c3ae1a2a9570dfc8615abSupport reusable JAX driver initialization and runtime batches (#1380)editLLM_prompts/pytest_workflow.mdaddtests/pytests/auto_llm_generated_pytests/test_scm_jax_driver_test.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_driver_error_window.pyaddclubb_jax/src/clubb_driver_test.pyaddclubb_jax/tests/run_driver_extensions_test.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_driver_lifecycle.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_driver_test_frontend.pyeditclubb_jax/README.mdeditclubb_jax/src/Input_fields/namelist.pyeditclubb_jax/src/clubb_standalone.pyedittests/run_jax_comparison_mutation_test.pyeditclubb_jax/src/clubb_case_initalization.pyeditclubb_jax/run_jax.pyeditLLM_prompts/jenkins_workflow.mdeditclubb_jax/src/CLUBB_core/parameters_tunable.pyeditclubb_jax/src/advance_clubb_to_end.pyeditjenkins_tests/clubb_driver/Jenkinsfileeditrun_scripts/run_scm.pytests/README.mdclubb_jax/src/clubb_case_initalization.pyclubb_jax/pytests/auto_llm_generated_pytests/test_restart.pytests/pytests/auto_llm_generated_pytests/test_run_restart_test.pyclubb_jax/pytests/auto_llm_generated_pytests/test_unsupported_config_guards.pyclubb_jax/src/Input_fields/input_fields.pyclubb_jax/README.mdclubb_jax/pytests/auto_llm_generated_pytests/test_restart_input_validation.pyjenkins_tests/clubb_restart/Jenkinsfiletests/run_restart_test.pyclubb_jax/RESTART_PORT_NOTES.md7666fd0f4e1bf2c8c46194dcbaa31fedf8f3c8241791325897000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comPort JAX restart initialization and test normal and SILHS continuation (#1381) This makes jax restarts work. Also adding jax restart test stages in the existing jenkins restart test. * Port JAX restart initialization and exercise native and SILHS restarts * Describe restart validation and dependencies for the focused PR * Describe JAX restart scenarios and their native source equivalents * Keep JAX restart validation in the shared harness and exercise distinct columns 2026-10-06 17:31:37 -05007666fd0f4e1bf2c8c46194dcbaa31fedf8f3c824Port JAX restart initialization and test normal and SILHS continuation (#1381)editclubb_jax/README.mdedittests/run_restart_test.pyaddclubb_jax/src/Input_fields/input_fields.pyedittests/README.mdaddclubb_jax/pytests/auto_llm_generated_pytests/test_restart.pyaddtests/pytests/auto_llm_generated_pytests/test_run_restart_test.pyaddclubb_jax/RESTART_PORT_NOTES.mdaddclubb_jax/pytests/auto_llm_generated_pytests/test_restart_input_validation.pyeditclubb_jax/src/clubb_case_initalization.pyeditjenkins_tests/clubb_restart/Jenkinsfileeditclubb_jax/pytests/auto_llm_generated_pytests/test_unsupported_config_guards.pyclubb_python_api/tests/clubb_loss_driver_test.pyclubb_python_api/README.mdclubb_jax/run_jax.pytuner/clubb_loss_driver.pytests/README.mdclubb_python_api/pytests/auto_llm_generated_pytests/test_loss_frontend.pyrun_scripts/run_scm_loss.pytuner/pytests/auto_llm_generated_pytests/test_case_window_overrides.pyclubb_jax/tests/test_loss_driver.pyclubb_jax/src/clubb_standalone_loss.pyclubb_jax/pytests/auto_llm_generated_pytests/test_loss_port_structure.pyclubb_python_api/clubb_python/clubb_standalone_loss.pyclubb_python_api/CMakeLists.txttuner/clubb_loss_driver_test.pyutilities/README.mdjenkins_tests/clubb_stats_output_consistency/Jenkinsfileutilities/loss_metrics.pyclubb_jax/src/clubb_loss_driver.pyclubb_jax/TUNER_PORT.mdutilities/pytests/auto_llm_generated_pytests/test_loss_cli.pytests/pytests/auto_llm_generated_pytests/test_run_loss_output_consistency.pyclubb_jax/tests/test_silhs_loss_driver.pyclubb_jax/pytests/auto_llm_generated_pytests/test_loss_driver.pytuner/README.mdclubb_jax/README.mdtuner/case_defaults.pytests/run_loss_output_consistency.py04ff5df702bc2ad372325353ee19dde5a2fc3fc11791344832000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comPort standalone JAX loss evaluation and consistency checks (#1382) This adds the capability for the jax to run and compute loss vs les data the same as fortran does. Fortran uses the "loss driver" which does this, and has some additional testing code and a clubb_standalone_loss program that supports that, so this was basically just porting more of the high level fortran code to jax and hooking it up with some of the high level python scripts the tuner uses. * Support reusable JAX driver state and runtime batches * Add standalone JAX loss evaluation and consistency coverage * Keep standalone loss CLI coverage separate from tuning * Remove trailing whitespace from extracted loss CLI tests * Run JAX loss help checks in the JAX pytest suite * Keep JAX lifecycle coverage with native driver tests and document its origins * Document loss test scenarios, native counterparts and JAX extensions * Keep the native loss executable path intact in the test description * Mirror the native driver lifecycle test and compare complete JAX statistics * Run JAX driver extensions as an independent step in the lifecycle stage * Update the C8 comparison mutation for indexed parameter loading * Reject unsupported loss restarts before opening model resources * Clean up merged loss launcher state and document early restart rejection * Move loss frontends and tests out of the tuner package Call the existing Fortran Python API directly from its installed standalone loss frontend, and keep the JAX standalone frontend with its source port. Share unchanged table formatting, relocate lifecycle and CLI coverage, and update runners and documentation. 2026-10-06 22:47:12 -050004ff5df702bc2ad372325353ee19dde5a2fc3fc1Port standalone JAX loss evaluation and consistency checks (#1382)addtuner/pytests/auto_llm_generated_pytests/test_case_window_overrides.pyeditclubb_python_api/README.mdaddtests/pytests/auto_llm_generated_pytests/test_run_loss_output_consistency.pydeletetuner/clubb_loss_driver_test.pyaddutilities/pytests/auto_llm_generated_pytests/test_loss_cli.pyaddclubb_jax/src/clubb_standalone_loss.pyedittests/run_loss_output_consistency.pyaddclubb_python_api/pytests/auto_llm_generated_pytests/test_loss_frontend.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_loss_port_structure.pyeditclubb_jax/run_jax.pyedittuner/case_defaults.pyaddclubb_jax/src/clubb_loss_driver.pyaddclubb_python_api/clubb_python/clubb_standalone_loss.pydeletetuner/clubb_loss_driver.pyaddclubb_jax/tests/test_loss_driver.pyeditclubb_jax/README.mdeditclubb_python_api/CMakeLists.txteditrun_scripts/run_scm_loss.pyeditjenkins_tests/clubb_stats_output_consistency/Jenkinsfileedittests/README.mdeditutilities/loss_metrics.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_loss_driver.pyaddclubb_python_api/tests/clubb_loss_driver_test.pyaddclubb_jax/TUNER_PORT.mdedittuner/README.mdeditutilities/README.mdaddclubb_jax/tests/test_silhs_loss_driver.pygithttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerfalse8https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/8/6https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/6/Started by user Gunther HueblerhueblerGunther Huebler6350a98e42b5a193c8471cc67c288bce95e7f7ac0350a98e42b5a193c8471cc67c288bce95e7f7ac0refs/remotes/origin/master350a98e42b5a193c8471cc67c288bce95e7f7ac0350a98e42b5a193c8471cc67c288bce95e7f7ac0refs/remotes/origin/master350a98e42b5a193c8471cc67c288bce95e7f7ac0350a98e42b5a193c8471cc67c288bce95e7f7ac0refs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#6757343013433486clubb_generalized_grid #66false610073FAILURE1791306239854https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/6/https://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerfalse7https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/7/5https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/5/Started by user Gunther HueblerhueblerGunther Hueblerfalse#51637313433486clubb_generalized_grid #55false59994FAILURE1791302496739https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/5/https://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerfalse6https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/6/4https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/4/Started by an SCM change4350a98e42b5a193c8471cc67c288bce95e7f7ac0350a98e42b5a193c8471cc67c288bce95e7f7ac0refs/remotes/origin/master350a98e42b5a193c8471cc67c288bce95e7f7ac0350a98e42b5a193c8471cc67c288bce95e7f7ac0refs/remotes/origin/master350a98e42b5a193c8471cc67c288bce95e7f7ac0350a98e42b5a193c8471cc67c288bce95e7f7ac0refs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#41369962613433486clubb_generalized_grid #44false49900FAILURE1791275172453https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/4/utilities/convert_acc_to_omp.bashe83e7d62179dd6c710b77216aea55df37600f8201791236009000https://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhuebler@uwm.eduFix OpenMP GPU host_data conversion 2026-10-05 16:33:29 -0500e83e7d62179dd6c710b77216aea55df37600f820Fix OpenMP GPU host_data conversioneditutilities/convert_acc_to_omp.bashclubb_jax/backends/cpu.pyclubb_jax/pytests/auto_llm_generated_pytests/test_backends.pyclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pytests/pytests/auto_llm_generated_pytests/test_compile_compiler_selection.pyclubb_jax/pytests/auto_llm_generated_pytests/test_rocm_runtime.pyBUILD.mdclubb_jax/backends/metal.pyclubb_jax/run_jax.pyclubb_jax/pytests/auto_llm_generated_pytests/test_portable_cholesky.pyclubb_jax/backends/__init__.pyclubb_jax/backends/cuda.pyclubb_jax/backends/rocm.pyclubb_jax/src/CLUBB_core/matrix_operations.pyclubb_jax/requirements-rocm.txtclubb_jax/README.mdclubb_jax/backends/common.pycompile.pytests/run_jax_vs_fortran_cases.pyclubb_jax/pytests/auto_llm_generated_pytests/test_runtime_info.pyclubb_jax/runtime_info.pyda614f85c180af844a77e80ddd4b61a94ce716b91791238822000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAMD/ROCM Support for Jax (#1376) This does 2 things: adds support for running on ROCM systems, this is the AMD GPU equivalent of cuda organize specific-device backend setup files, e.g GPU on nvidia needs cuda jax libraries, Apple needs metal, AMD needs rocm The only complication was the jax cholesky not working on AMD GPUs. Seems like a bug that's out of our control, so I left en environment flag to switch between the jax linalg call and a custom "portable" one. The portable one still passes the jax_vs_fortran comparison tests. Commits --- * Support native AMD ROCm JAX on CachyOS * Keep ROCm crash fixes and remove Morrison rounding workarounds * Separate JAX launcher and inspection backend policies 2026-10-05 17:20:22 -0500da614f85c180af844a77e80ddd4b61a94ce716b9AMD/ROCM Support for Jax (#1376)addclubb_jax/backends/cuda.pyeditclubb_jax/src/CLUBB_core/matrix_operations.pyeditcompile.pyaddclubb_jax/backends/metal.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_backends.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_portable_cholesky.pyeditclubb_jax/runtime_info.pyaddclubb_jax/backends/cpu.pyaddclubb_jax/backends/rocm.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_rocm_runtime.pyeditBUILD.mdeditclubb_jax/run_jax.pyaddtests/pytests/auto_llm_generated_pytests/test_compile_compiler_selection.pyedittests/run_jax_vs_fortran_cases.pyaddclubb_jax/requirements-rocm.txtaddclubb_jax/backends/common.pyeditclubb_jax/README.mdaddclubb_jax/backends/__init__.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_runtime_info.pyclubb_jax/pytests/auto_llm_generated_pytests/test_compute_sigma_sqd_w.pyclubb_jax/pytests/auto_llm_generated_pytests/test_component_corr_ip.pyclubb_jax/pytests/auto_llm_generated_pytests/test_diagnose_correlations.pyclubb_jax/pytests/auto_llm_generated_pytests/test_kk_autoconversion.pyclubb_jax/pytests/auto_llm_generated_pytests/test_limits_f_x_responder.pyclubb_jax/pytests/auto_llm_generated_pytests/test_compute_uv_tndcy.pyclubb_jax/pytests/auto_llm_generated_pytests/test_trivar_NNL_covar_eq.pyclubb_jax/pytests/auto_llm_generated_pytests/test_pdf_binormal_moments.pyclubb_jax/pytests/auto_llm_generated_pytests/test_Nc_Ncn_eqns.pyclubb_jax/pytests/auto_llm_generated_pytests/test_radiation_port_structure.pyclubb_jax/pytests/auto_llm_generated_pytests/test_liq_water_path.pyclubb_jax/pytests/auto_llm_generated_pytests/test_jit_compile.pyclubb_jax/pytests/auto_llm_generated_pytests/test_sunray_sw.pyclubb_jax/pytests/auto_llm_generated_pytests/test_simple_rad.pyclubb_jax/pytests/auto_llm_generated_pytests/test_comp_corr_norm.pyclubb_jax/pytests/auto_llm_generated_pytests/test_windm_edsclrm_rhs.pyclubb_jax/pytests/auto_llm_generated_pytests/test_remapping_ppm.pyclubb_jax/pytests/auto_llm_generated_pytests/test_simple_rad_lba.pyclubb_jax/tests/run_morrison_interface_test.pyclubb_jax/pytests/auto_llm_generated_pytests/test_ice_dfsn.pyclubb_jax/pytests/auto_llm_generated_pytests/test_clip_variance.pyclubb_jax/pytests/auto_llm_generated_pytests/test_adg1_adg2_responder_params.pyclubb_jax/pytests/auto_llm_generated_pytests/test_calc_ice_cloud_frac_component.pyclubb_jax/pytests/auto_llm_generated_pytests/test_sfc_varnce.pyclubb_jax/pytests/auto_llm_generated_pytests/test_rad_extended_atmosphere.pyclubb_jax/pytests/auto_llm_generated_pytests/test_compute_rtp2_from_chi.pyclubb_jax/pytests/auto_llm_generated_pytests/test_max_cubic_root.pyclubb_jax/pytests/auto_llm_generated_pytests/test_KK_Nrm_tendencies.pyclubb_jax/pytests/auto_llm_generated_pytests/test_param_names.pyclubb_jax/pytests/auto_llm_generated_pytests/test_pvertinterp.pyclubb_jax/pytests/auto_llm_generated_pytests/test_no_dead_functions.pyclubb_jax/pytests/auto_llm_generated_pytests/test_silhs_port_structure.pyclubb_jax/pytests/auto_llm_generated_pytests/test_denorm_transform_corr.pyclubb_jax/pytests/auto_llm_generated_pytests/test_pdf_params_pack_roundtrip.pyclubb_jax/pytests/auto_llm_generated_pytests/test_clip_skewness.pyclubb_jax/pytests/auto_llm_generated_pytests/test_microphysics_integration.pyclubb_jax/pytests/auto_llm_generated_pytests/test_NNL_covar_const_vs_MM.pyclubb_jax/pytests/auto_llm_generated_pytests/test_xp2_xpyp_terms.pyclubb_jax/pytests/auto_llm_generated_pytests/test_interpolation.pyclubb_jax/pytests/auto_llm_generated_pytests/test_constants.pyclubb_jax/pytests/auto_llm_generated_pytests/test_penta_faithful.pyclubb_jax/pytests/auto_llm_generated_pytests/test_mpace_b_lba_tndcy.pyclubb_jax/pytests/auto_llm_generated_pytests/test_T_in_K.pyclubb_jax/pytests/auto_llm_generated_pytests/test_config_flags_complete.pyclubb_jax/pytests/auto_llm_generated_pytests/test_update_xp2_mc.pyclubb_jax/README.mdclubb_jax/pytests/auto_llm_generated_pytests/test_calculate_w_responder_params.pyclubb_jax/pytests/auto_llm_generated_pytests/test_setter_var_params.pyclubb_jax/pytests/auto_llm_generated_pytests/test_diagnose_upxp.pyclubb_jax/pytests/auto_llm_generated_pytests/test_rcm_sat_adj.pyclubb_jax/pytests/auto_llm_generated_pytests/test_no_dead_imports.pyclubb_jax/pytests/auto_llm_generated_pytests/test_bivar_LL_covar_partial.pyclubb_jax/pytests/auto_llm_generated_pytests/test_hydrometp2_zt.pyclubb_jax/pytests/auto_llm_generated_pytests/test_mixed_moment_pdf_integrals.pyclubb_jax/pytests/auto_llm_generated_pytests/test_sponge_damp_xp23.pyclubb_jax/pytests/auto_llm_generated_pytests/test_calc_wp3_on_wp2.pyclubb_jax/pytests/auto_llm_generated_pytests/test_inverse_hydrostatic.pyclubb_jax/pytests/auto_llm_generated_pytests/test_diagnostic_cache.pyclubb_jax/pytests/auto_llm_generated_pytests/test_standalone_jax.pyclubb_jax/pytests/auto_llm_generated_pytests/test_kk_local_means.pyclubb_jax/pytests/auto_llm_generated_pytests/test_calc_roots.pyclubb_jax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_mean.pyclubb_jax/pytests/auto_llm_generated_pytests/test_cholesky_corr_mtx_approx.pyclubb_jax/pytests/auto_llm_generated_pytests/test_pdf_utilities.pyclubb_jax/pytests/auto_llm_generated_pytests/test_pdf_moment_integrals.pyclubb_jax/pytests/auto_llm_generated_pytests/test_lba_sfclyr.pyclubb_jax/pytests/auto_llm_generated_pytests/test_hydromet_pdf_parameter.pyclubb_jax/tests/run_standalone_no_bindings_test.pyclubb_jax/pytests/auto_llm_generated_pytests/test_new_pdf.pyclubb_jax/pytests/auto_llm_generated_pytests/test_numerics_autodiff.pyLLM_prompts/pytest_workflow.mdclubb_jax/pytests/auto_llm_generated_pytests/test_adg2_driver.pyclubb_jax/pytests/auto_llm_generated_pytests/test_routine_placement.pyclubb_jax/pytests/auto_llm_generated_pytests/test_calendar.pyclubb_jax/pytests/auto_llm_generated_pytests/test_microphysics_error_paths.pyclubb_jax/pytests/auto_llm_generated_pytests/test_compute_xp3.pyclubb_jax/pytests/auto_llm_generated_pytests/test_mean_adv.pyclubb_jax/pytests/auto_llm_generated_pytests/test_mono_flux_limiter.pyclubb_jax/pytests/auto_llm_generated_pytests/test_microphysics_port_structure.pyclubb_jax/pytests/auto_llm_generated_pytests/test_responder_params.pyclubb_jax/pytests/auto_llm_generated_pytests/test_corr_varnce.pyclubb_jax/pytests/auto_llm_generated_pytests/test_calc_comp_corrs_binormal.pyclubb_jax/pytests/auto_llm_generated_pytests/test_cloud_feedback_sfclyr.pyclubb_jax/pytests/auto_llm_generated_pytests/test_cholesky_factor.pyclubb_jax/pytests/auto_llm_generated_pytests/test_fill_holes_autodiff.pyclubb_jax/pytests/auto_llm_generated_pytests/test_advance_helper_extras.pyclubb_jax/pytests/auto_llm_generated_pytests/test_close_luhar_pdf.pyclubb_jax/pytests/auto_llm_generated_pytests/test_saturation.pyclubb_jax/pytests/auto_llm_generated_pytests/test_kk_upscaled_variances.pyclubb_jax/pytests/auto_llm_generated_pytests/test_new_tsdadg_pdf.pyclubb_jax/pytests/auto_llm_generated_pytests/test_set_sfc_value_of_flux_profiles.pyclubb_jax/pytests/auto_llm_generated_pytests/test_calc_corr_norm_cholesky.pyclubb_jax/pytests/auto_llm_generated_pytests/test_coefs_semiimpl.pyclubb_jax/pytests/auto_llm_generated_pytests/test_trivar_NLL_mean_eq.pyclubb_jax/pytests/auto_llm_generated_pytests/test_calc_xprcp_component.pyclubb_jax/pytests/auto_llm_generated_pytests/test_pdf_integrals_all_mm.pyclubb_jax/pytests/auto_llm_generated_pytests/test_stats_writer.pyclubb_jax/pytests/auto_llm_generated_pytests/test_new_hybrid_pdf_main.pyclubb_jax/pytests/auto_llm_generated_pytests/test_advance_xp3_simplified.py350a98e42b5a193c8471cc67c288bce95e7f7ac01791244216000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comPrune inherited JAX pytests and remove binding dependencies (#1379) This just prunes lots of outdated and unneccesary pytests. These are all LLM generated and I just never went through them before. Probably still needs cleanup. 2026-10-05 18:50:16 -0500350a98e42b5a193c8471cc67c288bce95e7f7ac0Prune inherited JAX pytests and remove binding dependencies (#1379)editclubb_jax/pytests/auto_llm_generated_pytests/test_hydrometeor_mixed_moments.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_fill_holes_mean.pydeleteclubb_jax/pytests/auto_llm_generated_pytests/test_pvertinterp.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_quadrivar_covar_const_limits.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_cos_solar_zen.pydeleteclubb_jax/pytests/auto_llm_generated_pytests/test_skx_func.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_spurious_source.pydeleteclubb_jax/pytests/auto_llm_generated_pytests/test_xp2_xpyp_terms.pydeleteclubb_jax/pytests/auto_llm_generated_pytests/test_new_hybrid_pdf_main.pydeleteclubb_jax/pytests/auto_llm_generated_pytests/test_xpyp_term_ta_godunov.pydeleteclubb_jax/pytests/auto_llm_generated_pytests/test_mixing_length.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_constants.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_remapping_module.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_advance_helper_extras.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_cloud_feedback_sfclyr.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_calc_corr_norm_cholesky.pydeleteclubb_jax/pytests/auto_llm_generated_pytests/test_penta_faithful.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_ice_dfsn.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_update_xp2_mc.pydeleteclubb_jax/pytests/auto_llm_generated_pytests/test_xpyp_term_ta_pdf.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_precip_fraction.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_setter_var_params.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_cholesky_corr_mtx_approx.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_sponge_damp_xp23.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_binormal_moments.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_calc_corr_w_hm_n.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_gabls3_night_stability.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_component_precip_frac_specify.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_adg1_adg2_responder_params.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_hydrometp2_zt.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_NNL_covar_vs_MM.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_close_luhar_pdf.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_numerical_check_setters.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_pdf_params_pack_roundtrip.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_Nc_Ncn_eqns.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_microphysics_error_paths.pydeleteclubb_jax/pytests/auto_llm_generated_pytests/test_diagnostic_cache.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_rad_extended_atmosphere.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_fill_holes_autodiff.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_kk_local_means.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_compute_rtp2_from_chi.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_new_pdf_main.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_rcm_sat_adj.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_max_cubic_root.pyeditclubb_jax/README.mdeditclubb_jax/pytests/auto_llm_generated_pytests/test_NNL_covar_const_limits.pydeleteclubb_jax/pytests/auto_llm_generated_pytests/test_hydrostatic.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_responder_params.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_silhs_surface_schemes.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_remapping_ppm.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_sfc_flux.pydeleteclubb_jax/pytests/auto_llm_generated_pytests/test_smooth_heaviside.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_hydromet_pdf_parameter.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_stats_output_time.pydeleteclubb_jax/pytests/auto_llm_generated_pytests/test_compute_sigma_sqd_w.pyaddclubb_jax/tests/run_standalone_no_bindings_test.pydeleteclubb_jax/pytests/auto_llm_generated_pytests/test_calculate_thvm.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_lba_sfclyr.pydeleteclubb_jax/pytests/auto_llm_generated_pytests/test_compute_xp3.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_param_names.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_splatting_autodiff.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_microphysics_port_structure.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_interpolation.pydeleteclubb_jax/pytests/auto_llm_generated_pytests/test_mono_flux_limiter.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_fill_holes_sliding_window.pydeleteclubb_jax/pytests/auto_llm_generated_pytests/test_cloud_correlate.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_penta_solver.pyaddclubb_jax/tests/run_morrison_interface_test.pyeditclubb_jax/pytests/auto_llm_gen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Hueblerfalse5https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/5/3https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/3/Started by an SCM change3feb2438c46510eaadecd3e0c3bdede3df2939ac1feb2438c46510eaadecd3e0c3bdede3df2939ac1refs/remotes/origin/masterfeb2438c46510eaadecd3e0c3bdede3df2939ac1feb2438c46510eaadecd3e0c3bdede3df2939ac1refs/remotes/origin/masterfeb2438c46510eaadecd3e0c3bdede3df2939ac1feb2438c46510eaadecd3e0c3bdede3df2939ac1refs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#31179838213433486clubb_generalized_grid #33false39796FAILURE1791188772409https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/3/clubb_jax/AGENTS.mdLLM_prompts/script_cli_conventions.mdLLM_prompts/update_python_api_and_drivers.mdLLM_prompts/jenkins_workflow.mdLLM_prompts/dash_app_workflow.mdLLM_prompts/port_underlying_fortran_to_other_languages.md.agents/skills/clubb-jax-port/SKILL.mdLLM_prompts/numerical_regression_workflow.mdLLM_prompts/README.mdAGENTS.md.agents/skills/clubb-script-cli/SKILL.mdLLM_prompts/fortran_column_refactor.mdLLM_prompts/SHORTCUTS.mdLLM_prompts/update_host_models_after_clubb_changes.mdLLM_prompts/jax_porting_workflow.mdd1c3f80378f8621f388662593c7e5a47f1847b351791138711000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comImprove agent workflow discovery and completion evidence (#1375) This is just a rework of out LLM shortcuts. I had chatgpt go through a bunch of sessions and investigate my inefficiencies in my workflow (like how often I have to ask for corrections for things that were already instructions in these shortcuts), and had it rework our shortcuts. The things done seem to make sense - they're a little shorter and more concise, broken up a bit better, include some extra things. Hard to say if any of it's effective though - hopefully I'll notice an improvement with things 2026-10-04 13:31:51 -0500d1c3f80378f8621f388662593c7e5a47f1847b35Improve agent workflow discovery and completion evidence (#1375)add.agents/skills/clubb-jax-port/SKILL.mdeditLLM_prompts/port_underlying_fortran_to_other_languages.mdaddLLM_prompts/script_cli_conventions.mdeditAGENTS.mdaddLLM_prompts/jenkins_workflow.mdeditLLM_prompts/update_python_api_and_drivers.mdaddLLM_prompts/fortran_column_refactor.mdaddLLM_prompts/jax_porting_workflow.mdaddLLM_prompts/numerical_regression_workflow.mdaddLLM_prompts/README.mdaddclubb_jax/AGENTS.mdadd.agents/skills/clubb-script-cli/SKILL.mdeditLLM_prompts/dash_app_workflow.mdeditLLM_prompts/SHORTCUTS.mdeditLLM_prompts/update_host_models_after_clubb_changes.mdclubb_jax/src/CLUBB_core/precipitation_fraction.pyclubb_jax/src/Microphys/cloud_sed_module.pyclubb_jax/tests/test_silhs_fortran_oracle.pyclubb_jax/tests/test_microphysics_port_structure.pyclubb_jax/tests/test_silhs_sampling.pyclubb_jax/src/Microphys/ice_dfsn_module.pyclubb_jax/src/Microphys/KK_microphys_module.pyclubb_jax/src/SILHS/latin_hypercube_arrays.pyclubb_jax/src/SILHS/est_kessler_microphys_module.pyclubb_jax/src/SILHS/silhs_api_module.pyclubb_jax/src/SILHS/lh_microphys_var_covar_module.pyclubb_jax/src/Microphys/estimate_scm_microphys_module.pyclubb_jax/tests/test_silhs_driver.pyclubb_jax/tests/test_silhs_diagnostics.pyclubb_jax/JAX_CONVERSION_PLAN.mdtests/run_jax_vs_fortran_cases.pyclubb_jax/src/CLUBB_core/fill_holes.pyclubb_jax/tests/test_microphysics_error_paths.pyclubb_jax/src/clubb_case_initalization.pyclubb_jax/src/Input_fields/corr_varnce_input_reader.pysrc/SILHS/latin_hypercube_driver_module.F90clubb_jax/tests/test_microphysics_integration.pyclubb_jax/README.mdclubb_jax/src/SILHS/__init__.pyclubb_jax/src/SILHS/parameters_silhs.pyclubb_jax/src/Microphys/advance_microphys_module.pytests/pytests/test_jax_compare_forwarding.pyclubb_jax/src/CLUBB_core/setup_clubb_pdf_params.pyclubb_jax/src/Microphys/gfdl_activation.pyclubb_jax/src/SILHS/latin_hypercube_driver_module.pyclubb_jax/src/Microphys/microphys_driver.pyclubb_jax/src/CLUBB_core/jax_stats.pyclubb_jax/src/Microphys/lh_microphys_driver_module.pyclubb_jax/src/Microphys/silhs_category_variance_module.pyLLM_prompts/SHORTCUTS.mdLLM_prompts/update_host_models_after_clubb_changes.mdclubb_jax/tests/test_silhs_port_structure.pysrc/SILHS/parameters_silhs.F90clubb_jax/tests/test_microphysics_host_errors.pyclubb_jax/src/Microphys/parameters_microphys.pyclubb_jax/src/SILHS/silhs_importance_sample_module.pyclubb_jax/src/SILHS/math_utilities.pysrc/Microphys/microphys_init_cleanup.F90clubb_jax/src/SILHS/generate_uniform_sample_module.pyclubb_jax/src/Microphys/pdf_hydromet_microphys_wrapper.pyclubb_jax/src/Microphys/morrison_microphys_module.pysrc/SILHS/generate_uniform_sample_module.F90clubb_jax/src/SILHS/transform_to_pdf_module.pyclubb_jax/SILHS_PORT_NOTES.mdclubb_jax/src/Microphys/microphys_init_cleanup.pyclubb_jax/src/CLUBB_core/stats_clubb_utilities.pyclubb_jax/src/Microphys/mixed_moment_PDF_integrals.pyclubb_jax/src/advance_clubb_to_end.pyclubb_jax/src/Microphys/coamps_microphys_driver_module.pyf51ab963e7cde71123d3afd8f77d077a35cf211f1791158488000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comJax silhs (#1372) Adding silhs to jax. To avoid randomness issues I added a silhs flag, l_lh_deterministic_test, that causes samples and random numbers to be generated in a deterministic order that is pretty basic but seems like a fine enough sampling method for a test that only matters for comparing jax to fortran matching. This required changing the fortran to have this deterministic test sample generation. I added 3 new silhs tests: rico_silhs with a 60s timestep matches up to 360 timestpes (6 hours) lba_kk_silhs (lba with kk microphys instead of defauly morrison) passes up to 270ish steps, I set test to 240 steps lba_silhs (with morrison) passes <80, from past exploration this seems mainly due to morrison being in single precision * Port SILHS sampling and microphysics coupling to JAX Add native JAX Latin-hypercube sampling with explicit persistent permutation state and case-owned initialization. Couple sampled states to KK and Morrison microphysics in interactive and diagnostic modes, with weighted statistics, substep averaging, and fatal-path/configuration guards. Preserve Fortran routine structure, argument grouping, and source comments throughout SILHS and the microphysics interface layer. Leave Fortran, MT95, and the KK/Morrison numerical cores unchanged. Validation: 103 focused sampling/interface/error-path checks and eight real SILHS driver checks pass. Earlier interface/support validation and the 20-pair disabled-SILHS JAX/Fortran comparison also pass. Enabled SILHS random stream parity is deferred to a future common-random-input comparison. * Add deterministic SILHS comparisons and initialize JAX output grids Add a default-off l_lh_deterministic_test flag to Fortran and JAX. Use ordered strata and a shared four-value, binary-exact draw cycle in the high-level LHS and overlap-pool routines, preserving sequence reuse and leaving the native random generators unchanged. Reject independent importance sampling and random starts in this comparison mode. Add interactive RICO, LBA KK and native LBA Morrison configurations to the JAX/Fortran comparison suite without relaxing the existing tolerances. Initialize SILHS host statistics from JAX case setup so reduced statistics files also contain Fortran's lh_zt and lh_sample_number coordinates. Validation: Fortran build and source checks pass; 581 raw sampling values match exactly; 59 sampler/contract/forwarding checks and 46 output/support checks pass. RICO matches through 360 steps at 60s with standard statistics and with reduced statistics at debug 0. Document the remaining comparison limits: LBA KK's repeating-cycle Nrp2 difference starts at saved prefix 274, while its configured cap remains 275. Native Morrison's selected scope was verified with midpoint inputs; the repeating-cycle comparison was not rerun after the requested stop. * Match Fortran SILHS sampling precision and overlap Preserve default-real rounding in inverse-normal coefficients before promotion to the sample dtype. Apply vertical overlap to starting-level straight Monte Carlo samples and retain source sampling failure status. Add a live Fortran inverse-normal oracle and regressions for overlap and the source sample-count check. Keep comparison limits and tolerances. * Restore SILHS diagnostics and microphysics host error guards Carry weight-limiter and Kessler diagnostic failures through compiled returns and ErrInfo. Preserve Fortran debug guards at the host boundaries so negative-debug tracing can retain per-column failure status. Write ordered microphysics/SILHS settings and approximate correlations from initialization into the standalone setup file. Keep report lifetime and output-name resolution outside the timestep driver. Add focused failure/report regressions and update the port notes with repeating-input comparisons and the native Morrison compiler sensitivity. * Document deterministic SILHS comparison patterns Explain the ordered permutation, repeating within-stratum offsets and overlap pool at every Fortran deterministic randomness override. Mirror the explanation in JAX, including index phases, sequence reuse and independence from RNG state. Executable statements are unchanged in both implementations; source/AST checks confirm these changes only add comments. * Use definition decorators for microphysics JIT boundaries Move the existing PDF preparation, scheme tendency and hydrometeor transport JIT boundaries onto their routine definitions with @partial(jax.jit, ...). Keep the static arguments unchanged and call the source-named routines directly from the standalone driver. Update host injection and source-order checks for the canonical routine names. Lightweight error/feedback fixtures still check eager and compiled routine bodies; real standalone runs exercise the decorated entry points. Validation: 140 focused tests; 28 passed, 2435 warnings in 453.39s (0:07:33); unchanged RICO360/LBAKK275 strict comparisons; supported whole-driver and reverse-mode tracing. * Simplify deterministic SILHS sampling comments Describe the repeatable-testing branches directly, with their base values and index offsets. Show the first twelve pool entries for four columns, grouped by sample, and use the same concise descriptions in the Fortran and JAX mirrors. Only comments and argument documentation change; executable code is unchanged. * Exclude E3SM from host compatibility updates Keep the exclusion visible in shortcut discovery and the host workflow. Treat sys_admin mappings as synchronization metadata, not the active host list. * Shortening tests timesteps a bit and adding a space for niceness 2026-10-04 19:01:28 -0500f51ab963e7cde71123d3afd8f77d077a35cf211fJax silhs (#1372)editclubb_jax/tests/test_microphysics_error_paths.pyeditclubb_jax/src/CLUBB_core/precipitation_fraction.pyeditsrc/SILHS/latin_hypercube_driver_module.F90addclubb_jax/src/SILHS/silhs_importance_sample_module.pyaddclubb_jax/src/SILHS/latin_hypercube_arrays.pyeditsrc/Microphys/microphys_init_cleanup.F90editclubb_jax/src/Microphys/advance_microphys_module.pyeditclubb_jax/src/Microphys/gfdl_activation.pyeditclubb_jax/tests/test_microphysics_integration.pyaddclubb_jax/tests/test_silhs_driver.pyeditclubb_jax/src/Microphys/parameters_microphys.pyaddclubb_jax/tests/test_silhs_fortran_oracle.pyeditclubb_jax/src/CLUBB_core/jax_stats.pyeditsrc/SILHS/parameters_silhs.F90addclubb_jax/src/SILHS/est_kessler_microphys_module.pyeditclubb_jax/src/Microphys/KK_microphys_module.pyeditLLM_prompts/update_host_models_after_clubb_changes.mdaddclubb_jax/src/SILHS/lh_microphys_var_covar_module.pyaddclubb_jax/src/SILHS/transform_to_pdf_module.pyaddclubb_jax/SILHS_PORT_NOTES.mdedittests/run_jax_vs_fortran_cases.pyeditclubb_jax/src/Microphys/ice_dfsn_module.pyedittests/pytests/test_jax_compare_forwarding.pyeditsrc/SILHS/generate_uniform_sample_module.F90addclubb_jax/tests/test_silhs_sampling.pyaddclubb_jax/src/SILHS/parameters_silhs.pyaddclubb_jax/src/SILHS/silhs_api_module.pyaddclubb_jax/src/SILHS/latin_hypercube_driver_module.pyeditclubb_jax/README.mdeditLLM_prompts/SHORTCUTS.mdeditclubb_jax/tests/test_microphysics_port_structure.pyaddclubb_jax/tests/test_silhs_port_structure.pyeditclubb_jax/src/Microphys/microphys_driver.pyeditclubb_jax/src/Microphys/mixed_moment_PDF_integrals.pyeditclubb_jax/src/Microphys/estimate_scm_microphys_module.pyeditclubb_jax/src/Microphys/pdf_hydromet_microphys_wrapper.pyaddclubb_jax/src/SILHS/__init__.pyeditclubb_jax/src/Microphys/morrison_microphys_module.pyeditclubb_jax/src/Microphys/microphys_init_cleanup.pyaddclubb_jax/tests/test_silhs_diagnostics.pyeditclubb_jax/src/advance_clubb_to_end.pyeditclubb_jax/JAX_CONVERSION_PLAN.mdaddclubb_jax/src/SILHS/math_utilities.pyeditclubb_jax/src/CLUBB_core/setup_clubb_pdf_params.pyeditclubb_jax/src/Microphys/cloud_sed_module.pyeditclubb_jax/src/CLUBB_core/stats_clubb_utilities.pyeditclubb_jax/src/CLUBB_core/fill_holes.pyeditclubb_jax/src/Microphys/silhs_category_variance_module.pyeditclubb_jax/src/clubb_case_initalization.pyaddclubb_jax/src/SILHS/generate_uniform_sample_module.pyeditclubb_jax/src/Input_fields/corr_varnce_input_reader.pyeditclubb_jax/src/Microphys/coamps_microphys_driver_module.pyeditclubb_jax/src/Microphys/lh_microphys_driver_module.pyaddclubb_jax/tests/test_microphysics_host_errors.pyclubb_jax/src/advance_clubb_to_end.pyclubb_jax/SILHS_PORT_NOTES.md9233e347a33c4422eaadde0503786b7f6134ebcf1791167559000https://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhuebler@uwm.eduClarify current SILHS comparison limits Separate current LBA test caps from earlier longer validation runs. Remove trailing spaces from the radiation-call blank line. 2026-10-04 21:32:39 -05009233e347a33c4422eaadde0503786b7f6134ebcfClarify current SILHS comparison 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pytest admission, ownership and Jenkins coverage (#1377) * Organize pytest coverage, generated admission and Jenkins ownership * Tidy moved pytest helper formatting * Isolate native JAX pytest failures and fix migration validation * Prepare Dash CI Node runtime without system npm * Prune incidental UI assertions and clarify required-input failures * Keep pytest promotion paths stable and validate API fixtures * Apply pytest review revisions and consolidate JAX CI * Keep pytest discovery and admission in the runners * Limit Jenkins additions to focused pytest stages * Keep component-specific validation beside Dash and JAX 2026-10-04 22:34:54 -05009afedd80dbc4a1f64989768f1f5124eb03483513Organize pytest admission, ownership and Jenkins coverage 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threadseditsrc/CLUBB_core/stats_netcdf.F90run_scripts/run_tuner.pyrun_scripts/run_clubb_w_varying_flags.pyjenkins_tests/clubb_python/Jenkinsfilejenkins_tests/clubb_tuner/Jenkinsfilerun_scripts/README.mdtests/test_monoflux_limiter_GPU.pytests/pytests/test_bindiff_report.pyutilities/pytests/test_time_clubb.pyCMakeLists.txtexperimental/experimental_pdfs/python/dash_additions/utilities/refresh_pdf9_parcel_ensemble_lab.pytests/README.mdtests/run_clubb_conv_test.pyrun_scripts/run_scm_loss.pypostprocessing/latin_hypercube_plotting/variance_analysis_scripts/rms_vs_sample_points/silhs_varying_sp_output.shtests/check_budget_balance.pyutilities/time_clubb.pyutilities/pytests/test_run_script_arguments.pyutilities/create_case_namelist.pydash_app/pytests/test_pyplotgen_export.pytests/run_jax_vs_fortran_cases.pydash_app/tune_tab/runtime.pyjenkins_tests/clubb_plots/Jenkinsfiletests/test_fire_tuner.pyjenkins_tests/clubb_column_mirror/Jenkinsfilejenkins_tests/clubb_generalized_grid/Jenkinsfiletuner/tune_clubb.pydash_app/compile_tab/runtime.pytests/run_thread_test.pyjenkins_tests/clubb_jax/Jenkinsfiletests/check_mirrored_multi_col_output.pyjenkins_tests/clubb_single_prec_build/Jenkinsfiletests/run_G_unit_tests.pypostprocessing/pyplotgen/README.mdrun_scripts/convergence_run/convergence_config.pypostprocessing/pyplotgen/pyplotgen.pytests/run_python_vs_fortran_cases.pyclubb_jax/tests/test_jax_cli_options.pyclubb_jax/tests/test_runtime_info.pyjenkins_tests/clubb_driver/Jenkinsfiledash_app/compile_tab/build_selector.pyinput/flag_sets/README.mdclubb_jax/README.mdrun_scripts/run_tuner_job.pytests/run_restart_test.pytuner/presets.pydash_app/pytests/test_profile_tab.pytests/run_loss_output_consistency.pytuner/job_runtime.pytests/pytests/test_jax_compare_forwarding.pyutilities/parse_argument_list/replace_err_code_type.pytuner/system_defaults.pyclubb_jax/run_jax.pyutilities/print_tunable_parameters_table.pytests/run_jax_comparison_mutation_test.pytests/run_bindiff_w_flags.pyjenkins_tests/clubb_gpu_async_output_matching/Jenkinsfileutilities/benchmark_converter.pyjenkins_tests/run_bindiff_w_varying_flags_against_master/Jenkinsfileutilities/api_analysis/run_full_api_diagnostics.bashutilities/split_stats_to_legacy.pyutilities/CLUBBStandardsCheck.pyjenkins_tests/clubb_basic_full_run/Jenkinsfilerun_scripts/run_scm_all.pyrun_scripts/run_clubb_and_pyplotgen.pydash_app/profile_tab/runtime.pyjenkins_tests/clubb_gpu_vs_cpu_diffness/Jenkinsfiletests/run_stats_output_consistency.pydash_app/pytests/test_compile_tab_build_status.pycompile.pyclubb_jax/runtime_info.pyclubb_jax/tests/test_kk_rico_oracle.pyutilities/api_analysis/create_module_table.pyutilities/api_analysis/api_commitment_test.pyutilities/setup_python_venv.pydash_app/run_tab/runtime.pyLLM_prompts/update_python_api_and_drivers.mdutilities/convert_to_async.pytests/pytests/test_column_mirror.pytests/run_silhs_test.pydash_app/plot_tab/pyplotgen_runtime.pyjenkins_tests/clubb_G_unit/Jenkinsfiletests/analyze_tuner_sample_history.pyrun_scripts/run_scm.pyrun_scripts/run_bindiff_all.pytests/pytests/test_run_clubb_conv_test.pypostprocessing/pyplotgen/config/Style_definitions.pyutilities/create_multi_col_params.pytuner/README.mdpostprocessing/pyplotgen/src/CaseGallerySetup.py1d1abb1d2fcf29eef75bfe3182b8b213a1c6001e1791075166000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comStandardize script arguments (#1373) This is mainly changing the names of arguments to be clearer and more consistent, and replacing the usage of double dash options with single ones (I just like it better that way). * Standardize script arguments and worker defaults * Forward model options through the Python comparison harness * Reuse existing modules for script argument helpers * Fix script argument cleanup integration regressions * Update API commitment wrapper for renamed exclusion option 2026-10-03 19:52:46 -05001d1abb1d2fcf29eef75bfe3182b8b213a1c6001eStandardize script arguments (#1373)edittests/run_stats_output_consistency.pyeditrun_scripts/README.mdedittests/pytests/test_bindiff_report.pyeditutilities/api_analysis/api_commitment_test.pyeditdash_app/profile_tab/runtime.pyeditdash_app/pytests/test_pyplotgen_export.pyeditutilities/parse_argument_list/replace_err_code_type.pyeditrun_scripts/run_scm.pyeditutilities/create_multi_col_params.pyeditutilities/create_case_namelist.pyeditclubb_jax/tests/test_runtime_info.pyeditjenkins_tests/clubb_basic_full_run/Jenkinsfileedittests/run_jax_comparison_mutation_test.pyeditjenkins_tests/clubb_single_prec_build/Jenkinsfileedittests/check_mirrored_multi_col_output.pyeditdash_app/plot_tab/pyplotgen_runtime.pyeditutilities/split_stats_to_legacy.pyeditdash_app/pytests/test_compile_tab_build_status.pyedittuner/system_defaults.pyedittuner/job_runtime.pyeditCMakeLists.txteditpostprocessing/pyplotgen/config/Style_definitions.pyeditutilities/setup_python_venv.pyedittests/pytests/test_column_mirror.pyeditrun_scripts/run_bindiff_all.pyeditjenkins_tests/clubb_column_mirror/Jenkinsfileedittests/README.mdedittests/run_python_vs_fortran_cases.pyeditutilities/benchmark_converter.pyeditclubb_jax/runtime_info.pyeditcompile.pyeditjenkins_tests/clubb_driver/Jenkinsfileeditpostprocessing/pyplotgen/src/CaseGallerySetup.pyeditdash_app/tune_tab/runtime.pyeditjenkins_tests/clubb_jax/Jenkinsfileedittuner/tune_clubb.pyaddutilities/pytests/test_run_script_arguments.pyeditclubb_jax/tests/test_kk_rico_oracle.pyeditdash_app/run_tab/runtime.pyeditrun_scripts/run_tuner_job.pyeditdash_app/pytests/test_profile_tab.pyeditrun_scripts/run_scm_loss.pyeditutilities/api_analysis/run_full_api_diagnostics.basheditdash_app/compile_tab/build_selector.pyedittests/run_clubb_conv_test.pyeditjenkins_tests/clubb_tuner/Jenkinsfileeditutilities/pytests/test_time_clubb.pyeditpostprocessing/pyplotgen/pyplotgen.pyedittests/run_bindiff_w_flags.pyeditexperimental/experimental_pdfs/python/dash_additions/utilities/refresh_pdf9_parcel_ensemble_lab.pyeditrun_scripts/run_tuner.pyedittests/run_silhs_test.pyedittests/test_monoflux_limiter_GPU.pyedittests/run_loss_output_consistency.pyedittests/check_budget_balance.pyeditLLM_prompts/update_python_api_and_drivers.mdeditclubb_jax/run_jax.pyedittests/analyze_tuner_sample_history.pyeditutilities/CLUBBStandardsCheck.pyeditpostprocessing/latin_hypercube_plotting/variance_analysis_scripts/rms_vs_sample_points/silhs_varying_sp_output.sheditclubb_jax/tests/test_jax_cli_options.pyeditjenkins_tests/clubb_gpu_vs_cpu_diffness/Jenkinsfileedittests/run_restart_test.pyedittuner/presets.pyeditjenkins_tests/clubb_G_unit/Jenkinsfileeditjenkins_tests/clubb_generalized_grid/Jenkinsfileeditutilities/convert_to_async.pyeditinput/flag_sets/README.mdeditclubb_jax/README.mdeditpostprocessing/pyplotgen/README.mdeditrun_scripts/run_clubb_w_varying_flags.pyedittests/run_G_unit_tests.pyedittests/pytests/test_jax_compare_forwarding.pyeditutilities/print_tunable_parameters_table.pyedittests/run_jax_vs_fortran_cases.pyeditjenkins_tests/clubb_gpu_async_output_matching/Jenkinsfileeditjenkins_tests/clubb_plots/Jenkinsfileeditrun_scripts/run_scm_all.pyeditjenkins_tests/run_bindiff_w_varying_flags_against_master/Jenkinsfileeditrun_scripts/convergence_run/convergence_config.pyeditutilities/time_clubb.pyeditdash_app/compile_tab/runtime.pyeditrun_scripts/run_clubb_and_pyplotgen.pyeditutilities/api_analysis/create_module_table.pyedittuner/README.mdedittests/run_thread_test.pyedittests/test_fire_tuner.pyedittests/pytests/test_run_clubb_conv_test.pyeditjenkins_tests/clubb_python/Jenkinsfilegithttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther 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Huebler1ec38f6a3b0805ee6ac8db48d845ddee0e7d11ac3ec38f6a3b0805ee6ac8db48d845ddee0e7d11ac3refs/remotes/origin/masterec38f6a3b0805ee6ac8db48d845ddee0e7d11ac3ec38f6a3b0805ee6ac8db48d845ddee0e7d11ac3refs/remotes/origin/masterec38f6a3b0805ee6ac8db48d845ddee0e7d11ac3ec38f6a3b0805ee6ac8db48d845ddee0e7d11ac3refs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#11627156913433486clubb_generalized_grid #11false19451FAILURE1790993188462https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/1/false2https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/2/Build stability: All recent builds failed.icon-health-00to19health-00to19.png0falseStarted by an SCM change000605985043285871.0379987998168369512fcc6487603491e12ac13376de2aec2a0b8369512fcc6487603491e12ac13376de2aec2a0brefs/remotes/origin/master8369512fcc6487603491e12ac13376de2aec2a0b8369512fcc6487603491e12ac13376de2aec2a0brefs/remotes/origin/master8369512fcc6487603491e12ac13376de2aec2a0b8369512fcc6487603491e12ac13376de2aec2a0brefs/remotes/origin/masterhttps://github.com/larson-group/clubb.gittrue#16013433486clubb_generalized_grid #1616false16111331792484769900https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/16/src/generalized_grid_test.F90src/CLUBB_core/setup_clubb_pdf_params.F90clubb_python_api/clubb_f2py.pyfsrc/CLUBB_core/fill_holes.F90clubb_python_api/f2py_fortran_wrappers/precipitation_fraction_wrapper.F90clubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_precipitation_fraction.pysrc/G_unit_test_types/mu_sigma_hm_tests.F90src/Microphys/pdf_hydromet_microphys_wrapper.F90clubb_python_api/clubb_python/CLUBB_core/precipitation_fraction.pysrc/CLUBB_core/precipitation_fraction.F908369512fcc6487603491e12ac13376de2aec2a0b1792463005000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comClubb params 1d to 2d fix (#1392) * Fix: clubb params is a shape (ngrdcol,nparams) that is passed into subroutines that expect a 1d array Also fixed dependent other places in code and changed the python api. This is BIT_CHANGING for multicol. If a 2d array is passed into a function that expects the arr to be 1d fortran just passes the first col of the arr. Therefore the changes dont affect single col runs. For multicol runs other indexing is needed * fill_holes_vertical_api expects the passed gr%dzt to have shape(ngrdcol,nz) but the code passes the whole gr%dzt array although each column is traversed one by one. So ngrdcol=1 is passed each time. No effect on single col, as with ngrdcol = 1, gr%dzt and gr%dzt(1:1,:) are the same. Affects multicol if l_hole_fill = .true. and the hydrometeor is a mixing ratio (name starts with r) and some value is actually negative Therefore BIT_CHANGING 2026-10-19 21:23:25 -05008369512fcc6487603491e12ac13376de2aec2a0bClubb params 1d to 2d fix (#1392)editclubb_python_api/clubb_f2py.pyfeditsrc/CLUBB_core/fill_holes.F90editsrc/generalized_grid_test.F90editsrc/CLUBB_core/setup_clubb_pdf_params.F90editclubb_python_api/f2py_fortran_wrappers/precipitation_fraction_wrapper.F90editclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_precipitation_fraction.pyeditsrc/Microphys/pdf_hydromet_microphys_wrapper.F90editclubb_python_api/clubb_python/CLUBB_core/precipitation_fraction.pyeditsrc/CLUBB_core/precipitation_fraction.F90editsrc/G_unit_test_types/mu_sigma_hm_tests.F90githttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblertrue15https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/15/Started by an SCM change000012914478173309961.3445636563615ec5e8070d3173282a6317b067f8673a657a1eb6fec5e8070d3173282a6317b067f8673a657a1eb6frefs/remotes/origin/masterec5e8070d3173282a6317b067f8673a657a1eb6fec5e8070d3173282a6317b067f8673a657a1eb6frefs/remotes/origin/masterec5e8070d3173282a6317b067f8673a657a1eb6fec5e8070d3173282a6317b067f8673a657a1eb6frefs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#151291447813433486clubb_generalized_grid #1515false1511023FAILURE1792398368289https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/15/.agents/skills/clubb-bit-changing/SKILL.md.agents/skills/clubb-jax-port/SKILL.md.agents/skills/clubb-finalization/SKILL.mdAGENTS.md.agents/skills/clubb-documentation/change-messages/SKILL.md.agents/skills/clubb-testing-and-reporting/SKILL.mdccafe4f166f956eed26b91f7fdacd5600f60f5b21792344464000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comDefine when to declare bit-changing commits (#1403) * Define conservative bit-change declarations Centralize the policy around intentional Fortran numerical answer changes, with named affected BFB tests or precise untested conditions. Preserve standalone coverage and the current JAX parity boundary, keep declarations sparse, and separate answer-changing edits from preserving cleanup. Route message writing, validation and branch finalization to one owner. Skill schemas, local links, heading anchors, parser examples and manual decision scenarios were checked; no model or CI code changes. * Define the optimization level for bitwise preservation Use -O0 as the normal preservation standard. Differences confined to optimized builds do not require an answer-change declaration when -O0 is verified BFB; report known optimized-only differences and their configuration in the PR. The changed skill schema and whitespace checks pass. Inspected current debug compile flags and manually reviewed the optimized-only decision scenario; documentation only, no numerical rerun. 2026-10-18 12:27:44 -0500ccafe4f166f956eed26b91f7fdacd5600f60f5b2Define when to declare bit-changing commits (#1403)edit.agents/skills/clubb-documentation/change-messages/SKILL.mdedit.agents/skills/clubb-finalization/SKILL.mdedit.agents/skills/clubb-testing-and-reporting/SKILL.mdedit.agents/skills/clubb-jax-port/SKILL.mdeditAGENTS.mdadd.agents/skills/clubb-bit-changing/SKILL.mdclubb_jax/src/clubb_standalone.pyclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyrun_scripts/README.mdutilities/clubb_case_runner.pyutilities/pytests/test_time_clubb.pytests/run_timestep_sweep.pyclubb_jax/pytests/auto_llm_generated_pytests/test_case_cache_reuse.pyclubb_python_driver/clubb_standalone.pysrc/clubb_standalone.F90tests/README.mdrun_scripts/run_scm_loss.pyutilities/time_clubb.py.agents/skills/clubb-testing-and-reporting/SKILL.mdutilities/create_case_namelist.pyutilities/pytests/test_create_case_namelist.pytests/run_stats_output_consistency.pytests/run_jax_vs_fortran_cases.py.agents/skills/clubb-fortran-port/SKILL.mdclubb_jax/src/clubb_case_initalization.pytests/case_runner_lifecycle_test.pyutilities/README.mdutilities/pytests/auto_llm_generated_pytests/test_timing_workers.pyclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.py.agents/skills/clubb-numerical-diagnosis/SKILL.mdutilities/pytests/auto_llm_generated_pytests/test_loss_cli.pytests/pytests/auto_llm_generated_pytests/test_scm_jax_driver_test.pyrun_scripts/run_scm.py.agents/skills/clubb-fortran-format/SKILL.md.agents/skills/clubb-finalization/SKILL.mdAGENTS.mdclubb_jax/src/Microphys/microphys_init_cleanup.pyjenkins_tests/clubb_driver/Jenkinsfileutilities/timing_profiles.pyclubb_jax/README.mdrun_scripts/run_tuner_job.pyutilities/pytests/auto_llm_generated_pytests/test_clubb_case_runner.pytests/run_restart_test.pyutilities/pytests/timing_test_inputs.pyclubb_jax/src/CLUBB_core/calc_pressure.pytests/run_loss_output_consistency.py4f8368a377989b649fc0ed53c26957e193d210671792350419000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd reusable case runners for timing (#1400) We have multiple entry points now for clubb standalone (fortran,python,jax), and there's additional logic that chooses which fortran installation to use (gfortran,ifort,nvhpc,etc). All of this has historically (~1 year) been done by run_scm.py, but we have a number of other scripts that need this same kind of logic, so instead of making run_scm.py more complicated and letting other scripts import it's pieces, we've made a `clubb_case_runner`. `clubb_case_runner` is a python object that abstracts the backend decisions. The "flow" is roughly: - high level script wants to run a clubb case some how - generates one or more case namelists (arm.in, bomex.in, etc) - creates a `clubb_case_runner` by passing it whatever runtime options (-jax/-python/-exe) the user requested - runs a case by passing this `clubb_case_runner` whatever namelists it wants to run. In addition to deduplicating runtime setting logic, this allows python scripts to create these high level `clubb_case_runner` objects and use those to do things that usually requires duplicate multiprocessesing and error code parsing logic. 2026-10-18 14:06:59 -05004f8368a377989b649fc0ed53c26957e193d21067Add reusable case runners for timing (#1400)edittests/run_jax_vs_fortran_cases.pyeditrun_scripts/run_scm.pyaddutilities/pytests/timing_test_inputs.pyeditrun_scripts/README.mdeditutilities/create_case_namelist.pyeditutilities/time_clubb.pyeditclubb_jax/src/clubb_standalone.pyeditsrc/clubb_standalone.F90addtests/case_runner_lifecycle_test.pyedit.agents/skills/clubb-finalization/SKILL.mdaddclubb_jax/pytests/auto_llm_generated_pytests/test_case_cache_reuse.pyeditjenkins_tests/clubb_driver/Jenkinsfileeditutilities/pytests/auto_llm_generated_pytests/test_loss_cli.pyeditutilities/timing_profiles.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyedit.agents/skills/clubb-testing-and-reporting/SKILL.mdeditclubb_python_driver/clubb_standalone.pyedit.agents/skills/clubb-numerical-diagnosis/SKILL.mdeditAGENTS.mdedit.agents/skills/clubb-fortran-port/SKILL.mdeditclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyeditrun_scripts/run_tuner_job.pyaddutilities/clubb_case_runner.pyedit.agents/skills/clubb-fortran-format/SKILL.mdedittests/pytests/auto_llm_generated_pytests/test_scm_jax_driver_test.pyeditutilities/pytests/test_time_clubb.pyeditclubb_jax/src/Microphys/microphys_init_cleanup.pyedittests/run_stats_output_consistency.pyeditrun_scripts/run_scm_loss.pyaddutilities/pytests/auto_llm_generated_pytests/test_clubb_case_runner.pyeditclubb_jax/src/CLUBB_core/calc_pressure.pyedittests/README.mdeditutilities/README.mdeditclubb_jax/src/clubb_case_initalization.pyedittests/run_loss_output_consistency.pyedittests/run_restart_test.pyeditclubb_jax/README.mdaddutilities/pytests/auto_llm_generated_pytests/test_timing_workers.pyeditutilities/pytests/test_create_case_namelist.pyedittests/run_timestep_sweep.pyclubb_jax/src/clubb_case_initalization.pyclubb_jax/src/clubb_standalone.pyutilities/README.mdclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyclubb_jax/pytests/auto_llm_generated_pytests/test_code_timer_module.pyclubb_jax/src/clubb_loss_driver.pyrun_scripts/README.mdclubb_jax/view_profile.pyclubb_jax/run_jax.pyclubb_jax/pytests/auto_llm_generated_pytests/test_profile_cli.pyclubb_jax/src/CLUBB_core/code_timer_module.pyutilities/time_clubb.pyclubb_jax/src/advance_clubb_to_end.pyclubb_jax/src/clubb_driver_test.pyclubb_jax/README.mdec5e8070d3173282a6317b067f8673a657a1eb6f1792362852000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd JAX timing and profiling (#1393) * Add JAX timing and persistent benchmark workers Write Fortran-format CPU timing summaries and optional XProf/Perfetto traces from JAX driver phases. Use synchronized persistent workers for full-case warmups and repetitions across Fortran, Python and JAX. Retain compiled JAX programs when initialization settings are unchanged. Validation: 243 focused checks and CPU case workflows passed. Repeated five-step BOMEX/RICO_SILHS numeric outputs matched fresh controls exactly. The two-column BOMEX JAX/Fortran comparison passed 1e-7 absolute and percent thresholds. BFB against the parent is not established by these comparisons. GPU and GPTL execution remain untested. * Making jax timer use wall clock time instead of cpu/process time * Keep JAX timing separate from reusable runners Move process persistence, cache reuse and Python timing adapters to the case-runner branch. Keep JAX wall-clock summaries, optional deep profiles, driver instrumentation and the parser change that reads their clock label. The timing-only shared suite and a three-step CPU BOMEX run pass. BFB against master is not established; physics expressions are unchanged. * Add reusable case runners for timing and tuning Share runtime selection and persistent standalone sessions between SCM, timing and tuning. Support namelist replacement and empty model reruns, plus parameter matrices for loss sessions. Synchronize timing cohorts and record retained-model initialization separately. Use executable loss workers for native tuning instead of requiring F2PY. Restore microphysics defaults between cases (BIT_CHANGING for sessions that previously inherited settings). Short native/CPU JAX sessions match fresh same-backend stats values exactly; broader BFB is not established. Native build, focused suites and repeated loss/tuner/timing workflows pass. * Use F2PY for reusable Fortran loss runs Run persistent Fortran loss sessions through the existing Python API. Restore the native loss standalone and remove its parameter namelist reader and result writers. Python workers pass arrays directly into F2PY; ordinary standalone persistence and JAX execution remain available. Fifteen native loss metric arrays match saved results exactly. Native and CPU JAX repeated loss/tuning workflows, tuner shutdown, the native build, 454 shared checks and four API checks pass. Broader BFB is not established. * Keep case runners persistent without retaining model state Run each ordinary request through full initialization, advancement and cleanup while keeping the process alive for in-memory JIT reuse. Remove retained-model commands, transport, timing/UI options and extra bindings. Restore tuning and loss frontends to their existing allocation-reusing APIs. The native build, 445 shared checks, 121 focused JAX checks and 85 Dash checks pass. Short native/JAX/Python reused-process stats match fresh controls exactly; tuning and synchronized timing sweeps pass. Two full 16-column JAX repeats log no new compilations. These comparisons do not establish blanket BFB. * Separate microphysics initialization fixes from case runners Move native default resets to their own branch/PR and keep the runner focused on shared runtime selection and full-case process reuse. Record the mixed-case native test's dependency on that fix. Refresh the timing base and master, and clarify runner, driver and test documentation under the current skills. The shared checks pass, including output drainage, cancellation, synchronized warmup/repetition barriers and CLI forwarding. Python AST checks confirm the remaining audit edits change only documentation. Jenkins validation follows this published checkpoint. * Complete 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. * Separate 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). * Add JAX timing after the case runner Restore the audited wall-clock summaries and optional execution tracing on top of the independent case runner. Keep the existing implementation and review history while reversing the PR merge order. * Add a JAX profiling option and viewer commands Enable captures with -jax=profile and print commands after cleanup. Keep capture export in the timer and viewing in view_profile.py. 181 focused checks pass. CPU BOMEX captures preserve numeric stats; both viewers were verified in-browser. Large full-Python Perfetto exports can truncate; XProf retained all five tested timesteps. * Clarify JAX timing usage and cleanup Document the timer lifecycle, failure handling and Dash wall-time comparison metric. Executable Python AST is unchanged. 2026-10-18 17:34:12 -0500ec5e8070d3173282a6317b067f8673a657a1eb6fAdd JAX timing and profiling (#1393)addclubb_jax/src/CLUBB_core/code_timer_module.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_profile_cli.pyeditclubb_jax/src/clubb_case_initalization.pyeditutilities/README.mdeditclubb_jax/src/advance_clubb_to_end.pyaddclubb_jax/view_profile.pyeditclubb_jax/src/clubb_driver_test.pyeditutilities/time_clubb.pyeditclubb_jax/README.mdaddclubb_jax/pytests/auto_llm_generated_pytests/test_code_timer_module.pyeditclubb_jax/src/clubb_standalone.pyeditrun_scripts/README.mdeditclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyeditclubb_jax/run_jax.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyeditclubb_jax/src/clubb_loss_driver.pygithttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerfalse16https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/16/14https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/14/Started by an SCM change000012914478173309961.3445636563615ec5e8070d3173282a6317b067f8673a657a1eb6fec5e8070d3173282a6317b067f8673a657a1eb6frefs/remotes/origin/masterec5e8070d3173282a6317b067f8673a657a1eb6fec5e8070d3173282a6317b067f8673a657a1eb6frefs/remotes/origin/masterec5e8070d3173282a6317b067f8673a657a1eb6fec5e8070d3173282a6317b067f8673a657a1eb6frefs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#151291447813433486clubb_generalized_grid #1515false1511023FAILURE1792398368289https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/15/.agents/skills/clubb-bit-changing/SKILL.md.agents/skills/clubb-jax-port/SKILL.md.agents/skills/clubb-finalization/SKILL.mdAGENTS.md.agents/skills/clubb-documentation/change-messages/SKILL.md.agents/skills/clubb-testing-and-reporting/SKILL.mdccafe4f166f956eed26b91f7fdacd5600f60f5b21792344464000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comDefine when to declare bit-changing commits (#1403) * Define conservative bit-change declarations Centralize the policy around intentional Fortran numerical answer changes, with named affected BFB tests or precise untested conditions. Preserve standalone coverage and the current JAX parity boundary, keep declarations sparse, and separate answer-changing edits from preserving cleanup. Route message writing, validation and branch finalization to one owner. Skill schemas, local links, heading anchors, parser examples and manual decision scenarios were checked; no model or CI code changes. * Define the optimization level for bitwise preservation Use -O0 as the normal preservation standard. Differences confined to optimized builds do not require an answer-change declaration when -O0 is verified BFB; report known optimized-only differences and their configuration in the PR. The changed skill schema and whitespace checks pass. Inspected current debug compile flags and manually reviewed the optimized-only decision scenario; documentation only, no numerical rerun. 2026-10-18 12:27:44 -0500ccafe4f166f956eed26b91f7fdacd5600f60f5b2Define when to declare bit-changing commits (#1403)edit.agents/skills/clubb-documentation/change-messages/SKILL.mdedit.agents/skills/clubb-finalization/SKILL.mdedit.agents/skills/clubb-testing-and-reporting/SKILL.mdedit.agents/skills/clubb-jax-port/SKILL.mdeditAGENTS.mdadd.agents/skills/clubb-bit-changing/SKILL.mdclubb_jax/src/clubb_standalone.pyclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyrun_scripts/README.mdutilities/clubb_case_runner.pyutilities/pytests/test_time_clubb.pytests/run_timestep_sweep.pyclubb_jax/pytests/auto_llm_generated_pytests/test_case_cache_reuse.pyclubb_python_driver/clubb_standalone.pysrc/clubb_standalone.F90tests/README.mdrun_scripts/run_scm_loss.pyutilities/time_clubb.py.agents/skills/clubb-testing-and-reporting/SKILL.mdutilities/create_case_namelist.pyutilities/pytests/test_create_case_namelist.pytests/run_stats_output_consistency.pytests/run_jax_vs_fortran_cases.py.agents/skills/clubb-fortran-port/SKILL.mdclubb_jax/src/clubb_case_initalization.pytests/case_runner_lifecycle_test.pyutilities/README.mdutilities/pytests/auto_llm_generated_pytests/test_timing_workers.pyclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.py.agents/skills/clubb-numerical-diagnosis/SKILL.mdutilities/pytests/auto_llm_generated_pytests/test_loss_cli.pytests/pytests/auto_llm_generated_pytests/test_scm_jax_driver_test.pyrun_scripts/run_scm.py.agents/skills/clubb-fortran-format/SKILL.md.agents/skills/clubb-finalization/SKILL.mdAGENTS.mdclubb_jax/src/Microphys/microphys_init_cleanup.pyjenkins_tests/clubb_driver/Jenkinsfileutilities/timing_profiles.pyclubb_jax/README.mdrun_scripts/run_tuner_job.pyutilities/pytests/auto_llm_generated_pytests/test_clubb_case_runner.pytests/run_restart_test.pyutilities/pytests/timing_test_inputs.pyclubb_jax/src/CLUBB_core/calc_pressure.pytests/run_loss_output_consistency.py4f8368a377989b649fc0ed53c26957e193d210671792350419000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd reusable case runners for timing (#1400) We have multiple entry points now for clubb standalone (fortran,python,jax), and there's additional logic that chooses which fortran installation to use (gfortran,ifort,nvhpc,etc). All of this has historically (~1 year) been done by run_scm.py, but we have a number of other scripts that need this same kind of logic, so instead of making run_scm.py more complicated and letting other scripts import it's pieces, we've made a `clubb_case_runner`. `clubb_case_runner` is a python object that abstracts the backend decisions. The "flow" is roughly: - high level script wants to run a clubb case some how - generates one or more case namelists (arm.in, bomex.in, etc) - creates a `clubb_case_runner` by passing it whatever runtime options (-jax/-python/-exe) the user requested - runs a case by passing this `clubb_case_runner` whatever namelists it wants to run. In addition to deduplicating runtime setting logic, this allows python scripts to create these high level `clubb_case_runner` objects and use those to do things that usually requires duplicate multiprocessesing and error code parsing logic. 2026-10-18 14:06:59 -05004f8368a377989b649fc0ed53c26957e193d21067Add reusable case runners for timing (#1400)edittests/run_jax_vs_fortran_cases.pyeditrun_scripts/run_scm.pyaddutilities/pytests/timing_test_inputs.pyeditrun_scripts/README.mdeditutilities/create_case_namelist.pyeditutilities/time_clubb.pyeditclubb_jax/src/clubb_standalone.pyeditsrc/clubb_standalone.F90addtests/case_runner_lifecycle_test.pyedit.agents/skills/clubb-finalization/SKILL.mdaddclubb_jax/pytests/auto_llm_generated_pytests/test_case_cache_reuse.pyeditjenkins_tests/clubb_driver/Jenkinsfileeditutilities/pytests/auto_llm_generated_pytests/test_loss_cli.pyeditutilities/timing_profiles.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyedit.agents/skills/clubb-testing-and-reporting/SKILL.mdeditclubb_python_driver/clubb_standalone.pyedit.agents/skills/clubb-numerical-diagnosis/SKILL.mdeditAGENTS.mdedit.agents/skills/clubb-fortran-port/SKILL.mdeditclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyeditrun_scripts/run_tuner_job.pyaddutilities/clubb_case_runner.pyedit.agents/skills/clubb-fortran-format/SKILL.mdedittests/pytests/auto_llm_generated_pytests/test_scm_jax_driver_test.pyeditutilities/pytests/test_time_clubb.pyeditclubb_jax/src/Microphys/microphys_init_cleanup.pyedittests/run_stats_output_consistency.pyeditrun_scripts/run_scm_loss.pyaddutilities/pytests/auto_llm_generated_pytests/test_clubb_case_runner.pyeditclubb_jax/src/CLUBB_core/calc_pressure.pyedittests/README.mdeditutilities/README.mdeditclubb_jax/src/clubb_case_initalization.pyedittests/run_loss_output_consistency.pyedittests/run_restart_test.pyeditclubb_jax/README.mdaddutilities/pytests/auto_llm_generated_pytests/test_timing_workers.pyeditutilities/pytests/test_create_case_namelist.pyedittests/run_timestep_sweep.pyclubb_jax/src/clubb_case_initalization.pyclubb_jax/src/clubb_standalone.pyutilities/README.mdclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyclubb_jax/pytests/auto_llm_generated_pytests/test_code_timer_module.pyclubb_jax/src/clubb_loss_driver.pyrun_scripts/README.mdclubb_jax/view_profile.pyclubb_jax/run_jax.pyclubb_jax/pytests/auto_llm_generated_pytests/test_profile_cli.pyclubb_jax/src/CLUBB_core/code_timer_module.pyutilities/time_clubb.pyclubb_jax/src/advance_clubb_to_end.pyclubb_jax/src/clubb_driver_test.pyclubb_jax/README.mdec5e8070d3173282a6317b067f8673a657a1eb6f1792362852000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd JAX timing and profiling (#1393) * Add JAX timing and persistent benchmark workers Write Fortran-format CPU timing summaries and optional XProf/Perfetto traces from JAX driver phases. Use synchronized persistent workers for full-case warmups and repetitions across Fortran, Python and JAX. Retain compiled JAX programs when initialization settings are unchanged. Validation: 243 focused checks and CPU case workflows passed. Repeated five-step BOMEX/RICO_SILHS numeric outputs matched fresh controls exactly. The two-column BOMEX JAX/Fortran comparison passed 1e-7 absolute and percent thresholds. BFB against the parent is not established by these comparisons. GPU and GPTL execution remain untested. * Making jax timer use wall clock time instead of cpu/process time * Keep JAX timing separate from reusable runners Move process persistence, cache reuse and Python timing adapters to the case-runner branch. Keep JAX wall-clock summaries, optional deep profiles, driver instrumentation and the parser change that reads their clock label. The timing-only shared suite and a three-step CPU BOMEX run pass. BFB against master is not established; physics expressions are unchanged. * Add reusable case runners for timing and tuning Share runtime selection and persistent standalone sessions between SCM, timing and tuning. Support namelist replacement and empty model reruns, plus parameter matrices for loss sessions. Synchronize timing cohorts and record retained-model initialization separately. Use executable loss workers for native tuning instead of requiring F2PY. Restore microphysics defaults between cases (BIT_CHANGING for sessions that previously inherited settings). Short native/CPU JAX sessions match fresh same-backend stats values exactly; broader BFB is not established. Native build, focused suites and repeated loss/tuner/timing workflows pass. * Use F2PY for reusable Fortran loss runs Run persistent Fortran loss sessions through the existing Python API. Restore the native loss standalone and remove its parameter namelist reader and result writers. Python workers pass arrays directly into F2PY; ordinary standalone persistence and JAX execution remain available. Fifteen native loss metric arrays match saved results exactly. Native and CPU JAX repeated loss/tuning workflows, tuner shutdown, the native build, 454 shared checks and four API checks pass. Broader BFB is not established. * Keep case runners persistent without retaining model state Run each ordinary request through full initialization, advancement and cleanup while keeping the process alive for in-memory JIT reuse. Remove retained-model commands, transport, timing/UI options and extra bindings. Restore tuning and loss frontends to their existing allocation-reusing APIs. The native build, 445 shared checks, 121 focused JAX checks and 85 Dash checks pass. Short native/JAX/Python reused-process stats match fresh controls exactly; tuning and synchronized timing sweeps pass. Two full 16-column JAX repeats log no new compilations. These comparisons do not establish blanket BFB. * Separate microphysics initialization fixes from case runners Move native default resets to their own branch/PR and keep the runner focused on shared runtime selection and full-case process reuse. Record the mixed-case native test's dependency on that fix. Refresh the timing base and master, and clarify runner, driver and test documentation under the current skills. The shared checks pass, including output drainage, cancellation, synchronized warmup/repetition barriers and CLI forwarding. Python AST checks confirm the remaining audit edits change only documentation. Jenkins validation follows this published checkpoint. * Complete 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. * Separate 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). * Add JAX timing after the case runner Restore the audited wall-clock summaries and optional execution tracing on top of the independent case runner. Keep the existing implementation and review history while reversing the PR merge order. * Add a JAX profiling option and viewer commands Enable captures with -jax=profile and print commands after cleanup. Keep capture export in the timer and viewing in view_profile.py. 181 focused checks pass. CPU BOMEX captures preserve numeric stats; both viewers were verified in-browser. Large full-Python Perfetto exports can truncate; XProf retained all five tested timesteps. * Clarify JAX timing usage and cleanup Document the timer lifecycle, failure handling and Dash wall-time comparison metric. Executable Python AST is unchanged. 2026-10-18 17:34:12 -0500ec5e8070d3173282a6317b067f8673a657a1eb6fAdd JAX timing and profiling (#1393)addclubb_jax/src/CLUBB_core/code_timer_module.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_profile_cli.pyeditclubb_jax/src/clubb_case_initalization.pyeditutilities/README.mdeditclubb_jax/src/advance_clubb_to_end.pyaddclubb_jax/view_profile.pyeditclubb_jax/src/clubb_driver_test.pyeditutilities/time_clubb.pyeditclubb_jax/README.mdaddclubb_jax/pytests/auto_llm_generated_pytests/test_code_timer_module.pyeditclubb_jax/src/clubb_standalone.pyeditrun_scripts/README.mdeditclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyeditclubb_jax/run_jax.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyeditclubb_jax/src/clubb_loss_driver.pygithttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerfalse16https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/16/14https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/14/Started by an SCM change000012914478173309961.3445636563615ec5e8070d3173282a6317b067f8673a657a1eb6fec5e8070d3173282a6317b067f8673a657a1eb6frefs/remotes/origin/masterec5e8070d3173282a6317b067f8673a657a1eb6fec5e8070d3173282a6317b067f8673a657a1eb6frefs/remotes/origin/masterec5e8070d3173282a6317b067f8673a657a1eb6fec5e8070d3173282a6317b067f8673a657a1eb6frefs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#151291447813433486clubb_generalized_grid #1515false1511023FAILURE1792398368289https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/15/.agents/skills/clubb-bit-changing/SKILL.md.agents/skills/clubb-jax-port/SKILL.md.agents/skills/clubb-finalization/SKILL.mdAGENTS.md.agents/skills/clubb-documentation/change-messages/SKILL.md.agents/skills/clubb-testing-and-reporting/SKILL.mdccafe4f166f956eed26b91f7fdacd5600f60f5b21792344464000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comDefine when to declare bit-changing commits (#1403) * Define conservative bit-change declarations Centralize the policy around intentional Fortran numerical answer changes, with named affected BFB tests or precise untested conditions. Preserve standalone coverage and the current JAX parity boundary, keep declarations sparse, and separate answer-changing edits from preserving cleanup. Route message writing, validation and branch finalization to one owner. Skill schemas, local links, heading anchors, parser examples and manual decision scenarios were checked; no model or CI code changes. * Define the optimization level for bitwise preservation Use -O0 as the normal preservation standard. Differences confined to optimized builds do not require an answer-change declaration when -O0 is verified BFB; report known optimized-only differences and their configuration in the PR. The changed skill schema and whitespace checks pass. Inspected current debug compile flags and manually reviewed the optimized-only decision scenario; documentation only, no numerical rerun. 2026-10-18 12:27:44 -0500ccafe4f166f956eed26b91f7fdacd5600f60f5b2Define when to declare bit-changing commits (#1403)edit.agents/skills/clubb-documentation/change-messages/SKILL.mdedit.agents/skills/clubb-finalization/SKILL.mdedit.agents/skills/clubb-testing-and-reporting/SKILL.mdedit.agents/skills/clubb-jax-port/SKILL.mdeditAGENTS.mdadd.agents/skills/clubb-bit-changing/SKILL.mdclubb_jax/src/clubb_standalone.pyclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyrun_scripts/README.mdutilities/clubb_case_runner.pyutilities/pytests/test_time_clubb.pytests/run_timestep_sweep.pyclubb_jax/pytests/auto_llm_generated_pytests/test_case_cache_reuse.pyclubb_python_driver/clubb_standalone.pysrc/clubb_standalone.F90tests/README.mdrun_scripts/run_scm_loss.pyutilities/time_clubb.py.agents/skills/clubb-testing-and-reporting/SKILL.mdutilities/create_case_namelist.pyutilities/pytests/test_create_case_namelist.pytests/run_stats_output_consistency.pytests/run_jax_vs_fortran_cases.py.agents/skills/clubb-fortran-port/SKILL.mdclubb_jax/src/clubb_case_initalization.pytests/case_runner_lifecycle_test.pyutilities/README.mdutilities/pytests/auto_llm_generated_pytests/test_timing_workers.pyclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.py.agents/skills/clubb-numerical-diagnosis/SKILL.mdutilities/pytests/auto_llm_generated_pytests/test_loss_cli.pytests/pytests/auto_llm_generated_pytests/test_scm_jax_driver_test.pyrun_scripts/run_scm.py.agents/skills/clubb-fortran-format/SKILL.md.agents/skills/clubb-finalization/SKILL.mdAGENTS.mdclubb_jax/src/Microphys/microphys_init_cleanup.pyjenkins_tests/clubb_driver/Jenkinsfileutilities/timing_profiles.pyclubb_jax/README.mdrun_scripts/run_tuner_job.pyutilities/pytests/auto_llm_generated_pytests/test_clubb_case_runner.pytests/run_restart_test.pyutilities/pytests/timing_test_inputs.pyclubb_jax/src/CLUBB_core/calc_pressure.pytests/run_loss_output_consistency.py4f8368a377989b649fc0ed53c26957e193d210671792350419000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd reusable case runners for timing (#1400) We have multiple entry points now for clubb standalone (fortran,python,jax), and there's additional logic that chooses which fortran installation to use (gfortran,ifort,nvhpc,etc). All of this has historically (~1 year) been done by run_scm.py, but we have a number of other scripts that need this same kind of logic, so instead of making run_scm.py more complicated and letting other scripts import it's pieces, we've made a `clubb_case_runner`. `clubb_case_runner` is a python object that abstracts the backend decisions. The "flow" is roughly: - high level script wants to run a clubb case some how - generates one or more case namelists (arm.in, bomex.in, etc) - creates a `clubb_case_runner` by passing it whatever runtime options (-jax/-python/-exe) the user requested - runs a case by passing this `clubb_case_runner` whatever namelists it wants to run. In addition to deduplicating runtime setting logic, this allows python scripts to create these high level `clubb_case_runner` objects and use those to do things that usually requires duplicate multiprocessesing and error code parsing logic. 2026-10-18 14:06:59 -05004f8368a377989b649fc0ed53c26957e193d21067Add reusable case runners for timing (#1400)edittests/run_jax_vs_fortran_cases.pyeditrun_scripts/run_scm.pyaddutilities/pytests/timing_test_inputs.pyeditrun_scripts/README.mdeditutilities/create_case_namelist.pyeditutilities/time_clubb.pyeditclubb_jax/src/clubb_standalone.pyeditsrc/clubb_standalone.F90addtests/case_runner_lifecycle_test.pyedit.agents/skills/clubb-finalization/SKILL.mdaddclubb_jax/pytests/auto_llm_generated_pytests/test_case_cache_reuse.pyeditjenkins_tests/clubb_driver/Jenkinsfileeditutilities/pytests/auto_llm_generated_pytests/test_loss_cli.pyeditutilities/timing_profiles.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyedit.agents/skills/clubb-testing-and-reporting/SKILL.mdeditclubb_python_driver/clubb_standalone.pyedit.agents/skills/clubb-numerical-diagnosis/SKILL.mdeditAGENTS.mdedit.agents/skills/clubb-fortran-port/SKILL.mdeditclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyeditrun_scripts/run_tuner_job.pyaddutilities/clubb_case_runner.pyedit.agents/skills/clubb-fortran-format/SKILL.mdedittests/pytests/auto_llm_generated_pytests/test_scm_jax_driver_test.pyeditutilities/pytests/test_time_clubb.pyeditclubb_jax/src/Microphys/microphys_init_cleanup.pyedittests/run_stats_output_consistency.pyeditrun_scripts/run_scm_loss.pyaddutilities/pytests/auto_llm_generated_pytests/test_clubb_case_runner.pyeditclubb_jax/src/CLUBB_core/calc_pressure.pyedittests/README.mdeditutilities/README.mdeditclubb_jax/src/clubb_case_initalization.pyedittests/run_loss_output_consistency.pyedittests/run_restart_test.pyeditclubb_jax/README.mdaddutilities/pytests/auto_llm_generated_pytests/test_timing_workers.pyeditutilities/pytests/test_create_case_namelist.pyedittests/run_timestep_sweep.pyclubb_jax/src/clubb_case_initalization.pyclubb_jax/src/clubb_standalone.pyutilities/README.mdclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyclubb_jax/pytests/auto_llm_generated_pytests/test_code_timer_module.pyclubb_jax/src/clubb_loss_driver.pyrun_scripts/README.mdclubb_jax/view_profile.pyclubb_jax/run_jax.pyclubb_jax/pytests/auto_llm_generated_pytests/test_profile_cli.pyclubb_jax/src/CLUBB_core/code_timer_module.pyutilities/time_clubb.pyclubb_jax/src/advance_clubb_to_end.pyclubb_jax/src/clubb_driver_test.pyclubb_jax/README.mdec5e8070d3173282a6317b067f8673a657a1eb6f1792362852000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd JAX timing and profiling (#1393) * Add JAX timing and persistent benchmark workers Write Fortran-format CPU timing summaries and optional XProf/Perfetto traces from JAX driver phases. Use synchronized persistent workers for full-case warmups and repetitions across Fortran, Python and JAX. Retain compiled JAX programs when initialization settings are unchanged. Validation: 243 focused checks and CPU case workflows passed. Repeated five-step BOMEX/RICO_SILHS numeric outputs matched fresh controls exactly. The two-column BOMEX JAX/Fortran comparison passed 1e-7 absolute and percent thresholds. BFB against the parent is not established by these comparisons. GPU and GPTL execution remain untested. * Making jax timer use wall clock time instead of cpu/process time * Keep JAX timing separate from reusable runners Move process persistence, cache reuse and Python timing adapters to the case-runner branch. Keep JAX wall-clock summaries, optional deep profiles, driver instrumentation and the parser change that reads their clock label. The timing-only shared suite and a three-step CPU BOMEX run pass. BFB against master is not established; physics expressions are unchanged. * Add reusable case runners for timing and tuning Share runtime selection and persistent standalone sessions between SCM, timing and tuning. Support namelist replacement and empty model reruns, plus parameter matrices for loss sessions. Synchronize timing cohorts and record retained-model initialization separately. Use executable loss workers for native tuning instead of requiring F2PY. Restore microphysics defaults between cases (BIT_CHANGING for sessions that previously inherited settings). Short native/CPU JAX sessions match fresh same-backend stats values exactly; broader BFB is not established. Native build, focused suites and repeated loss/tuner/timing workflows pass. * Use F2PY for reusable Fortran loss runs Run persistent Fortran loss sessions through the existing Python API. Restore the native loss standalone and remove its parameter namelist reader and result writers. Python workers pass arrays directly into F2PY; ordinary standalone persistence and JAX execution remain available. Fifteen native loss metric arrays match saved results exactly. Native and CPU JAX repeated loss/tuning workflows, tuner shutdown, the native build, 454 shared checks and four API checks pass. Broader BFB is not established. * Keep case runners persistent without retaining model state Run each ordinary request through full initialization, advancement and cleanup while keeping the process alive for in-memory JIT reuse. Remove retained-model commands, transport, timing/UI options and extra bindings. Restore tuning and loss frontends to their existing allocation-reusing APIs. The native build, 445 shared checks, 121 focused JAX checks and 85 Dash checks pass. Short native/JAX/Python reused-process stats match fresh controls exactly; tuning and synchronized timing sweeps pass. Two full 16-column JAX repeats log no new compilations. These comparisons do not establish blanket BFB. * Separate microphysics initialization fixes from case runners Move native default resets to their own branch/PR and keep the runner focused on shared runtime selection and full-case process reuse. Record the mixed-case native test's dependency on that fix. Refresh the timing base and master, and clarify runner, driver and test documentation under the current skills. The shared checks pass, including output drainage, cancellation, synchronized warmup/repetition barriers and CLI forwarding. Python AST checks confirm the remaining audit edits change only documentation. Jenkins validation follows this published checkpoint. * Complete 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. * Separate 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). * Add JAX timing after the case runner Restore the audited wall-clock summaries and optional execution tracing on top of the independent case runner. Keep the existing implementation and review history while reversing the PR merge order. * Add a JAX profiling option and viewer commands Enable captures with -jax=profile and print commands after cleanup. Keep capture export in the timer and viewing in view_profile.py. 181 focused checks pass. CPU BOMEX captures preserve numeric stats; both viewers were verified in-browser. Large full-Python Perfetto exports can truncate; XProf retained all five tested timesteps. * Clarify JAX timing usage and cleanup Document the timer lifecycle, failure handling and Dash wall-time comparison metric. Executable Python AST is unchanged. 2026-10-18 17:34:12 -0500ec5e8070d3173282a6317b067f8673a657a1eb6fAdd JAX timing and profiling (#1393)addclubb_jax/src/CLUBB_core/code_timer_module.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_profile_cli.pyeditclubb_jax/src/clubb_case_initalization.pyeditutilities/README.mdeditclubb_jax/src/advance_clubb_to_end.pyaddclubb_jax/view_profile.pyeditclubb_jax/src/clubb_driver_test.pyeditutilities/time_clubb.pyeditclubb_jax/README.mdaddclubb_jax/pytests/auto_llm_generated_pytests/test_code_timer_module.pyeditclubb_jax/src/clubb_standalone.pyeditrun_scripts/README.mdeditclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyeditclubb_jax/run_jax.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyeditclubb_jax/src/clubb_loss_driver.pygithttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyhttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerfalse16https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/16/14https://carson.math.uwm.edu/jenkins/job/clubb_generalized_grid/14/17falsefalsefalsefalse