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* Little UI improvements to compile tab, and adding a dashboard launch script that installs the python dependencies for you in a local python venv

* Little dash fixes to compile tab

* Fixing little path bug in the old tuner script and the thread test script

* Update dash app README with alternative run command

* Little UI improvements to compile tab, and adding a dashboard launch script that installs the python dependencies for you in a local python venv

* Little compile tab stlying and adding UI element to warn user of violated coding standards. Also improving README

* Making the standards check error log viewable from the dash app

* Little fix for mac

* Plot updates, mainly default settings but a little slider UI

* One more little default setting update

---------

Co-authored-by: Vincent Larson &lt;vlarson@users.noreply.github.com&gt;
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Removed the version control identifier from the file.
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* Upgrading CLUBBs timer system. Now we either can use gptl just by compiling with it, or we use a cpu_time based fallback that was designed to be a crude copy

* Giving up on using the build system to detect stale build, switching to a method that just compares timestamps on directories

* Fixing small UI bug and removing a bit of dead code in the dash app, also fixing a gptl compiling issue on mac

* Little fix for python

* Adding a bit about the new timing output in the output section of the README

* Improving print statements and disabling timing and iteration prints when debug=-1

---------

Co-authored-by: Gunther Huebler &lt;guntherhuebler@frankie.uits.uwm.edu&gt;
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dash updates (#1327)

* Cross-platform updates to help with running on Macs mainly. The biggest difference is that now our code expects the les data in input/, and I've added a symlink that points to the normal pub directory for it. This makes everything work the same, but also makes it so someone can download the les data and store it anywhere, then just change the symlink.

* Little UI improvements

* Small UI fix

* Small fix needed for a different python version and a little UI update

* Another tiny cross platform fix

* Updating build removal method and adding a mac specific bit for GPTL compiling that fixes environment issues

* Removing accidentally added file
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additions (#1324)

* Starting new additions for tuner - specifically an overall history of all samples and loss metrics with the eventual goal of having fancy SVD and spline things we can do with that

* Adding plots to tune tab to visualize data in the overall sample outputs

* Adding the enhanced simulated annealed to the tuner. Only real tweak it that it runs workers x batch_size chains independently so that we can utilize the CPU fully

* Filtering big values in parameter plot view and making default window length 3600s (1 hour)

* Bug fix to metric report - a 0 correlation was able to throw things off, which could occur when a field from either result (clubb or LES) is all 0 without the other one being all zero. Also some small display improvements

* Adding sensitivity plots

* Updating flag/param selecting method by created a general input/tunable_parameters directory that contains subdirectories for different flag set combos. These can be used by passing in their name to run_scm.py with -config. Also updating references to these files since they moved and also making tests and scripts default to using -override instead of editting files with sed.

* Adding buttons to select param/flag config in the tuner

* Quality of life improvements for plot tab - now view settings and UI settings are retained when reloading the same case

* Fixing missed comment change

* Various small UI improvements

* Improving tuner history check and little UI fix in run_tab

* Fixing tuner environment setup

* Fixing little netcdf version issue and adding new test for loss metrics consistency check

* Renaming tunable_parameters to parameter_and_flag_configs, also adding -config example to run_scripts README
</comment><date>2026-07-02 23:06:14 -0500</date><id>95d5d12aef49035170773f0714a97f4109bcccdd</id><msg>Tuner additions 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_class='hudson.plugins.git.GitChangeSet'><affectedPath>dash_app/run_tab/tab.py</affectedPath><affectedPath>dash_app/compile_tab/discovery.py</affectedPath><affectedPath>dash_app/app.py</affectedPath><affectedPath>dash_app/assets/10_theme.css</affectedPath><affectedPath>dash_app/compile_tab/runtime.py</affectedPath><affectedPath>clubb_python_api/README.md</affectedPath><affectedPath>dash_app/run_tab/layout.py</affectedPath><affectedPath>dash_app/assets/30_run_ui_resize.js</affectedPath><affectedPath>dash_app/compile_tab/tab.py</affectedPath><affectedPath>dash_app/assets/14_tab_compile_theme.css</affectedPath><affectedPath>run_scripts/run_scm.py</affectedPath><affectedPath>dash_app/assets/20_autoscroll.js</affectedPath><affectedPath>dash_app/compile_tab/callbacks.py</affectedPath><affectedPath>dash_app/compile_tab/layout.py</affectedPath><affectedPath>run_scripts/run_scm_loss.py</affectedPath><affectedPath>clubb_python_api/run_pytests.sh</affectedPath><affectedPath>dash_app/plot_tab/plot_types/base_plot.py</affectedPath><affectedPath>dash_app/tune_tab/layout.py</affectedPath><affectedPath>dash_app/assets/11_tab_run_theme.css</affectedPath><affectedPath>dash_app/compile_tab/state.py</affectedPath><affectedPath>dash_app/compile_tab/__init__.py</affectedPath><affectedPath>clubb_python_api/CMakeLists.txt</affectedPath><commitId>31446891daef22d1f1ac63262df21583933565b9</commitId><timestamp>1782963365000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Dash compile tab (#1323)

* Fixing small UI issues and adding tab that currently only can compile, but the plan is to have to be compile + run tests

* Improving compile tab - mainly implementing the ability to select existing builds to use as the version to run with.

* Tiny fixes to run tab UI

* Improvements to rebuilding - there were tiny bugs.

* Updating method of installing python compiles - now we package the python .so libraries with the install build. This makes things simple to import and fixes compilation issues when switching between compilers

* Cleanup - reverting various unneccesary things

---------

Co-authored-by: Gunther Huebler &lt;guntherhuebler@Gunthers-MacBook-Pro-2.local&gt;
</comment><date>2026-07-01 22:36:05 -0500</date><id>31446891daef22d1f1ac63262df21583933565b9</id><msg>Dash compile tab 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Also adding a temporary handoff file and improving the python api fix shortcut

(cherry picked from commit 47106db56945d6d0c1f962cc77d205db99d60f4f)
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(cherry picked from commit f5c3b99d56499acc2a706cf024dd802f73030dd2)
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Huebler</fullName></author><authorEmail>huebler@uwm.edu</authorEmail><comment>advance_clubb_core.py cleanup and removing strange compat_kwargs usages that seem like artifacts of laziness

(cherry picked from commit 9056400901e270333b80ee8f66af055d395b8020)
</comment><date>2026-06-25 23:05:35 -0500</date><id>e73f5d17f344ccfbf4741d978a7e0dd60a06fb25</id><msg>advance_clubb_core.py cleanup and removing strange compat_kwargs usages that seem like artifacts of laziness</msg><path><editType>edit</editType><file>clubb_python_api/clubb_f2py.pyf</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_stats_accumulate.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_udt_return_contract.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/ly93_pdf.py</file></path><path><editType>edit</editType><file>clubb_python_driver/advance_clubb_core.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/diffusion.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_advance_xm_wpxp.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_advance_xp2_xpyp.py</file></path><path><editType>edit</editType><file>clubb_python_api/f2py_fortran_wrappers/pdf_closure_module_wrapper.F90</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/pdf_parameter_module.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_advance_windm_edsclrm.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_ly93.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/stats_netcdf.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_new_hybrid_pdf.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_stats.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_skx.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/advance_wp2_wp3.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_new_pdf.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_mono_flux.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/advance_xp2_xpyp.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/adg1_adg2_3d_luhar_pdf.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/new_tsdadg_pdf.py</file></path><path><editType>edit</editType><file>clubb_python_api/f2py_fortran_wrappers/new_hybrid_pdf_main_wrapper.F90</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_remap.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/matrix_solver_wrapper.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/prescribe_forcings.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_advance_core_subs.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_transport.py</file></path><path><editType>edit</editType><file>clubb_python_api/f2py_fortran_wrappers/advance_wp2_wp3_module_wrapper.F90</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/advance_helper.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_advance_xp3.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_advance_wp2_wp3.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/radiation.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_advance_core.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/err_info_type_module.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/sponge_layer_damping.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/calc_pressure.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/new_pdf.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/remapping_module.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/advance_clubb_core.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_luhar.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_precipitation_fraction.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/clubb_api.py</file></path><path><editType>edit</editType><file>clubb_python_driver/advance_clubb_to_end.py</file></path><path><editType>edit</editType><file>clubb_python_driver/clubb_case_initalization.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_mixing_length.py</file></path><path><editType>edit</editType><file>clubb_jax/clubb_case_initalization.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_c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Huebler</fullName></author><authorEmail>huebler@uwm.edu</authorEmail><comment>Improving audit script even more, fixing issues it found. Also making advance_clubb_core.py nice and making an LLM shortcut for how to repeat the process

(cherry picked from commit 25b41435d7bfbbe03f2736440bdcbf4330f863ab)
</comment><date>2026-06-25 23:49:56 -0500</date><id>1fa8fdebc019e2807e0031f7233ef85243f80ad6</id><msg>Improving audit script even more, fixing issues it found. Also making advance_clubb_core.py nice and making an LLM shortcut for how to repeat the process</msg><path><editType>edit</editType><file>clubb_python_api/f2py_fortran_wrappers/clubb_loss_driver_wrapper.F90</file></path><path><editType>edit</editType><file>clubb_python_driver/advance_clubb_to_end.py</file></path><path><editType>add</editType><file>LLM_prompts/port_underlying_fortran_to_other_languages.md</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/sponge_layer_damping.py</file></path><path><editType>edit</editType><file>clubb_python_driver/clubb_case_initalization.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_precipitation_fraction.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/loss_driver.py</file></path><path><editType>edit</editType><file>clubb_jax/clubb_case_initalization.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_advance_xm_wpxp.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_new_pdf.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_mono_flux.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_advance_xp2_xpyp.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/diffusion.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_advance_xp3.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_advance_wp2_wp3.py</file></path><path><editType>edit</editType><file>clubb_jax/advance_clubb_core.py</file></path><path><editType>edit</editType><file>clubb_jax/advance_clubb_to_end.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/pdf_parameter_module.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/advance_xp2_xpyp.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/pdf_closure.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_stats_accumulate.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/clubb_api.py</file></path><path><editType>edit</editType><file>LLM_prompts/SHORTCUTS.md</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/remapping_module.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_advance_core_subs.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_pdf_closure_driver.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_mixing_length.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/mixing_length.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/new_pdf_main.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/stats_netcdf.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/prescribe_forcings.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/error_code.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/parameters_tunable.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/argument_list_enforcer/argument_contract_audit.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_luhar.py</file></path><path><editType>edit</editType><file>clubb_python_driver/advance_clubb_core.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_stats.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/advance_clubb_core.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/new_hybrid_pdf_main.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_advance_windm_edsclrm.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/adg1_adg2_3d_luhar_pdf.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_matrix_solver_wrapper.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_f2py.pyf</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_argument_contract_audit.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/matrix_solver_wrapper.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/advance_wp2_wp3.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/mono_flux_limiter.py</file></path></item><item 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up run_scripts (#1320)

* Cleaning up run_scripts by removing old bash files, also moving many scripts into a new tests/ directory, since those are tests. Fixing a small bug in clubb_driver as well, just needed to move a print statement, otherwise it tries writing to a closed file.

* A little cleanup and better READMEs for run_scripts and tests
</comment><date>2026-06-25 21:06:57 -0500</date><id>e04956358685c2869358db8b6d46d16cf9744b03</id><msg>Cleaning up run_scripts 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_class='hudson.plugins.git.GitChangeSet'><affectedPath>run_scripts/README</affectedPath><affectedPath>src/CMakeLists.txt</affectedPath><affectedPath>src/jacobian.F90</affectedPath><affectedPath>README</affectedPath><affectedPath>input_misc/jacobian.in</affectedPath><affectedPath>run_scripts/run_jacobian.bash</affectedPath><commitId>5512bff0caa1b179b2a03a5512fc3de2c866b0cb</commitId><timestamp>1782441296000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/huebler</absoluteUrl><fullName>Gunther Huebler</fullName></author><authorEmail>huebler@uwm.edu</authorEmail><comment>Removing jacobian code - it has not worked in a long time
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</comment><date>2026-06-25 21:49:39 -0500</date><id>0ed15803474cd7d3d8228a642e9e2599a840707d</id><msg>Removing ifdefs that are only for E3SM and only on a specific machine</msg><path><editType>edit</editType><file>src/CLUBB_core/lapack_wrap.F90</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>src/CLUBB_core/advance_clubb_core_module.F90</affectedPath><affectedPath>src/generalized_grid_test.F90</affectedPath><affectedPath>src/CLUBB_core/clubb_api_module.F90</affectedPath><affectedPath>src/CLUBB_core/mixing_length.F90</affectedPath><commitId>86f7a6081cc525e6d953cebc42d4e5962d7e24f2</commitId><timestamp>1782443428000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/huebler</absoluteUrl><fullName>Gunther Huebler</fullName></author><authorEmail>huebler@uwm.edu</authorEmail><comment>Removing the CLUBBND_CAM option, not sure what it was for, it's not defined in this repo or any of our host model repos
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</comment><date>2026-06-23 15:51:04 -0500</date><id>2ca3ddc3ece9ae81f9b9acc08d3be93c4aab01fb</id><msg>Recently clubb_BFB_varying_flags_gfortran_test failed due to a script bug, dispite it being BFB. 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_class='hudson.plugins.git.GitChangeSet'><affectedPath>clubb_python_api/clubb_python/clubb_api.py</affectedPath><affectedPath>src/CLUBB_core/pdf_closure_module.F90</affectedPath><affectedPath>dash_app/assets/37_run_console_state.js</affectedPath><affectedPath>clubb_python_api/f2py_fortran_wrappers/stats_netcdf_wrapper.F90</affectedPath><affectedPath>dash_app/tune_tab/__init__.py</affectedPath><affectedPath>dash_app/tune_tab/callbacks_display.py</affectedPath><affectedPath>dash_app/assets/13_tab_tune_theme.css</affectedPath><affectedPath>src/clubb_loss_driver_test.F90</affectedPath><affectedPath>dash_app/run_tab/callbacks_console.py</affectedPath><affectedPath>src/CLUBB_core/error_code.F90</affectedPath><affectedPath>dash_app/plot_tab/profile_loss.py</affectedPath><affectedPath>tuner/clubb_loss_driver.py</affectedPath><affectedPath>tuner/taylor_metrics.py</affectedPath><affectedPath>run_scripts/run_scm_loss.py</affectedPath><affectedPath>tuner/case_defaults.json</affectedPath><affectedPath>src/clubb_driver_test.F90</affectedPath><affectedPath>run_scripts/run_benchmark_converter_test.py</affectedPath><affectedPath>dash_app/tune_tab/tab.py</affectedPath><affectedPath>clubb_python_api/clubb_python/CLUBB_core/stats_netcdf.py</affectedPath><affectedPath>dash_app/plot_tab/plot_types/shared.py</affectedPath><affectedPath>dash_app/tune_tab/runtime.py</affectedPath><affectedPath>tuner/clubb_loss_driver_test.py</affectedPath><affectedPath>tuner/tune_clubb.py</affectedPath><affectedPath>tuner/tuning_worker.py</affectedPath><affectedPath>utilities/loss_metrics.py</affectedPath><affectedPath>run_scripts/create_case_namelist.py</affectedPath><affectedPath>jenkins_tests/LLM_FAILURE_AUTOMATION_DESIGN.md</affectedPath><affectedPath>tuner/paths.py</affectedPath><affectedPath>src/SILHS/latin_hypercube_driver_module.F90</affectedPath><affectedPath>tuner/status.py</affectedPath><affectedPath>dash_app/run_tab/layout.py</affectedPath><affectedPath>dash_app/plot_tab/benchmark_overlay.py</affectedPath><affectedPath>clubb_python_driver/clubb_case_initalization.py</affectedPath><affectedPath>run_scripts/create_multi_col_params.py</affectedPath><affectedPath>run_scripts/run_loss_output_consistency.py</affectedPath><affectedPath>dash_app/plot_tab/callbacks_grid.py</affectedPath><affectedPath>src/CLUBB_core/clubb_api_module.F90</affectedPath><affectedPath>dash_app/tune_tab/callbacks_runs.py</affectedPath><affectedPath>dash_app/tune_tab/layout.py</affectedPath><affectedPath>clubb_python_api/clubb_f2py.pyf</affectedPath><affectedPath>dash_app/tune_tab/discovery.py</affectedPath><affectedPath>dash_app/requirements.txt</affectedPath><affectedPath>jenkins_tests/clubb_new_tuner_test/Jenkinsfile</affectedPath><affectedPath>tuner/case_defaults.py</affectedPath><affectedPath>run_scripts/run_tuner_job.py</affectedPath><affectedPath>dash_app/plot_tab/plot_types/timeheight_plot.py</affectedPath><affectedPath>dash_app/assets/36_tune_ui_resize.js</affectedPath><affectedPath>dash_app/plot_tab/state.py</affectedPath><affectedPath>tuner/job_runtime.py</affectedPath><affectedPath>utilities/__init__.py</affectedPath><affectedPath>tuner/test_tuning_strategy.py</affectedPath><affectedPath>src/CLUBB_core/stats_netcdf.F90</affectedPath><affectedPath>tuner/__init__.py</affectedPath><affectedPath>dash_app/tune_tab/callbacks_settings.py</affectedPath><affectedPath>dash_app/README.md</affectedPath><affectedPath>tuner/tuning_strategy.py</affectedPath><affectedPath>run_scripts/run_stats_output_consistency.py</affectedPath><affectedPath>tuner/request.py</affectedPath><affectedPath>utilities/benchmark_converter.py</affectedPath><affectedPath>dash_app/plot_tab/plot_types/budget_plot.py</affectedPath><affectedPath>clubb_python_api/clubb_python/_runtime_loader.py</affectedPath><affectedPath>dash_app/plot_tab/layout.py</affectedPath><affectedPath>clubb_python_api/clubb_python/CLUBB_core/loss_driver.py</affectedPath><affectedPath>dash_app/plot_tab/callbacks_controls.py</affectedPath><affectedPath>dash_app/plot_tab/callbacks_params.py</affectedPath><affectedPath>clubb_python_api/f2py_fortran_wrappers/clubb_loss_driver_wrapper.F90</affectedPath><affectedPath>dash_app/app.py</affectedPath><affectedPath>jenkins_tests/clubb_stats_output_consistency_gfortran_test/Jenkinsfile</affectedPath><affectedPath>clubb_python_api/clubb_python/__init__.py</affectedPath><affectedPath>dash_app/plot_tab/plot_types/profile_plot.py</affectedPath><affectedPath>clubb_python_driver/advance_clubb_to_end.py</affectedPath><affectedPath>run_scripts/run_scm.py</affectedPath><affectedPath>src/clubb_standalone_loss.F90</affectedPath><affectedPath>dash_app/plot_tab/plot_types/subcolumn_plot.py</affectedPath><affectedPath>run_scripts/run_bindiff_all.py</affectedPath><affectedPath>src/clubb_driver.F90</affectedPath><affectedPath>README</affectedPath><affectedPath>tuner/tuning_scheduler.py</affectedPath><affectedPath>dash_app/assets/12_tab_plots_theme.css</affectedPath><affectedPath>src/CMakeLists.txt</affectedPath><affectedPath>tuner/README.md</affectedPath><affectedPath>dash_app/plot_tab/callbacks_case.py</affectedPath><affectedPath>src/clubb_loss_driver.F90</affectedPath><affectedPath>dash_app/tune_tab/state.py</affectedPath><commitId>2a334f87922dfaceb7d3a37b1924d374f1b986d5</commitId><timestamp>1781756186000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Clubb loss driver (#1303)

* First set of commits for the new loss driver.

* Improvements

* Batching capabilities

* Lot's of cleanup, simplifications, and consolidation

* More testing

* Python interfaces for the loss driver

* Interface for tuner and tuner with modes.

* Nice updates

* Missed file

* Little updates to fix inconsistencies in the plots and averaging ranges

* Adding a script that converts sam and coamps netcdf files to a clubb named version, including things that need to be calculated. This fixes a bug where fields were being averaged before being calculated, see https://github.com/larson-group/clubb/issues/1284, but is currently only wired up in the new tuner and the dash app plotter

* Making some things public for nvhpc

* Organization and consistency test fix

* Adding taylor diagram to tune tab, this needs taylor metrics to be computed so the loss driver needed to output this info.

* Adding more fancy loss functions based on Taylor metrics and a way to switch how the loss is computed in the dash tuner

* Making NaN in code not an issue

* Mostly dash app improvements to plotting, also made subwindows for tuning

* Tuner tracking by case

* Removing stats time-variance code

* Simplifying loss driver output - now loss metrics are output explicitly rather than as packaged taylor_metrics and having different versions for subwindows and such

* Mainly ui updates and small simplifications

* Improving comments and cleaning things up a bit

* Removing strictness on stats window vs output interval, and adding a stats consistency test to tests for issues with batch size and output frequency and the windowing mode

* Fixing openmp bug and making incomplete stats intervals not output, as it was before

* Making jenkins test use standard stats, and fixing tiny bug that caused error running with debug+no rcp2 stats

* Adding gate around bindiff, there's an edge case where a cosmetic diff can trigger a full-diff even in a failed case, which should otherwise be considered BFB and skipped.

* Adding some README entries for the dash app and a python requirements file

* Adding comments and little bug fix to dash app

* Update to loss consistency test, making it simpler since stats consistency test covers most things. Also adding it to the stats consistency jenkins test since it is still similar

* Cleanup and code consolidation, new jenkins test for tuner

* Adding comments

* Fixing little bugs

* Slight improvement to stats_api

* Small bug fix

* Consolidating stats time setting
</comment><date>2026-06-17 23:16:26 -0500</date><id>2a334f87922dfaceb7d3a37b1924d374f1b986d5</id><msg>Clubb loss driver 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_class='org.jenkinsci.plugins.displayurlapi.actions.RunDisplayAction'></action><action _class='org.jenkinsci.plugins.pipeline.modeldefinition.actions.RestartDeclarativePipelineAction'></action><action></action><action _class='org.jenkinsci.plugins.workflow.job.views.FlowGraphAction'></action><action></action><action></action><action></action><building>false</building><displayName>#52</displayName><duration>611913</duration><estimatedDuration>603251</estimatedDuration><fullDisplayName>clubb_plot_solver_compare #52</fullDisplayName><id>52</id><keepLog>false</keepLog><number>52</number><queueId>4876</queueId><result>SUCCESS</result><timestamp>1781683568702</timestamp><url>http://carson.math.uwm.edu/jenkins/job/clubb_plot_solver_compare/52/</url><changeSet _class='hudson.plugins.git.GitChangeSetList'><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>src/clubb_driver.F90</affectedPath><commitId>d4fbf466f74b11ca7b5a81575427768beebc3f5b</commitId><timestamp>1781661933000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/huebler</absoluteUrl><fullName>Gunther Huebler</fullName></author><authorEmail>huebler@uwm.edu</authorEmail><comment>Fixing bug that caused incorrect times to be written to netcdf in cases where stats_tout (output interval) &gt; dt_main (timestep). This is BIT_CHANGING because of that, but only for the time variable (no field differences), and only for cases where we don't output each timestep.
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- utilities/convert_acc_to_omp.bash
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the old compile directory and docs directory (#1315)

- The old mkmf/make compile directory, the bash based compile scripts are no longer needed now that we have CMake
- Moved `convert_acc_to_omp.bash` to utilities/ directory
- The docs directory had an old copy of the website, but the website is backed up to a local drive on Carson
</comment><date>2026-06-10 13:51:07 -0500</date><id>beffd89a659bcbddc72da2c23fa57ff0bd34a424</id><msg>Deleted the old compile directory and docs directory 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outdated Matlab files (#1313)

- Removed plotting, utility, and post-processing Matlab scripts
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GrADS (.ctl, .dat) file format and reference to it (#1310)

- Made updates to Input Fields to remove GrADS. Master branch only worked for a small number of input variables, and after the changes when testing, worked just as well as the master branch. 
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* Removed perl and references to it

* Reverting changes to files/directories as requested
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</comment><date>2026-06-04 10:38:02 -0500</date><id>0d30e05f0411c43c5b0eecb8734433dd9a29deda</id><msg>Create README for python_sam_budgets_plotter folder</msg><path><editType>add</editType><file>postprocessing/python_sam_budgets_plotter/README</file></path></item><item 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plotgen (#1312)

* Removed entire plotgen directory 
</comment><date>2026-06-04 13:47:50 -0500</date><id>53893cabfda88eccc92204a3471b3855a4716aa6</id><msg>Removed plotgen (#1312)</msg><path><editType>delete</editType><file>postprocessing/plotgen/cases/cam/armcc.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/lba_subperiods/lba_deep.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/plotgen.pl</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/cgils_s12_p2k.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/sam_clubb/twpice_sam_standalone.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/sam_clubb/lba_subperiods/lba_budgets_early.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/cgils_s11_p2k.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/sam_clubb/bomex_budgets.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/dycoms2_rf02_ds_budgets.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/lba_subperiods/lba_morr_budgets_deep.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/mpace_b.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/read_netcdf_hoc_corr.m</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/sam_clubb/lba_budgets.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/DetermineExtension.m</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/dycoms2_rf01_coamps_budgets.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/mc3e_morr_budgets.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/sam_clubb/templates/template_morr_budget.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/wangara_budgets.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/wrf/arm.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/CaseReader.pm</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/gabls3_budgets.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/templates/template_all_sam.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/rico_coamps_budgets.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/cam/ne_pac_hi_iop_clubb.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/sam_clubb/cloud_feedback_s6_p2k_budgets.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/wrf/fire.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/read_grads_hoc_sfc_endian.m</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/sam_clubb/dycoms2_rf02_ds.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/dycoms2_rf02_do_budgets.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/read_netcdf_hoc.m</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/cgils_s06_p2k_budgets.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/gfdl/bomex.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/CaseFunctions/UseFirstArgIfExist.m</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/sam_clubb/lba_subperiods/lba_morr_budgets_early.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/sam_clubb/cloud_feedback_s12_budgets.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/gfdl/atex.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/mpace_b_silhs.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/cam/atex.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/lba_morr_budgets.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/twp_ice.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/sam_clubb/lba_morr_budgets.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/dycoms2_rf02_so.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/gfdl/dycoms2_rf01_fixed_sst.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/clubb/lba.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/gfdl/dycoms2_rf01.case</file></path><path><editType>delete</editType><file>postprocessing/plotgen/cases/sam_clubb/gate_shear_rlsf.case</file></path><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organization part3 (#1306)

* More BFB movements

* Reworking where sigma_sqd_w and gamma_Skw_fnc are computed - this should all be BFB. Also fixing the G_unit test that was failing due to sigma_sqd_w issues

* Correcting arg list

* Fixes after rebase

* Making sigma_sqd_w_zt BFB vs master when using iiPDF_type=7 (new hybrid)

* Fixing python API

* Changing name of compute_xp3 to diagnose_xp3 and moving a1_coef and a3_coef calculation back into advance routines

* Fixes for GPU code
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* Adding script that converts openacc directives to use async clauses and jenkins test to test that adding them does not change BFBness

* Small cleanup - fixing typo and adding comments.
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Clarified the role of clubb_python_api in the conversion process and improved the description of the test harness functionality.
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</comment><date>2026-05-27 13:49:11 -0500</date><id>73dc365c77ab4bf2405d753f167307ae9be330a0</id><msg>Removing unneccesary wp2_zt conversion that should've been removed already, but was accidentally added back in the last PR when trying to split BFB from non-BFB changes. 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organization part2 (#1304)

A number of fields were being calculated in `advance_clubb_core` (`wp2_zt` `wp3_on_wp2` `wp3_on_wp2_zt` `Skw_zm` `Skw_zt) then passed into other routines, however, all these fields depend on `wp2` and were not being updated after `wp2` was being updated by `calc_sfc_varnce`. This commit fixes that by moving where these fields are calculated - instead of computing in `advance_clubb_core` with the incoming `wp2`, we now calculate them "on-demand" where they are needed using the most recent value of `wp2`. 

Using our default flag set, there are no numerical differences caused by this change set, only a few stats differences. There are real differences that occur when `l_upwind_xpyp_ta = .false.` (a clubb_config_flag value) or when `l_explicit_turbulent_adv_xpyp = .true.` (a parameter in model_flags.F90), but these are small differences and do not visually affect plots for our stable cases. Changing the order of the `advance_` routines would also cause this to be BIT_CHANGING, since that also affects the update path for `wp2` - now these values that got moved would be using the newest `wp2` instead of being "stale", also causing small (but real) differences.

* Calculating wp2_zt and wp3_on_wp2 where needed, rather than passing those values around through advance_clubb_core. This is BIT_CHANGING for a handful of stats only variables be default: wp3_on_wp2, wp3_on_wp2_zt, wp3_on_wp2_cfl_num, term_wprtp2_explicit, term_wprtpthlp_explicit, and term_wpthlp2_explicit. Some Skw_ variables when using lmm_stepping, and has actual differences (not just in stats output) when swapping the order of the advance routines

* Moving things around, this seems to all be BFB except for the Skw_ movements, which is BIT_CHANGING if the advance_ order changes

* Fixing python API

* Reverting some BFB changes
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* More organization. Also moving some stats calls inside of pdf_closure_driver, which is BIT_CHANGING, but only for stats output and only when ipdf_call_placement=ipdf_pre_post_advance_fields

* Adding new flag set for testing

* Fixing python API and updating prompt
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</comment><date>2026-05-14 13:30:26 -0500</date><id>77d989d6d7397187825e263ed404e956c7598749</id><msg>This fixes the GPU BFB test that failed due to stats-only differences in rtm_ed and thlm_ed, and as a result is technically BIT_CHANGING. Also, the BFB with varying flags failed because flag set 1 changed to use the lapack solvers since the custom ones it set before are now default. 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cleanup (#1301)

* BFB cleanup stuff

* Adding some helper routines

* More BFB changes

* More BFB changes

* More BFB changes

* More BFB changes

* Fixing python API and adding an agent file and a prompt to fix python API in the future.

* Updating scripts and improving formatting

* Updating some scripts and adding new jenkins test to compare the current branch vs master with flags

* Restoring BFBness when using l_lmm_stepping=.true. by reimplementing an existing bug...

* Making run_clubb_w_varying_flags.py not remove output, it's just unneccesary

* Simplifying script changes

* Jenkins script update

* Little consolidation of code in pdf_closure_driver

* Fixing python API

* Fixing parameterization_check formatting
</comment><date>2026-05-13 15:00:40 -0500</date><id>34c6bb07afb6e445f60ea87dcc632969086f9fa1</id><msg>advance_clubb_core cleanup 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_class='hudson.plugins.git.GitChangeSet'><affectedPath>clubb_jax/advance_clubb_to_end.py</affectedPath><affectedPath>clubb_python_driver/advance_clubb_to_end.py</affectedPath><commitId>2fe6e56761356da5b20a7fba14c72ec69fdc9d02</commitId><timestamp>1778175927000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/huebler</absoluteUrl><fullName>Gunther Huebler</fullName></author><authorEmail>huebler@uwm.edu</authorEmail><comment>Switching default call to advance_clubb_core in python and jax drivers to use the python api version, rather than the python ported version.
</comment><date>2026-05-07 12:45:27 -0500</date><id>2fe6e56761356da5b20a7fba14c72ec69fdc9d02</id><msg>Switching default call to advance_clubb_core in python and jax drivers to use the python api version, rather than the python ported version.</msg><path><editType>edit</editType><file>clubb_jax/advance_clubb_to_end.py</file></path><path><editType>edit</editType><file>clubb_python_driver/advance_clubb_to_end.py</file></path></item><kind>git</kind></changeSet><culprit><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/huebler</absoluteUrl><fullName>Gunther Huebler</fullName></culprit><inProgress>false</inProgress><nextBuild><number>37</number><url>http://carson.math.uwm.edu/jenkins/job/clubb_plot_solver_compare/37/</url></nextBuild><previousBuild><number>35</number><url>http://carson.math.uwm.edu/jenkins/job/clubb_plot_solver_compare/35/</url></previousBuild></build><build _class='org.jenkinsci.plugins.workflow.job.WorkflowRun'><action _class='hudson.model.CauseAction'><cause 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Huebler</fullName></author><authorEmail>huebler@uwm.edu</authorEmail><comment>Fixing python api and python/jax driver. Also fixing bug that caused non-BFBness in stats outputs (only upwp_cl/vpwp_cl) when using l_predict_upwp_vpwp=.false., and adding ulimit -s 8388608 to fix GPU test (though it's unclear why exactly we need this all of a sudden for this test). RESOLVED:643d128a5613019595aecd643f1028e937ad4b76 RESOLVED:f146255f50732c445ccbd012ca45888a9ce44d0b, and since this changes stats this is technically BIT_CHANGING"
</comment><date>2026-05-05 17:22:01 -0500</date><id>5e3cfdd6efddf098dbddb41a5848e3ef4189aac8</id><msg>Fixing python api and python/jax driver. Also fixing bug that caused non-BFBness in stats outputs (only upwp_cl/vpwp_cl) when using l_predict_upwp_vpwp=.false., and adding ulimit -s 8388608 to fix GPU test (though it's unclear why exactly we need this all of a sudden for this test). RESOLVED:643d128a5613019595aecd643f1028e937ad4b76 RESOLVED:f146255f50732c445ccbd012ca45888a9ce44d0b, and since this changes stats this is technically BIT_CHANGING"</msg><path><editType>edit</editType><file>clubb_python_api/f2py_fortran_wrappers/clip_explicit_wrapper.F90</file></path><path><editType>edit</editType><file>jenkins_tests/clubb_plot_nvhpc_gpu_vs_cpu/Jenkinsfile</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_advance_core_subs.py</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_advance_xm_wpxp.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/advance_xm_wpxp.py</file></path><path><editType>edit</editType><file>clubb_python_api/f2py_fortran_wrappers/advance_xp2_xpyp_module_wrapper.F90</file></path><path><editType>edit</editType><file>clubb_python_driver/advance_clubb_core.py</file></path><path><editType>edit</editType><file>clubb_jax/advance_clubb_core.py</file></path><path><editType>edit</editType><file>jenkins_tests/clubb_BFB_multi_col_gpu_nvhpc_test/Jenkinsfile</file></path><path><editType>edit</editType><file>src/CLUBB_core/advance_windm_edsclrm_module.F90</file></path><path><editType>edit</editType><file>clubb_python_api/f2py_fortran_wrappers/advance_xm_wpxp_module_wrapper.F90</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_advance_windm_edsclrm.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/advance_windm_edsclrm.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/clip_explicit.py</file></path><path><editType>edit</editType><file>src/CLUBB_core/advance_clubb_core_module.F90</file></path><path><editType>edit</editType><file>clubb_python_api/f2py_fortran_wrappers/advance_windm_edsclrm_module_wrapper.F90</file></path><path><editType>edit</editType><file>clubb_python_api/tests/test_call_tree_advance_xp2_xpyp.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_python/CLUBB_core/advance_xp2_xpyp.py</file></path><path><editType>edit</editType><file>jenkins_tests/clubb_driver_test/Jenkinsfile</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_f2py.pyf</file></path></item><kind>git</kind></changeSet><culprit><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/huebler</absoluteUrl><fullName>Gunther 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_class='hudson.plugins.git.GitChangeSet'><affectedPath>src/CLUBB_core/advance_clubb_core_module.F90</affectedPath><affectedPath>src/CLUBB_core/advance_xm_wpxp_module.F90</affectedPath><affectedPath>src/CLUBB_core/advance_windm_edsclrm_module.F90</affectedPath><affectedPath>src/G_unit_test_types/spurious_source_test.F90</affectedPath><affectedPath>src/CLUBB_core/setup_clubb_pdf_params.F90</affectedPath><affectedPath>src/CLUBB_core/clip_explicit.F90</affectedPath><affectedPath>src/Microphys/pdf_hydromet_microphys_wrapper.F90</affectedPath><affectedPath>src/CLUBB_core/advance_xp2_xpyp_module.F90</affectedPath><commitId>643d128a5613019595aecd643f1028e937ad4b76</commitId><timestamp>1777923494000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Clip covar simplifications (#1297)

* Initial clip covar changes

* Slightly nicer clipping count behavior
</comment><date>2026-05-04 14:38:14 -0500</date><id>643d128a5613019595aecd643f1028e937ad4b76</id><msg>Clip covar simplifications (#1297)</msg><path><editType>edit</editType><file>src/CLUBB_core/clip_explicit.F90</file></path><path><editType>edit</editType><file>src/Microphys/pdf_hydromet_microphys_wrapper.F90</file></path><path><editType>edit</editType><file>src/CLUBB_core/advance_clubb_core_module.F90</file></path><path><editType>edit</editType><file>src/CLUBB_core/advance_xm_wpxp_module.F90</file></path><path><editType>edit</editType><file>src/CLUBB_core/advance_windm_edsclrm_module.F90</file></path><path><editType>edit</editType><file>src/CLUBB_core/setup_clubb_pdf_params.F90</file></path><path><editType>edit</editType><file>src/CLUBB_core/advance_xp2_xpyp_module.F90</file></path><path><editType>edit</editType><file>src/G_unit_test_types/spurious_source_test.F90</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>src/clubb_driver.F90</affectedPath><affectedPath>README</affectedPath><affectedPath>cmake/deps/NetcdfFortranDependency.cmake</affectedPath><affectedPath>run_scripts/README</affectedPath><affectedPath>src/CMakeLists.txt</affectedPath><affectedPath>postprocessing/plotgen/cases/README</affectedPath><affectedPath>compile.py</affectedPath><affectedPath>run_scripts/run_scm.py</affectedPath><commitId>f146255f50732c445ccbd012ca45888a9ce44d0b</commitId><timestamp>1777938051000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Cmake netcdf fallback (#1294)

* WIP: Compile w/o NetCDF

- Currently failing from a 'version' error, but actually it's because the fortran cmake is testing a small c program to test functionality, but the C hasn't been built yet

* CMake configuration phase works for netcdf, but build fails

* Compiles almost all the way and has the executable clubb_standalone

* No errors to compile w/o netcdf

- CMake configure and build phase ran with no errors

- Clubb was functional after the build

* Fixed to work as a fresh user

- Worked with no netcdf and a clean clone of this branch

* Added blank line

* Got compile.py to run on gfortran, nvhpc, ifort, ifx

 - Needs testing for with/without netcdf pre-installed

* Fixed compiler logic

 - Basically, if not matching the default (gfortran) netcdf, and can't find a different one, then go from scratch.

* Small bug fixes

* Cleaned up code, all lines less than 100 characters

* Commented through code

* Removing redundancy

* Fixes to make -gptl flag work

* Improved comments, replaced .bash with .py in readme's
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* Possibly better string fix for python API

* Little test changes
</comment><date>2026-04-08 15:46:04 -0500</date><id>dc7d6ed92e27f14e4e64769a67a09a63b2783310</id><msg>Python update (#1291)</msg><path><editType>edit</editType><file>clubb_python_api/f2py_fortran_wrappers/stats_netcdf_wrapper.F90</file></path><path><editType>edit</editType><file>clubb_python_api/f2py_fortran_wrappers/parameters_tunable_wrapper.F90</file></path><path><editType>add</editType><file>clubb_python_api/tests/test_call_tree_t_in_k_module.py</file></path><path><editType>delete</editType><file>clubb_python_api/tests/test_hello_world.py</file></path><path><editType>add</editType><file>clubb_python_api/tests/test_string_conversion.py</file></path><path><editType>edit</editType><file>clubb_python_api/clubb_f2py.pyf</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>src/CLUBB_core/CMakeLists.txt</affectedPath><commitId>0ab371ba28cf647f279567c04786ddc925aa5a87</commitId><timestamp>1775682381000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Remove line to test python scripts
</comment><date>2026-04-08 16:06:21 -0500</date><id>0ab371ba28cf647f279567c04786ddc925aa5a87</id><msg>Remove line to test python scripts</msg><path><editType>edit</editType><file>src/CLUBB_core/CMakeLists.txt</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>src/CLUBB_core/CMakeLists.txt</affectedPath><commitId>2bac827cd3b91b3437ca62918583938237c9fd03</commitId><timestamp>1775696339000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Add blank line to test python scripts
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</comment><date>2026-04-06 13:28:13 -0500</date><id>9d56b4d0695c86980a6bfaaf9567449dbc4ccabd</id><msg>Space change for little test</msg><path><editType>edit</editType><file>License.txt</file></path></item><item 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fix (#1288)

* Fixing code to comply with clubb standards and making standards check output a little nicer

* Fixing unused variable compiler errors

* Removing ifdef GFDL option

* A bit of cleanup

* Little GPU fix

* Making the threadprivate check part of the standards, little script improvements, and adding more code to the standards check and also fixing it

* Adding missed cmake files

* Improving various subroutine edits
</comment><date>2026-04-06 14:02:51 -0500</date><id>1e25b23661f4235b8a0484bf76bc542cc1ab5f6d</id><msg>Standards fix 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/tests/test_call_tree_new_tsdadg.py</affectedPath><affectedPath>clubb_python_api/f2py_fortran_wrappers/numerical_check_wrapper.F90</affectedPath><affectedPath>clubb_python_api/clubb_python/CLUBB_core/skx_module.py</affectedPath><affectedPath>clubb_python_api/clubb_python/derived_types/pdf_params.py</affectedPath><commitId>14926dd026f178cacec4336a6389e3c59c2eb4d4</commitId><timestamp>1775506956000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Clubb f2py (#1274)

* Initial python clubb driver. Currently BFB for bomex. This is using a hugely simplified clubb_driver currently.

* Fixes

* Making work with cmake, and generalizing for more cases to work (arm, bomex, wangara tested and correct)

* Lots of new interfaces, not all complete though.

* Bit better structure and read grid_class.py

* Improvements, mainly to pdf_closure stack

* Making UDTs handled more correctly - lots of python interfaces were missing them as aguements, which is needed for pushing/pulling

* Better pdf_params (implicit too) python type

* Various cleanup and simplifications

* Fixing up argument list orders

* Breakup up clubb driver and making real radiation call

* Improving run_bindiff script

* Small improvements

* Folder restructuring

* Fixing sclr/edsclr code

* Small fixes

* Better output directory config and python vs fortran driver test script

* Various small improvements to run scripts and dash app

* Improvements to sclr/edsclr/hydromet handling using a _transport variable. Most cases (3/8) in run_python_vs_fortran_cases.py matching now with multiple columns.

* Various cleanup

* Various improvements and cleanup

* Sync f2py branch with master radiation changes

* Fixing things after merge conflict

* Commenting run_bindiff_all better

* Small changes and rough draft of README

* Improvements to various things

* Various improvements and adding a python converted advance_clubb_core for fun

* Adding more apis for missed things and a nice script which checks for missed things

* Stuctural changes and better READMEs

* Little fixes

* Aligning inouts/outs

* Renaming jenkins test

* Adding script

* Little tweaks

* Small updates

* Better readme and api diagram

* Better readme and api diagram again

* Adding clubb_jax directory, just a copy of the python driver right now with some instructions/tips for the conversion process

* Final little changes to readme and renaming various things
</comment><date>2026-04-06 15:22:36 -0500</date><id>14926dd026f178cacec4336a6389e3c59c2eb4d4</id><msg>Clubb f2py 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</comment><date>2026-04-06 17:30:01 -0500</date><id>89a78e3c137f74f6b8ed0c02875651646e6b0fd8</id><msg>Added blank line to trigger git update scripts</msg><path><editType>edit</editType><file>src/Lapack/CMakeLists.txt</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>Changes_M2005</affectedPath><commitId>9d534983ad611d90632f67b0e85b7bf738786c58</commitId><timestamp>1775514643000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Removed blank line to trigger git update scripts
</comment><date>2026-04-06 17:30:43 -0500</date><id>9d534983ad611d90632f67b0e85b7bf738786c58</id><msg>Removed blank line to trigger git update scripts</msg><path><editType>edit</editType><file>Changes_M2005</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>src/SILHS/CMakeLists.txt</affectedPath><commitId>ea158fd73790b07ad91600595adf0a10f0bccd04</commitId><timestamp>1775514734000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Add blank line to trigger git update scripts
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</comment><date>2026-04-06 17:33:08 -0500</date><id>170ad3f0b10539e37efd2f19c76f51b6bec3a255</id><msg>Add blank line to trigger git update scripts</msg><path><editType>edit</editType><file>input/stats/README</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>input/tunable_parameters/configurable_model_flags.in</affectedPath><commitId>8759dedaf6cd411a4d4943c3d8525b022ca00986</commitId><timestamp>1775514902000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Add blank line to trigger git update scripts
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* Adding BFB test with varying flags

* Space diff

* Script fix

* Space diff

* Removing output .gitignore, we don't need it and it's annoying
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* Making matrix solve checks also trigger if l_implemented is true so that they always are done in CAM, regardless of debug level

* Reworking rcond flag in advance_windm

* Updating l_implemented flag comments

* Adding printouts to make clear where the NaN are (if any) in the soln vector.
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</comment><date>2026-03-22 00:56:32 -0500</date><id>9f2b1e6c9370a897e1da1320521fbc27baf6ff31</id><msg>GPUizing most of radiation code</msg><path><editType>edit</editType><file>src/CLUBB_core/interpolation.F90</file></path><path><editType>edit</editType><file>src/Radiation/rad_lwsw_module.F90</file></path><path><editType>edit</editType><file>src/Radiation/radiation_module.F90</file></path><path><editType>edit</editType><file>src/Radiation/bugsrad_driver.F90</file></path><path><editType>edit</editType><file>src/Radiation/radiation_variables_module.F90</file></path><path><editType>edit</editType><file>src/Radiation/soil_vegetation.F90</file></path><path><editType>edit</editType><file>src/clubb_driver.F90</file></path><path><editType>edit</editType><file>src/Radiation/simple_rad_module.F90</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>src/Radiation/radiation_module.F90</affectedPath><commitId>149e61f9bab26c5cb4518fd7bada9b1f4064482e</commitId><timestamp>1774236539000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/huebler</absoluteUrl><fullName>Gunther Huebler</fullName></author><authorEmail>huebler@uwm.edu</authorEmail><comment>Fixing multicol radiation stats bug.
</comment><date>2026-03-22 22:28:59 -0500</date><id>149e61f9bab26c5cb4518fd7bada9b1f4064482e</id><msg>Fixing multicol radiation stats bug.</msg><path><editType>edit</editType><file>src/Radiation/radiation_module.F90</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>dash_app/run_tab/callbacks_runs.py</affectedPath><affectedPath>dash_app/run_tab/runtime.py</affectedPath><affectedPath>dash_app/run_tab/layout.py</affectedPath><commitId>0fc97f413d522aabb24db8c4a289aa5e5471256d</commitId><timestamp>1774237949000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/huebler</absoluteUrl><fullName>Gunther Huebler</fullName></author><authorEmail>huebler@uwm.edu</authorEmail><comment>Adding max tasks option to dash app
</comment><date>2026-03-22 22:52:29 -0500</date><id>0fc97f413d522aabb24db8c4a289aa5e5471256d</id><msg>Adding max tasks option to dash app</msg><path><editType>edit</editType><file>dash_app/run_tab/layout.py</file></path><path><editType>edit</editType><file>dash_app/run_tab/callbacks_runs.py</file></path><path><editType>edit</editType><file>dash_app/run_tab/runtime.py</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>src/generalized_grid_test.F90</affectedPath><commitId>d9d887857da333c2c683aad09311ffcdb2d54440</commitId><timestamp>1774239145000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/huebler</absoluteUrl><fullName>Gunther Huebler</fullName></author><authorEmail>huebler@uwm.edu</authorEmail><comment>Increasing tolerance for check_flipped_results - this is used in the generalized_grid_test when we allow the matrices to be solved in different vertical modes
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</comment><date>2026-03-18 20:15:01 -0500</date><id>d3c5a22e8d71e7224d34ffe7c7d2276679df7492</id><msg>Now that the adg1_ routines prevent below threshold wp2 and xp2 values, we also need these max statements in this unit test too</msg><path><editType>edit</editType><file>src/G_unit_test_types/spurious_source_test.F90</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>run_scripts/run_bindiff_all.py</affectedPath><commitId>d20fd1daad5e5d921607794e258bfde151fd3c89</commitId><timestamp>1773884674000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/huebler</absoluteUrl><fullName>Gunther Huebler</fullName></author><authorEmail>huebler@uwm.edu</authorEmail><comment>Previous commit (49bd72c6b6ee57f27c7694b25facd1b0eb91bd09) fixed a stats bug that caused parameter names to not be stored in the netcdf file - so now run_bindiff_all.py has to ignore those. Fixed by ignoring all non-numeric variables.
</comment><date>2026-03-18 20:44:34 -0500</date><id>d20fd1daad5e5d921607794e258bfde151fd3c89</id><msg>Previous commit (49bd72c6b6ee57f27c7694b25facd1b0eb91bd09) fixed a stats bug that caused parameter names to not be stored in the netcdf file - so now run_bindiff_all.py has to ignore those. Fixed by ignoring all non-numeric variables.</msg><path><editType>edit</editType><file>run_scripts/run_bindiff_all.py</file></path></item><kind>git</kind></changeSet><culprit><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/huebler</absoluteUrl><fullName>Gunther Huebler</fullName></culprit><inProgress>false</inProgress><nextBuild><number>27</number><url>http://carson.math.uwm.edu/jenkins/job/clubb_plot_solver_compare/27/</url></nextBuild><previousBuild><number>25</number><url>http://carson.math.uwm.edu/jenkins/job/clubb_plot_solver_compare/25/</url></previousBuild></build><build _class='org.jenkinsci.plugins.workflow.job.WorkflowRun'><action _class='hudson.model.CauseAction'><cause _class='hudson.model.Cause$UserIdCause'><shortDescription>Started by user Gunther Huebler</shortDescription><userId>huebler</userId><userName>Gunther Huebler</userName></cause></action><action _class='org.jenkinsci.plugins.workflow.libs.LibrariesAction'></action><action></action><action></action><action _class='hudson.plugins.git.util.BuildData'><buildsByBranchName><refsremotesoriginmaster _class='hudson.plugins.git.util.Build'><buildNumber>25</buildNumber><marked><SHA1>49bd72c6b6ee57f27c7694b25facd1b0eb91bd09</SHA1><branch><SHA1>49bd72c6b6ee57f27c7694b25facd1b0eb91bd09</SHA1><name>refs/remotes/origin/master</name></branch></marked><revision><SHA1>49bd72c6b6ee57f27c7694b25facd1b0eb91bd09</SHA1><branch><SHA1>49bd72c6b6ee57f27c7694b25facd1b0eb91bd09</SHA1><name>refs/remotes/origin/master</name></branch></revision></refsremotesoriginmaster></buildsByBranchName><lastBuiltRevision><SHA1>49bd72c6b6ee57f27c7694b25facd1b0eb91bd09</SHA1><branch><SHA1>49bd72c6b6ee57f27c7694b25facd1b0eb91bd09</SHA1><name>refs/remotes/origin/master</name></branch></lastBuiltRevision><remoteUrl>https://github.com/larson-group/clubb.git</remoteUrl><scmName></scmName></action><action></action><action _class='org.jenkinsci.plugins.workflow.cps.EnvActionImpl'></action><action></action><action></action><action></action><action></action><action _class='org.jenkinsci.plugins.displayurlapi.actions.RunDisplayAction'></action><action _class='org.jenkinsci.plugins.pipeline.modeldefinition.actions.RestartDeclarativePipelineAction'></action><action></action><action _class='org.jenkinsci.plugins.workflow.job.views.FlowGraphAction'></action><action></action><action></action><action></action><building>false</building><displayName>#25</displayName><duration>690572</duration><estimatedDuration>603251</estimatedDuration><fullDisplayName>clubb_plot_solver_compare #25</fullDisplayName><id>25</id><keepLog>false</keepLog><number>25</number><queueId>2264</queueId><result>SUCCESS</result><timestamp>1773878866872</timestamp><url>http://carson.math.uwm.edu/jenkins/job/clubb_plot_solver_compare/25/</url><changeSet _class='hudson.plugins.git.GitChangeSetList'><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>src/Radiation/soil_vegetation.F90</affectedPath><affectedPath>src/Radiation/bugsrad_driver.F90</affectedPath><affectedPath>src/Radiation/simple_rad_module.F90</affectedPath><affectedPath>src/Radiation/BUGSrad/variables_radiation_module.F90</affectedPath><affectedPath>src/Radiation/radiation_variables_module.F90</affectedPath><affectedPath>src/Radiation/extended_atmosphere_module.F90</affectedPath><affectedPath>src/Radiation/BUGSrad/bugs_rad.F</affectedPath><affectedPath>src/CLUBB_core/numerical_check.F90</affectedPath><affectedPath>src/soil_vegetation.F90</affectedPath><affectedPath>compile/file_list/clubb_bugsrad_files</affectedPath><affectedPath>compile/file_list/clubb_model_files</affectedPath><affectedPath>src/Radiation/CMakeLists.txt</affectedPath><affectedPath>src/Radiation/BUGSrad/driver_read.F</affectedPath><affectedPath>src/clubb_driver.F90</affectedPath><affectedPath>src/CMakeLists.txt</affectedPath><affectedPath>src/Radiation/BUGSrad/CMakeLists.txt</affectedPath><affectedPath>src/Radiation/radiation_module.F90</affectedPath><commitId>cbaf3b7cad36f5843a53f7e5ce77943ca7cc64c9</commitId><timestamp>1773867770000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Clubb radiation update (#1283)

* Compartmentalizing radiation code a bit

* More compartmentalizing

* Pushing loop into bugsrad because it makes things cleaner

* Small loop pushes

* Little cleanup

* Moving soil_veg code

* GPU fix and a little cleanup

* Missed a file to commit

* Making work with old build system

* Need zeroing routines for set_case_initial_conditions

* Adding comment explaining why advance_soil_veg is being packaged with Radiation code now
</comment><date>2026-03-18 16:02:50 -0500</date><id>cbaf3b7cad36f5843a53f7e5ce77943ca7cc64c9</id><msg>Clubb radiation update (#1283)</msg><path><editType>edit</editType><file>src/Radiation/CMakeLists.txt</file></path><path><editType>edit</editType><file>src/Radiation/radiation_module.F90</file></path><path><editType>delete</editType><file>src/Radiation/BUGSrad/variables_radiation_module.F90</file></path><path><editType>edit</editType><file>src/Radiation/extended_atmosphere_module.F90</file></path><path><editType>add</editType><file>src/Radiation/radiation_variables_module.F90</file></path><path><editType>add</editType><file>src/Radiation/soil_vegetation.F90</file></path><path><editType>edit</editType><file>src/CMakeLists.txt</file></path><path><editType>edit</editType><file>src/Radiation/simple_rad_module.F90</file></path><path><editType>edit</editType><file>src/CLUBB_core/numerical_check.F90</file></path><path><editType>edit</editType><file>src/Radiation/BUGSrad/bugs_rad.F</file></path><path><editType>edit</editType><file>compile/file_list/clubb_bugsrad_files</file></path><path><editType>edit</editType><file>compile/file_list/clubb_model_files</file></path><path><editType>edit</editType><file>src/Radiation/bugsrad_driver.F90</file></path><path><editType>edit</editType><file>src/Radiation/BUGSrad/driver_read.F</file></path><path><editType>edit</editType><file>src/Radiation/BUGSrad/CMakeLists.txt</file></path><path><editType>delete</editType><file>src/soil_vegetation.F90</file></path><path><editType>edit</editType><file>src/clubb_driver.F90</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>dash_app/plot_tab/state.py</affectedPath><affectedPath>dash_app/assets/33_run_param_rows.js</affectedPath><affectedPath>dash_app/run_tab/tab.py</affectedPath><affectedPath>dash_app/plot_tab/case_definitions.py</affectedPath><affectedPath>src/CLUBB_core/stats_netcdf.F90</affectedPath><affectedPath>dash_app/run_tab/callbacks_console.py</affectedPath><affectedPath>dash_app/tab_compare.py</affectedPath><affectedPath>dash_app/plot_tab/plot_types/registry.py</affectedPath><affectedPath>dash_app/plot_tab/plot_types/budget_plot.py</affectedPath><affectedPath>dash_app/plot_tab/plot_types/base_plot.py</affectedPath><affectedPath>dash_app/run_tab/namelist.py</affectedPath><affectedPath>dash_app/tab_run.py</affectedPath><affectedPath>dash_app/assets/11_tab_run_theme.css</affectedPath><affectedPath>dash_app/plot_tab/layout.py</affectedPath><affectedPath>dash_app/run_tab/callbacks_settings.py</affectedPath><affectedPath>dash_app/assets/31_plots_ui_resize.js</affectedPath><affectedPath>dash_app/tab_multicol.py</affectedPath><affectedPath>dash_app/plot_tab/callbacks_controls.py</affectedPath><affectedPath>dash_app/plot_tab/plot_types/shared.py</affectedPath><affectedPath>dash_app/run_tab/__init__.py</affectedPath><affectedPath>dash_app/assets/35_plots_keyboard.js</affectedPath><affectedPath>dash_app/plot_tab/callbacks_params.py</affectedPath><affectedPath>dash_app/plot_tab/plot_types/budget_groups.py</affectedPath><affectedPath>dash_app/plot_tab/__init__.py</affectedPath><affectedPath>dash_app/app.py</affectedPath><affectedPath>dash_app/assets/10_theme.css</affectedPath><affectedPath>dash_app/run_tab/runtime.py</affectedPath><affectedPath>dash_app/plot_tab/plot_types/__init__.py</affectedPath><affectedPath>dash_app/run_tab/callbacks_selection.py</affectedPath><affectedPath>dash_app/plot_tab/plot_types/profile_plot.py</affectedPath><affectedPath>dash_app/run_tab/layout.py</affectedPath><affectedPath>dash_app/plot_tab/benchmark_overlay.py</affectedPath><affectedPath>dash_app/run_tab/state.py</affectedPath><affectedPath>run_scripts/run_scm.py</affectedPath><affectedPath>dash_app/plot_tab/plot_types/subcolumn_plot.py</affectedPath><affectedPath>run_scripts/create_multi_col_params.py</affectedPath><affectedPath>dash_app/plot_tab/callbacks_grid.py</affectedPath><affectedPath>dash_app/run_tab/discovery.py</affectedPath><affectedPath>dash_app/case_definitions.py</affectedPath><affectedPath>dash_app/plot_tab/plot_types/specs.py</affectedPath><affectedPath>dash_app/assets/12_tab_plots_theme.css</affectedPath><affectedPath>dash_app/plot_tab/tab.py</affectedPath><affectedPath>dash_app/assets/32_plots_constant_param_rows.js</affectedPath><affectedPath>dash_app/run_tab/callbacks_runs.py</affectedPath><affectedPath>dash_app/assets/34_run_param_clientside.js</affectedPath><affectedPath>dash_app/plot_tab/callbacks_case.py</affectedPath><affectedPath>dash_app/plot_tab/plot_types/timeseries_plot.py</affectedPath><affectedPath>dash_app/plot_tab/plot_types/timeheight_plot.py</affectedPath><commitId>49bd72c6b6ee57f27c7694b25facd1b0eb91bd09</commitId><timestamp>1773872129000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Dash app improvements (#1280)

* Mainly dash app improvements, but also removing unused args from stats and improving run scripts

* Small update to ui in run tab

* Improvements to make plotting faster, fixing various bugs, making things more robust, and adding more run modification fields (out_dir/dt_main/etc)

* Adding les plotting capabilities, lots of tiny improvements

* Reverting run_bindiff_all.py

* Tiny quality of life improvements - fixing port conflict, opening in browser automatically, and defaulting to the run_tab instead of requiring a first click
</comment><date>2026-03-18 17:15:29 -0500</date><id>49bd72c6b6ee57f27c7694b25facd1b0eb91bd09</id><msg>Dash app improvements 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</comment><date>2026-03-17 13:14:11 -0500</date><id>02123793194ca95295bbd90c35129faf395b9525</id><msg>Toolchain names were changed, so the references to them should've changed in the jenkins tests.</msg><path><editType>edit</editType><file>jenkins_tests/clubb_nvhpc_gpu_column_mirror_test/Jenkinsfile</file></path><path><editType>edit</editType><file>jenkins_tests/clubb_nvhpc_gpu_vs_cpu_diffness/Jenkinsfile</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>run_scripts/test_monoflux_limiter_GPU.py</affectedPath><commitId>36ca61e3203b201832c5ca74ce764fc7e97786a8</commitId><timestamp>1773771352000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/huebler</absoluteUrl><fullName>Gunther Huebler</fullName></author><authorEmail>huebler@uwm.edu</authorEmail><comment>Toolchain names were changed, so the references to them should've changed in this test too.
</comment><date>2026-03-17 13:15:52 -0500</date><id>36ca61e3203b201832c5ca74ce764fc7e97786a8</id><msg>Toolchain names were changed, so the references to them should've changed in this test too.</msg><path><editType>edit</editType><file>run_scripts/test_monoflux_limiter_GPU.py</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>src/G_unit_test_types/pdf_parameter_tests.F90</affectedPath><affectedPath>src/G_unit_tests.F90</affectedPath><affectedPath>src/CLUBB_core/adg1_adg2_3d_luhar_pdf.F90</affectedPath><affectedPath>src/G_unit_test_types/spurious_source_test.F90</affectedPath><commitId>c15b1d3c005fdffa76902e976acdb5db5dbde012</commitId><timestamp>1773804486000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>ADG1_w_closure consistency fix (#1282)

* G_unit_test / ADG1_w_closure fix. A recent commit (bff619bdb2836f83ac658be8b8c258d41aaa6e14) introduced a change to ADG1_ADG2_responder_params that caused an inconsistency in the pdf calculations that the G_unit tests picked up on. This corrects it, but is also BIT_CHANGING, since it changes the calculation slightly when wp2 is exactly tolerance.

* Adding test to ensure err_info is correctly set by adg1 routines when calling with bad inputs - also moving wp2 check to ADG1_w_closure because it makes more sense there
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* Fixing error test by making the code check for NaNs in all solver cases - before it was only checking in Lapack. Also making a python version of the test and updating jenkins script to use it.

* A little cleanup

* Adding more comments and making a little data structure for the tests
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* Making compiler lookup a little more general, this allows us to compile on Derecho too. Now it uses LMOD_FAMILY_COMPILER by default, then tries FC as a backup, and has a map of names so that things like intel/intel-oneapi map to the same things. Also adding a toolchain for the cray compiler (cce).

* Removing old toolchains
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* Making compiling with gptl more robust. Before it could only compile when we used openmp too, but that's been worked around, and now it can compile on nvhpc too thanks to the static and disabled-shared flags that were added. Also works with gcc now.

* Adding comment

* Small cleanup and a better comment
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_class='hudson.plugins.git.GitChangeSet'><affectedPath>jenkins_tests/clubb_plot_nvhpc_gpu_vs_cpu/Jenkinsfile</affectedPath><affectedPath>src/CLUBB_core/pdf_closure_module.F90</affectedPath><affectedPath>src/G_unit_test_types/pdf_parameter_tests.F90</affectedPath><affectedPath>src/CLUBB_core/adg1_adg2_3d_luhar_pdf.F90</affectedPath><affectedPath>run_scripts/run_scm_all.py</affectedPath><affectedPath>jenkins_tests/clubb_nvhpc_gpu_column_mirror_test/Jenkinsfile</affectedPath><affectedPath>jenkins_tests/clubb_driver_test/Jenkinsfile</affectedPath><commitId>bff619bdb2836f83ac658be8b8c258d41aaa6e14</commitId><timestamp>1773630552000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Stability fix (#1276)

* Adding multiprocesses to run_scm_all.py, making the GPU jenkins tests only use 1 thread though, otherwise the different processes will fight for GPU usage

* Making the if statement in ADG1_ADG2_responder_params use a strict inequality - this was causing numerical issues when fields were close to tolerance. This will be slightly BIT_CHANGING for most cases.

* Adding comments to run_scm_all.py and removing the if-case in ADG1_ADG2_responder_params in favor of an explicit error check

* Changing nprocs to nproc and updating jenkins tests
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</comment><date>2026-03-13 18:47:34 -0500</date><id>e589c52f0d3f735c8a1f4206fce09e7e4b0f7578</id><msg>Added blank line</msg><path><editType>edit</editType><file>src/CLUBB_core/calendar.F90</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>src/CLUBB_core/LY93_pdf.F90</affectedPath><commitId>a1dd370ac9a7d03023289b7025c7e30eca0184d1</commitId><timestamp>1773453517000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Remove Id tag from LY93_pdf.F90 in order to trigger git update scripts

larson-group/sys_admin#848
</comment><date>2026-03-13 20:58:37 -0500</date><id>a1dd370ac9a7d03023289b7025c7e30eca0184d1</id><msg>Remove Id tag from LY93_pdf.F90 in order to trigger git update scripts</msg><path><editType>edit</editType><file>src/CLUBB_core/LY93_pdf.F90</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>src/SILHS/est_kessler_microphys_module.F90</affectedPath><commitId>02e8b46e176338e0beae7ab6fe3bb4ab2c11a7f2</commitId><timestamp>1773453655000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Remove unnecessary comments from est_kessler_microphys_module

in order to trigger git update scripts.  larson-group/sys_admin#848
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* Setting our solvers to use the new LU solvers by default instead of Lapack. This is BIT_CHANGING, but not answer changing.

* Also changing default in code
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</comment><date>2026-03-02 14:38:56 -0600</date><id>967e4c00c3609874bf0c9eecbd93781724252ce9</id><msg>Force-sync README to match SAM</msg><path><editType>edit</editType><file>src/Microphys/Morrison_microphys/README.MICRO_M2005</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>src/CLUBB_core/CMakeLists.txt</affectedPath><commitId>6340e0a542105e3612b9709f3192cdf3b88a55ec</commitId><timestamp>1772502018000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Add blank line to test python scripts

Testing python scripts from crontab
</comment><date>2026-03-02 19:40:18 -0600</date><id>6340e0a542105e3612b9709f3192cdf3b88a55ec</id><msg>Add blank line to test python scripts</msg><path><editType>edit</editType><file>src/CLUBB_core/CMakeLists.txt</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>Changes_M2005</affectedPath><commitId>8cb40c6a054a81383415a640c91d5effcc187d28</commitId><timestamp>1772502096000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Added blank line to test python update scripts

Testing python update scripts from crontab
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* First commit in removing legacy stats

* Removing accidentally added plots

* Updates to fix and improve various things. Removing grads handling from lots of test scripts

* Reverting old scripts to leave untouched

* More reversions

* More reversions

* Simplifications

* More reversions

* Simplifications

* Simplifications

* Simplification

* Simplification

* Simplification

* Simplification

* Small pyplotgen improvement

* Reverting case defs to use old scripts, removing need to unify old ones
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ectedPath><affectedPath>src/input_interpret.F90</affectedPath><affectedPath>src/Input_fields/input_fields.F90</affectedPath><affectedPath>src/clubb_thread_test.F90</affectedPath><affectedPath>src/soil_vegetation.F90</affectedPath><affectedPath>run_scripts/run_restart_test.py</affectedPath><affectedPath>run_scripts/run_scm.py</affectedPath><affectedPath>src/CLUBB_core/stats_sfc_module.F90</affectedPath><affectedPath>run_scripts/run_bindiff_all.py</affectedPath><affectedPath>run_scripts/run_thread_test.py</affectedPath><affectedPath>src/sounding.F90</affectedPath><affectedPath>jenkins_tests/clubb_nvhpc_gpu_multi_col_avg_test/Jenkinsfile</affectedPath><affectedPath>src/Microphys/silhs_category_variance_module.F90</affectedPath><affectedPath>run_scripts/test_monoflux_limiter_GPU.py</affectedPath><affectedPath>src/CLUBB_core/stats_zt_module.F90</affectedPath><affectedPath>src/CMakeLists.txt</affectedPath><affectedPath>src/error.F90</affectedPath><commitId>3d4d74a0d0295936253484c54693f9eac230f604</commitId><timestamp>1771386880000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>New stats system  (#1270)

* Initial commit for the new stats system

* Adding helper scripts

* Fixes and another script

* Updates

* Improvements

* Fixed bug in all_stats.in

* Updates

* Adding dash app

* Updates, also including new dash app since I'm finding it quite useful

* Improvements/fixes and adding missing variable to all_stats.in

* Updates

* Moving wp2sclrp, wpsclrp2, wpsclrprtp, and wpsclrpthlp to the zt netcdf output file, since those are zt variables. Also adding a missing variable, rcm_in_cloud, to all_stats.in and correcting a missing comma bug. This is technically BIT_CHANGING because the variables are moving files, but the stored data is identical from 1:nzt - the nzm level just had garbage for those variables and is now gone.

* Updates

* Updates

* The big stats pull, only new stats remains now

* Some cleanup

* Lot's of core rework, new index caching system speeds things up

* Missed files

* Small improvements a bug fix to the grid remapped output

* Fixing up logic and ordering things a bit better

* Little improvements

* Cleanup and simplications to new stats core

* Little improvements, mostly to dash app

* Mostly cleanup

* Making GPU code work

* Making more scripts work

* Fixing line lengths

* Bug fixes

* Bug fixes

* Bug fixes

* Bug fixes

* Bug fixes and script updates

* Jenkins script update

* Jenkins script update

* Jenkins script update

* Jenkins script update

* Jenkins script update

* Jenkins script update

* Script update

* Script update

* Script update

* Script update

* Script update

* Script update

* Script update

* Test update

* Jenkins script update

* Test update

* Fixing bug

* Fixing bug

* Fixing up comments

* Small fixes

* Jenkins script update

* CMake update

* Little fix for cmake

* Jenkins script update

* Jenkins script updateS

* Cmake update

* Jenkins script update

* Jenkins script update

* Jenkins script updates

* Adding new stats input

* Small fixes

* Fixing old compile scripts

* Jenkins script updates

* Jenkins script updates

* Jenkins script updates

* Little fixes

* Little cmake fix

* Little jenkins fix

* Mono flux test update and _api renamings

* Small Jenkins fix

* Adding missing comments back

* Even more comments

* stats updates

* Even more comments

* Various small improvements

* Removing test statsd

* Adding some things back to _api and adding structure explaining comment in stats files.

* Many more comments

* Removing plan file

* Spelling fix
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trad coriolis (#1267)

* Updating the clubb core and silhs version files

* Fixing bug. qclvar copying is handled by the api, but we were deleting it with an unstructured data statement. I added this due as a fix before thinking qclvar was a local variable, which happened because I mixed up the CLUBB_CAM and CLUBBND_CAM flags. https://github.com/larson-group/cam/issues/175

* Fixing GPU bug. There is a vertical dependency with wpxp. This is what was breaking the ECT test, see larson-group/cam#175

* Moving pdf_params copying to copyin. This is the data structure that contains pointers, and these pointers will be different on the host and device, so it is bad in theory to copy the structure back to the CPU as it might overwrite cpu memory pointers with gpu memory pointers. In practice though I've seen no problems caused by this, I'm just making this commit preemptively, and it has already been tested with the ECT test.

* Moving PosInf to clubb_model_settings.F90

* Updating the clubb core and silhs version files

* Add flags for the Coriolis terms.

* Pass fcory from api module into advance module

* Implement the traditional Coriolis terms

* Implement the nontraditional Coriolis terms

* Add stats variables for the Coriolis terms

* Compute Coriolis parameters from namelist latitude

* Create the coriolis_test case

* Tune the coriolis_test case. However, oscillation frequency is too slow

* Correct a coefficient in Coriolis. "coriolis_test" matches analytical

* Update advance_clubb_core_module.F90

Rename fcory as fcor_y and add description

* Update advance_wp2_wp3_module.F90

Rename fcory as fcor_y and add description

* Update advance_xm_wpxp_module.F90

Rename fcory as fcor_y and add description

* Update advance_xp2_xpyp_module.F90

Rename fcory as fcor_y and add description

* Update clubb_api_module.F90

Rename fcory as fcor_y and add description

* Update spurious_source_test.F90

Rename fcory as fcor_y and add description

* Update clubb_driver.F90

Rename fcor as fcor_y and add description.
Also, add description for the coriolis_test

* Update generalized_grid_test.F90

Rename fcory as fcor_y and add description.

* Update coriolis_test_model.in

Add description for the Coriolis test case

* Stablize the cgils_s6 case with smaller time step

* Create the ekman case

* Tune the ekman case to match LES

* Compute wp2up with PDF and pass along with wp2thvp

* Implement the nontraditional Coriolis term for wp3

* Fine-tune parameters for the ekman case

* Create the atex_long case

* Retune ekman case with l_vary_convect_depth = .true.

* Fine-tune the atex_long case

* Add atex_long case to pyplotgen

* Fine-tune atex_long case with less radical changes

* Updating the clubb core and silhs version files

* Small bug fix in the wp2up flip and adding new files to the cmakelist

* Renmaing, moving some files, and reverting change to cgils_s6 timestep

* Adding new flags to flag test file

* Updating comment for fcor_y calculation explanation

* Removing accidentally added file

---------

Co-authored-by: pickett &lt;larsongroupgithub@gmail.com&gt;
Co-authored-by: Hing Ong &lt;hing.ong@anl.gov&gt;
Co-authored-by: Hing Ong &lt;36782452+HingOng@users.noreply.github.com&gt;
</comment><date>2026-01-08 14:23:44 -0600</date><id>4902a5ccf6c0da1bf588ea853aaadbc9a776dfa2</id><msg>Non trad coriolis 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_class='hudson.plugins.git.GitChangeSet'><affectedPath>src/CLUBB_core/fill_holes.F90</affectedPath><affectedPath>src/CLUBB_core/advance_clubb_core_module.F90</affectedPath><affectedPath>src/CLUBB_core/grid_class.F90</affectedPath><affectedPath>run_scripts/run_bindiff_w_flags_config_core_flags.json</affectedPath><affectedPath>input/case_setups/arm_97_model.in</affectedPath><affectedPath>input/case_setups/arm_97_edsclr_sounding.in</affectedPath><commitId>418c202a9b0512fc8c4f421918cc978164db852d</commitId><timestamp>1766005108000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>Fixes for fill_holes and edsclr code (#1266)

* Fixing bugs in new hole fillers that caused error when ran in descending mode, the issue was that dz is negative in descending mode, so we need abs() around it when calculating the normalized mass. Also fixing a related bug in the way edsclr code calls the hole filler - it was not using the generalized bounds. Also removing the ifdef in favor of normal ifs

* Copying the rtm and thm values from arm_97_sounding.in to the edsclr_sounding file. This still allows arm_97 to catch the bugs we want it to.
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reverse matrix test (#1265)

* Making new flag l_force_descending_solves that forces us to use descending solves. Having it true keeps results BFB between ascending and descending when using -O0.

* renaming test

* Moving flag

* test fix

* test fix

* test fix

* Removing iteration limit on script and adding test error

* Removing test error, it was correctly caught

* Adding max statement to aid in single precision runs and removing accidentally commited file.
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 - Changes to this file are supposed to be made in sam_clubb
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* Adding multiprocesses to run_scm_all.py, making the GPU jenkins tests only use 1 thread though, otherwise the different processes will fight for GPU usage

* Making the if statement in ADG1_ADG2_responder_params use a strict inequality - this was causing numerical issues when fields were close to tolerance. This will be slightly BIT_CHANGING for most cases.

* Adding comments to run_scm_all.py and removing the if-case in ADG1_ADG2_responder_params in favor of an explicit error check

* Changing nprocs to nproc and updating jenkins tests
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 - Changes to this file are supposed to be made in sam_clubb
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 - Changes to this file are supposed to be made in sam_clubb
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* Adding multiprocesses to run_scm_all.py, making the GPU jenkins tests only use 1 thread though, otherwise the different processes will fight for GPU usage

* Making the if statement in ADG1_ADG2_responder_params use a strict inequality - this was causing numerical issues when fields were close to tolerance. This will be slightly BIT_CHANGING for most cases.

* Adding comments to run_scm_all.py and removing the if-case in ADG1_ADG2_responder_params in favor of an explicit error check

* Changing nprocs to nproc and updating jenkins tests
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