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Started by an SCM change
Obtained jenkins_tests/clubb_generalized_vert_grid_host_flags/Jenkinsfile from git https://github.com/larson-group/clubb.git
[Pipeline] Start of Pipeline
[Pipeline] node
Running on mitch in /home/jenkins/workspace/clubb_generalized_vert_grid_host_flags
[Pipeline] {
[Pipeline] stage
[Pipeline] { (Declarative: Checkout SCM)
[Pipeline] checkout
The recommended git tool is: git
No credentials specified
Cloning the remote Git repository
Cloning repository https://github.com/larson-group/clubb.git
 > git init /home/jenkins/workspace/clubb_generalized_vert_grid_host_flags # timeout=10
Fetching upstream changes from https://github.com/larson-group/clubb.git
 > git --version # timeout=10
 > git --version # 'git version 2.34.1'
 > git fetch --tags --force --progress -- https://github.com/larson-group/clubb.git +refs/heads/*:refs/remotes/origin/* # timeout=10
Avoid second fetch
Checking out Revision 034f61908b84f2574a06cc7da3db70d50696e69d (refs/remotes/origin/master)
 > git config remote.origin.url https://github.com/larson-group/clubb.git # timeout=10
 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
 > git rev-parse refs/remotes/origin/master^{commit} # timeout=10
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 034f61908b84f2574a06cc7da3db70d50696e69d # timeout=10
Commit message: "The old mixing length calculation seems to be making dycoms2_rf02 fail when using the bicgstab solver. This case was always unstable with bicgstab, so it seemed more like luck before that it was passing. This change just removes the failed output data to prevent pyplotgen from crashing"
 > git rev-list --no-walk 765ae7c30cda88e01b27cd1ee4277d54e4fcb752 # timeout=10
[Pipeline] }
[Pipeline] // stage
[Pipeline] withEnv
[Pipeline] {
[Pipeline] stage
[Pipeline] { (Enable Model Flag for Test)
[Pipeline] sh
+ sed -i 's:l_test_grid_generalization.*:l_test_grid_generalization = .true.:g' src/CLUBB_core/model_flags.F90
[Pipeline] sh
+ sed -i 's:l_force_descending_solves.*:l_force_descending_solves = .true.:g' src/CLUBB_core/model_flags.F90
[Pipeline] }
[Pipeline] // stage
[Pipeline] stage
[Pipeline] { (Turn Off Sponge Damping in Case Setups)
[Pipeline] sh
+ sed -i 's:thlm_sponge_damp_settings%l_sponge_damping.*:thlm_sponge_damp_settings%l_sponge_damping = .false.:g' input/case_setups/cgils_s6_model.in
[Pipeline] sh
+ sed -i 's:rtm_sponge_damp_settings%l_sponge_damping.*:rtm_sponge_damp_settings%l_sponge_damping = .false.:g' input/case_setups/cgils_s6_model.in
[Pipeline] sh
+ sed -i 's:thlm_sponge_damp_settings%l_sponge_damping.*:thlm_sponge_damp_settings%l_sponge_damping = .false.:g' input/case_setups/cgils_s11_model.in
[Pipeline] sh
+ sed -i 's:rtm_sponge_damp_settings%l_sponge_damping.*:rtm_sponge_damp_settings%l_sponge_damping = .false.:g' input/case_setups/cgils_s11_model.in
[Pipeline] sh
+ sed -i 's:thlm_sponge_damp_settings%l_sponge_damping.*:thlm_sponge_damp_settings%l_sponge_damping = .false.:g' input/case_setups/cgils_s12_model.in
[Pipeline] sh
+ sed -i 's:rtm_sponge_damp_settings%l_sponge_damping.*:rtm_sponge_damp_settings%l_sponge_damping = .false.:g' input/case_setups/cgils_s12_model.in
[Pipeline] }
[Pipeline] // stage
[Pipeline] stage
[Pipeline] { (Compile)
[Pipeline] sh
+ 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/
++ source /opt/lmod//lmod/lmod/init/bash
+++ '[' -z '' ']'
+++ case "$-" in
+++ __lmod_vx=x
+++ '[' -n x ']'
+++ set +x
Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for this output (/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-fq24mybyn2li6got2bxzk62ejh5d3p4z/lmod/lmod/init/bash)
Shell debugging restarted
+++ unset __lmod_vx
+++ find /usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core -print -quit
++ export MODULEPATH=/usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core
++ MODULEPATH=/usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core
+ module load intel netcdf-fortran
+ '[' -z '' ']'
+ case "$-" in
+ __lmod_sh_dbg=x
+ '[' -n x ']'
+ set +x
Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
Shell debugging restarted
+ unset __lmod_sh_dbg
+ return 0
+ ./compile.py -debug
-- The Fortran compiler identification is IntelLLVM 2023.2.0
-- The C compiler identification is IntelLLVM 2023.2.0
-- The CXX compiler identification is IntelLLVM 2023.2.0
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/intel-oneapi-compilers-2023.2.0-od6qbkw4h7zydnyvjahatxrprimcyseq/compiler/2023.2.0/linux/bin/ifx - skipped
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/intel-oneapi-compilers-2023.2.0-od6qbkw4h7zydnyvjahatxrprimcyseq/compiler/2023.2.0/linux/bin/icx - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/intel-oneapi-compilers-2023.2.0-od6qbkw4h7zydnyvjahatxrprimcyseq/compiler/2023.2.0/linux/bin/icpx - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Compiling with double precision
-- Performing Test NETCDF_ABI_COMPATIBLE
-- Performing Test NETCDF_ABI_COMPATIBLE - Success
-- SUCCESS: netcdf-fortran found.
--   -> Library : /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/oneapi-2023.2.0/netcdf-fortran-4.5.3-inkjvmgdy5ao7uwihl6lzsnlpstmyoyt/lib/libnetcdff.so
--   -> Modules : /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/oneapi-2023.2.0/netcdf-fortran-4.5.3-inkjvmgdy5ao7uwihl6lzsnlpstmyoyt/include
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    NetCDF_C_INCLUDE_DIR
    NetCDF_C_LIBRARY
    NetCDF_Fortran_INCLUDE_DIR
    NetCDF_Fortran_LIBRARY


-- Build files have been written to: /home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/build/intel_DEBUG_PRECdouble
Using inferred toolchain file: /home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/cmake/toolchains/linux_x86_64_intel.cmake
Setting CLUBB installation dir: /home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/build/intel_DEBUG_PRECdouble
Setting CLUBB installation dir: /home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble
about to cmnake /home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/build/intel_DEBUG_PRECdouble
Running CMake configure...
Scanning dependencies of target clubb_lapack_shared
Scanning dependencies of target clubb_lapack_double
Scanning dependencies of target scm_activation_lib
[  1%] Building Fortran object src/Lapack/Lapack_shared/CMakeFiles/clubb_lapack_shared.dir/lsame.f.o
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Scanning dependencies of target clubb_lapack_single
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/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/src/SILHS/silhs_importance_sample_module.F90(901): warning #5462: Global name too long, shortened from: silhs_importance_sample_moduleeight_cluster_allocation_mp_NUM_CATEGORIES_IN_CLUSTER to: s_importance_sample_moduleeight_cluster_allocation_mp_NUM_CATEGORIES_IN_CLUSTER
      num_categories_in_cluster = (/ 1, 1, 1, 1, 1, 1, 1, 1 /)
------^
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Install the project...
-- Install configuration: "Debug"
-- Installing: /home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/libclubb_driver_lib.a
-- Installing: /home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/clubb_tuner
-- Set runtime path of "/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/clubb_tuner" to "/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble:/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/lib:/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/lib64:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/oneapi-2023.2.0/netcdf-fortran-4.5.3-inkjvmgdy5ao7uwihl6lzsnlpstmyoyt/lib"
-- Installing: /home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/G_unit_tests
-- Set runtime path of "/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/G_unit_tests" to "/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble:/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/lib:/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/lib64:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/oneapi-2023.2.0/netcdf-fortran-4.5.3-inkjvmgdy5ao7uwihl6lzsnlpstmyoyt/lib"
-- Installing: /home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/clubb_thread_test
-- Set runtime path of "/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/clubb_thread_test" to "/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble:/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/lib:/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/lib64:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/oneapi-2023.2.0/netcdf-fortran-4.5.3-inkjvmgdy5ao7uwihl6lzsnlpstmyoyt/lib"
-- Installing: /home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/clubb_standalone
-- Set runtime path of "/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/clubb_standalone" to "/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble:/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/lib:/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/lib64:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/oneapi-2023.2.0/netcdf-fortran-4.5.3-inkjvmgdy5ao7uwihl6lzsnlpstmyoyt/lib"
-- Installing: /home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/clubb_driver_test
-- Set runtime path of "/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/clubb_driver_test" to "/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble:/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/lib:/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/lib64:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/oneapi-2023.2.0/netcdf-fortran-4.5.3-inkjvmgdy5ao7uwihl6lzsnlpstmyoyt/lib"
-- Installing: /home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/clubb_standalone_loss
-- Set runtime path of "/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/clubb_standalone_loss" to "/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble:/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/lib:/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/lib64:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/oneapi-2023.2.0/netcdf-fortran-4.5.3-inkjvmgdy5ao7uwihl6lzsnlpstmyoyt/lib"
-- Installing: /home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/clubb_loss_driver_test
-- Set runtime path of "/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/clubb_loss_driver_test" to "/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble:/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/lib:/home/jenkins/workspace/clubb_generalized_vert_grid_host_flags/install/intel_DEBUG_PRECdouble/lib64:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/oneapi-2023.2.0/netcdf-fortran-4.5.3-inkjvmgdy5ao7uwihl6lzsnlpstmyoyt/lib"
CLUBBStandardsCheck.py: beginning check on src
PASS: 0 checks failed for src
CLUBBStandardsCheck.py: beginning check on src/CLUBB_core
PASS: 0 checks failed for src/CLUBB_core
CLUBBStandardsCheck.py: beginning check on src/SILHS
PASS: 0 checks failed for src/SILHS
CLUBBStandardsCheck.py: beginning check on src/Benchmark_cases
PASS: 0 checks failed for src/Benchmark_cases
CLUBBStandardsCheck.py: beginning check on src/Radiation
PASS: 0 checks failed for src/Radiation
CLUBBStandardsCheck.py: beginning check on src/Microphys
PASS: 0 checks failed for src/Microphys
CLUBBStandardsCheck.py: beginning check on src/Microphys/KK_microphys
PASS: 0 checks failed for src/Microphys/KK_microphys
CLUBBStandardsCheck.py: beginning check on src/G_unit_test_types
PASS: 0 checks failed for src/G_unit_test_types

Build completed successfully, and all source code checks passed.
[Pipeline] }
[Pipeline] // stage
[Pipeline] stage
[Pipeline] { (Run)
[Pipeline] sh
+ python3 run_scripts/run_clubb_w_varying_flags.py -f input/flag_sets/run_bindiff_w_flags_config_host_flags.json
Reading settings from input/flag_sets/run_bindiff_w_flags_config_host_flags.json...
Running 124 run_scm.py task(s) with up to 8 worker(s)...
COMPLETE -- default / bomex
COMPLETE -- default / atex
COMPLETE -- default / arm
COMPLETE -- default / clex9_nov02
COMPLETE -- default / dycoms2_rf01_fixed_sst
COMPLETE -- default / dycoms2_rf01
COMPLETE -- default / clex9_oct14
COMPLETE -- default / dycoms2_rf02_nd
COMPLETE -- default / dycoms2_rf02_do
COMPLETE -- default / dycoms2_rf02_so
COMPLETE -- default / fire
COMPLETE -- default / cgils_s12
COMPLETE -- default / astex_a209
COMPLETE -- default / cgils_s11
COMPLETE -- default / dycoms2_rf02_ds
COMPLETE -- default / cgils_s6
COMPLETE -- default / jun25_altocu
COMPLETE -- default / gabls3_night
COMPLETE -- default / mpace_b
COMPLETE -- default / mpace_b_silhs
COMPLETE -- default / nov11_altocu
COMPLETE -- default / gabls3
COMPLETE -- default / rico
COMPLETE -- default / wangara
COMPLETE -- default / rico_silhs
COMPLETE -- flag1 / arm_97
COMPLETE -- default / lba
COMPLETE -- flag1 / arm
COMPLETE -- flag1 / atex
COMPLETE -- flag1 / bomex
COMPLETE -- flag1 / astex_a209
COMPLETE -- flag1 / cgils_s11
COMPLETE -- flag1 / cgils_s6
COMPLETE -- flag1 / clex9_nov02
COMPLETE -- flag1 / cgils_s12
COMPLETE -- default / gabls2
COMPLETE -- flag1 / dycoms2_rf01_fixed_sst
COMPLETE -- flag1 / clex9_oct14
COMPLETE -- flag1 / dycoms2_rf01
COMPLETE -- flag1 / dycoms2_rf02_nd
COMPLETE -- flag1 / fire
COMPLETE -- flag1 / dycoms2_rf02_so
COMPLETE -- flag1 / dycoms2_rf02_do
COMPLETE -- flag1 / dycoms2_rf02_ds
COMPLETE -- flag1 / jun25_altocu
COMPLETE -- flag1 / gabls3_night
COMPLETE -- default / twp_ice
COMPLETE -- flag1 / gabls3
COMPLETE -- default / mpace_a
COMPLETE -- flag1 / mpace_b
COMPLETE -- flag1 / lba
COMPLETE -- flag1 / nov11_altocu
COMPLETE -- flag1 / mpace_b_silhs
COMPLETE -- flag1 / rico
COMPLETE -- flag1 / wangara
COMPLETE -- flag1 / rico_silhs
COMPLETE -- flag2 / arm_97
COMPLETE -- flag2 / arm
COMPLETE -- flag2 / atex
COMPLETE -- flag2 / bomex
COMPLETE -- flag2 / astex_a209
COMPLETE -- default / arm_97
COMPLETE -- flag1 / gabls2
COMPLETE -- flag2 / clex9_nov02
COMPLETE -- flag2 / cgils_s11
COMPLETE -- flag1 / twp_ice
COMPLETE -- flag2 / clex9_oct14
COMPLETE -- flag2 / cgils_s12
COMPLETE -- flag2 / cgils_s6
COMPLETE -- flag2 / dycoms2_rf01_fixed_sst
COMPLETE -- flag2 / dycoms2_rf02_nd
COMPLETE -- flag2 / fire
COMPLETE -- flag2 / dycoms2_rf02_so
COMPLETE -- flag2 / dycoms2_rf01
COMPLETE -- flag2 / dycoms2_rf02_do
COMPLETE -- flag2 / dycoms2_rf02_ds
COMPLETE -- flag2 / jun25_altocu
COMPLETE -- flag2 / gabls3_night
COMPLETE -- flag2 / gabls3
COMPLETE -- flag1 / mpace_a
COMPLETE -- flag2 / mpace_b
COMPLETE -- flag2 / lba
COMPLETE -- flag2 / rico
COMPLETE -- flag2 / nov11_altocu
COMPLETE -- flag2 / mpace_b_silhs
COMPLETE -- flag2 / wangara
COMPLETE -- flag2 / rico_silhs
COMPLETE -- flag3 / arm_97
COMPLETE -- flag3 / arm
COMPLETE -- flag3 / atex
COMPLETE -- flag3 / bomex
COMPLETE -- flag3 / astex_a209
COMPLETE -- flag1 / mc3e
COMPLETE -- flag2 / gabls2
COMPLETE -- flag3 / clex9_nov02
COMPLETE -- flag3 / cgils_s6
COMPLETE -- flag3 / cgils_s11
COMPLETE -- flag3 / dycoms2_rf01_fixed_sst
COMPLETE -- flag3 / cgils_s12
COMPLETE -- flag3 / dycoms2_rf01
COMPLETE -- flag3 / clex9_oct14
COMPLETE -- flag3 / dycoms2_rf02_nd
COMPLETE -- flag3 / fire
COMPLETE -- flag3 / dycoms2_rf02_so
COMPLETE -- flag3 / dycoms2_rf02_do
COMPLETE -- flag3 / dycoms2_rf02_ds
COMPLETE -- flag3 / jun25_altocu
COMPLETE -- flag3 / gabls3_night
COMPLETE -- flag2 / twp_ice
COMPLETE -- flag2 / mpace_a
COMPLETE -- flag3 / gabls3
COMPLETE -- flag3 / mpace_b
COMPLETE -- flag3 / mpace_b_silhs
COMPLETE -- flag3 / nov11_altocu
COMPLETE -- flag3 / lba
COMPLETE -- flag3 / rico
COMPLETE -- flag3 / rico_silhs
COMPLETE -- flag3 / wangara
COMPLETE -- flag3 / gabls2
COMPLETE -- flag3 / twp_ice
COMPLETE -- flag3 / mpace_a
COMPLETE -- flag2 / mc3e
COMPLETE -- default / mc3e
COMPLETE -- flag3 / mc3e

=================== Runs Complete ===================
All flag sets ran to completion.

All CLUBB runs succeeded.
[Pipeline] }
[Pipeline] // stage
[Pipeline] stage
[Pipeline] { (Declarative: Post Actions)
[Pipeline] script
[Pipeline] {
[Pipeline] cleanWs
[WS-CLEANUP] Deleting project workspace...
[WS-CLEANUP] Deferred wipeout is used...
[WS-CLEANUP] done
[Pipeline] }
[Pipeline] // script
[Pipeline] }
[Pipeline] // stage
[Pipeline] }
[Pipeline] // withEnv
[Pipeline] }
[Pipeline] // node
[Pipeline] End of Pipeline
Finished: SUCCESS