Console Output
+ source /etc/profile.d/larson-group.sh
++ export GIT_EDITOR=vi
++ GIT_EDITOR=vi
++ export SVN_EDITOR=vi
++ SVN_EDITOR=vi
++ export OMP_STACKSIZE=1048579
++ OMP_STACKSIZE=1048579
++ export LMOD_ROOT=/opt/lmod/
++ LMOD_ROOT=/opt/lmod/
++ . /opt/lmod//lmod/lmod/init/profile
+++ '[' -z '' ']'
+++ LMOD_ALLOW_ROOT_USE=yes
+++ '[' -n '' ']'
+++ '[' yes '!=' yes ']'
+++ '[' -z '' ']'
+++ export MODULEPATH_ROOT=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles
+++ MODULEPATH_ROOT=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles
+++ export USER=jenkins
+++ USER=jenkins
++++ uname
+++ export LMOD_sys=Linux
+++ LMOD_sys=Linux
+++ '[' -z '' ']'
+++ '[' -f /etc/lmod/.modulespath ']'
+++ LMOD_MODULEPATH_INIT=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/init/.modulespath
+++ '[' -f /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/init/.modulespath ']'
++++ /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/libexec/addto --append MODULEPATH /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Linux /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Core
+++ export MODULEPATH=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Linux:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Core
+++ MODULEPATH=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Linux:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Core
++++ /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/libexec/addto --append MODULEPATH /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/modulefiles/Core
+++ export MODULEPATH=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Linux:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Core:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/modulefiles/Core
+++ MODULEPATH=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Linux:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Core:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/modulefiles/Core
+++ '[' -n '' ']'
+++ export BASH_ENV=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/init/bash
+++ BASH_ENV=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/init/bash
+++ '[' -z '' ']'
+++ export MANPATH=:
+++ MANPATH=:
++++ /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/libexec/addto MANPATH /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/share/man
+++ export MANPATH=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/share/man:
+++ MANPATH=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/share/man:
+++ findExec READLINK_CMD /usr/bin/readlink readlink
+++ Nm=READLINK_CMD
+++ confPath=/usr/bin/readlink
+++ execNm=readlink
+++ eval READLINK_CMD=/usr/bin/readlink
++++ READLINK_CMD=/usr/bin/readlink
+++ '[' '!' -x /usr/bin/readlink ']'
+++ unset Nm confPath execNm
+++ findExec PS_CMD /usr/bin/ps ps
+++ Nm=PS_CMD
+++ confPath=/usr/bin/ps
+++ execNm=ps
+++ eval PS_CMD=/usr/bin/ps
++++ PS_CMD=/usr/bin/ps
+++ '[' '!' -x /usr/bin/ps ']'
+++ unset Nm confPath execNm
+++ findExec EXPR_CMD /usr/bin/expr expr
+++ Nm=EXPR_CMD
+++ confPath=/usr/bin/expr
+++ execNm=expr
+++ eval EXPR_CMD=/usr/bin/expr
++++ EXPR_CMD=/usr/bin/expr
+++ '[' '!' -x /usr/bin/expr ']'
+++ unset Nm confPath execNm
+++ findExec BASENAME_CMD /usr/bin/basename basename
+++ Nm=BASENAME_CMD
+++ confPath=/usr/bin/basename
+++ execNm=basename
+++ eval BASENAME_CMD=/usr/bin/basename
++++ BASENAME_CMD=/usr/bin/basename
+++ '[' '!' -x /usr/bin/basename ']'
+++ unset Nm confPath execNm
+++ unset -f findExec
+++ '[' -f /proc/1370407/exe ']'
++++ /usr/bin/readlink /proc/1370407/exe
+++ my_shell=/usr/bin/bash
++++ /usr/bin/expr /usr/bin/bash : '-*\(.*\)'
+++ my_shell=/usr/bin/bash
++++ /usr/bin/basename /usr/bin/bash
+++ my_shell=bash
+++ case ${my_shell} in
+++ '[' -f /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/init/bash ']'
+++ . /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/init/bash
++++ '[' -z '' ']'
++++ case "$-" in
++++ __lmod_vx=x
++++ '[' -n x ']'
++++ set +x
Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for this output (/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/init/bash)
Shell debugging restarted
++++ unset __lmod_vx
+++ unset my_shell PS_CMD EXPR_CMD BASENAME_CMD MODULEPATH_INIT LMOD_ALLOW_ROOT_USE READLINK_CMD
+++ find /usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core -print -quit
++ export MODULEPATH=/usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core
++ MODULEPATH=/usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core
+ module load gcc netcdf-fortran
+ '[' -z '' ']'
+ case "$-" in
+ __lmod_sh_dbg=x
+ '[' -n x ']'
+ set +x
Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
Lmod Warning:
-------------------------------------------------------------------------------
The following dependent module(s) are not currently loaded:
gcc-runtime/13.1.0-wiuv7wc (required by: mpich/4.2.1, hdf5/1.14.3-cb5lzz7,
netcdf-c/4.9.2, netcdf-fortran/4.5.3), glibc/2.35-tdr5czg (required by:
mpich/4.2.1, hdf5/1.14.3-cb5lzz7, netcdf-c/4.9.2, netcdf-fortran/4.5.3)
-------------------------------------------------------------------------------
Shell debugging restarted
+ unset __lmod_sh_dbg
+ return 0
+ bash tests/run_pytests.sh -unit --junitxml=/home/jenkins/workspace/clubb_python/output/tests/pytests/unit.xml --durations=10
============================= test session starts ==============================
platform linux -- Python 3.12.3, pytest-9.1.1, pluggy-1.6.0
rootdir: /home/jenkins/workspace/clubb_python
collected 273 items
utilities/pytests/test_clubb_settings_resolution.py .......... [ 3%]
utilities/pytests/test_create_case_namelist.py ......................... [ 12%]
............ [ 17%]
utilities/pytests/test_create_multi_col_params.py ... [ 18%]
utilities/pytests/test_output_paths.py ..... [ 20%]
utilities/pytests/test_run_script_arguments.py .............. [ 25%]
utilities/pytests/test_settings_rules.py ................. [ 31%]
utilities/pytests/test_stats_json_to_namelist.py ......... [ 34%]
utilities/pytests/test_time_clubb.py ....................... [ 43%]
utilities/pytests/test_timing_profiles.py ....... [ 45%]
tuner/pytests/test_adam_baselines.py ............ [ 50%]
tuner/pytests/test_parameter_ranges.py ...... [ 52%]
tuner/pytests/test_presets.py ........... [ 56%]
tuner/pytests/test_tuning_strategy.py .................................. [ 68%]
........ [ 71%]
tuner/pytests/test_workspaces.py ...... [ 73%]
tests/pytests/test_bindiff_report.py .... [ 75%]
tests/pytests/test_column_mirror.py .................................... [ 88%]
..................... [ 96%]
tests/pytests/test_compile_install_aliases.py .. [ 97%]
tests/pytests/test_jax_compare_forwarding.py ...... [ 99%]
tests/pytests/test_run_clubb_conv_test.py .. [100%]
=============================== warnings summary ===============================
tests/pytests/test_bindiff_report.py::test_json_reports_paths_logs_and_exclusive_variable_categories
tests/pytests/test_bindiff_report.py::test_json_reports_paths_logs_and_exclusive_variable_categories
/home/jenkins/workspace/clubb_python/tests/pytests/test_bindiff_report.py:37: DeprecationWarning: Setting the shape on a NumPy array has been deprecated in NumPy 2.5.
As an alternative, you can create a new view using np.reshape (with copy=False if needed).
nc.createVariable("shape", "f8", ("time", "col"))[:] = np.ones((2, 2 if right else 1))
tests/pytests/test_column_mirror.py: 28 warnings
/home/jenkins/workspace/clubb_python/.venv-python/lib/python3.12/site-packages/numpy/ma/core.py:3511: DeprecationWarning: Setting the shape on a NumPy array has been deprecated in NumPy 2.5.
As an alternative, you can create a new view using np.reshape (with copy=False if needed).
super(MaskedArray, type(self)).shape.__set__(self, shape)
tests/pytests/test_column_mirror.py::test_runner_detects_first_column_state_leak[separator0-True]
tests/pytests/test_column_mirror.py::test_runner_detects_first_column_state_leak[separator1-True]
tests/pytests/test_column_mirror.py::test_diff_copies_align_raw_values_and_parameters_without_editing_originals
tests/pytests/test_column_mirror.py::test_diff_copies_align_raw_values_and_parameters_without_editing_originals
tests/pytests/test_column_mirror.py::test_diff_copies_align_raw_values_and_parameters_without_editing_originals
tests/pytests/test_column_mirror.py::test_saved_output_comparison_and_tolerance
tests/pytests/test_column_mirror.py::test_saved_output_comparison_and_tolerance
/home/jenkins/workspace/clubb_python/tests/check_mirrored_multi_col_output.py:197: DeprecationWarning: Setting the shape on a NumPy array has been deprecated in NumPy 2.5.
As an alternative, you can create a new view using np.reshape (with copy=False if needed).
var[:] = np.flip(var[:], axis=var.dimensions.index("col"))
tests/pytests/test_column_mirror.py::test_diff_copies_align_raw_values_and_parameters_without_editing_originals
/home/jenkins/workspace/clubb_python/tests/pytests/test_column_mirror.py:131: DeprecationWarning: Setting the shape on a NumPy array has been deprecated in NumPy 2.5.
As an alternative, you can create a new view using np.reshape (with copy=False if needed).
ds.createVariable('clubb_params', 'f8', ('param', 'col'))[:] = [[.8, .5, .2]]
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
- generated xml file: /home/jenkins/workspace/clubb_python/output/tests/pytests/unit.xml -
============================= slowest 10 durations =============================
1.41s call tests/pytests/test_column_mirror.py::test_incremental_build_reuses_objects_and_picks_up_source_changes
0.85s call utilities/pytests/test_time_clubb.py::test_continue_on_error_completes_remaining_sweep_points
0.80s call utilities/pytests/test_time_clubb.py::test_live_results_have_workload_metadata_before_benchmark_finishes
0.59s call utilities/pytests/test_time_clubb.py::test_failure_preserves_completed_and_failed_points
0.56s call tests/pytests/test_column_mirror.py::test_runner_detects_first_column_state_leak[separator1-True]
0.55s call tests/pytests/test_column_mirror.py::test_runner_detects_first_column_state_leak[separator0-True]
0.54s call utilities/pytests/test_time_clubb.py::test_warmups_are_aggregated_and_dash_ignores_them
0.53s call tests/pytests/test_column_mirror.py::test_failed_run_does_not_compare_stale_output
0.47s call utilities/pytests/test_time_clubb.py::test_failure_console_includes_namelist_error_without_launching_model
0.41s call utilities/pytests/test_time_clubb.py::test_fake_runner_is_concurrent_and_writes_isolated_csv_rows
======================= 273 passed, 38 warnings in 9.77s =======================
