Console Output

Started by an SCM change
Obtained jenkins_tests/clubb_BFB_gfortran_test/Jenkinsfile from git https://github.com/larson-group/clubb.git
[Pipeline] Start of Pipeline
[Pipeline] node
Still waiting to schedule task
Waiting for next available executor
Running on Jenkins in /home/jenkins/workspace/clubb_BFB_gfortran_test
[Pipeline] {
[Pipeline] stage
[Pipeline] { (Declarative: Checkout SCM)
[Pipeline] checkout
The recommended git tool is: git
Wiping out workspace first.
Cloning the remote Git repository
Cloning repository https://github.com/larson-group/clubb.git
 > git init /home/jenkins/workspace/clubb_BFB_gfortran_test # 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
 > 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
Avoid second fetch
 > git rev-parse refs/remotes/origin/master^{commit} # timeout=10
Checking out Revision 040e9961b5b422803a0aa816c5921be9576aa4a8 (refs/remotes/origin/master)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 040e9961b5b422803a0aa816c5921be9576aa4a8 # timeout=10
Commit message: "Small bug fix, but this is BIT_CHANGING because it affects stats output. Some zm fields (w_1_zm, w_2_zm, varnce_w_1_zm, varnce_w_2_zm, and mixt_frac_zm) were all nan in the netcdf output when l_call_pdf_closure_twice=.false., because those come from pdf_params_zm."
 > git rev-list --no-walk 61aa970643913037e2766554210e4527bb5e8171 # timeout=10
[Pipeline] }
[Pipeline] // stage
[Pipeline] withEnv
[Pipeline] {
[Pipeline] stage
[Pipeline] { (Update sys_admin Repo)
[Pipeline] sh
+ git -C /home/pub/jenkins_BFB_test_configs/sys_admin pull
Already up to date.
[Pipeline] }
[Pipeline] // stage
[Pipeline] stage
[Pipeline] { (Run Python Test)
[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 "$-" in
+++ __lmod_vx=x
+++ '[' -n x ']'
+++ set +x
Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for this output (/usr/local/spack/opt/spack/linux-pop22-cascadelake/gcc-12.2.0/lmod-8.7.37-bi3kyxcdrfgw3y7vv2k7c5rjxg75qzju/lmod/lmod/init/bash)
Shell debugging restarted
+++ unset __lmod_vx
+++ find /usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core -print -quit
++ export MODULEPATH=/usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core
++ MODULEPATH=/usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core
+ module load gcc netcdf-fortran
+ '[' -z '' ']'
+ case "$-" 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-gzedt3f (required by: mpich/4.2.1, hdf5/1.14.3-42x3zrv,
netcdf-c/4.9.2, netcdf-fortran/4.5.3)
-------------------------------------------------------------------------------



Shell debugging restarted
+ unset __lmod_sh_dbg
+ return 0
+ python3 /home/pub/jenkins_BFB_test_configs/sys_admin/python_nightly_test_suite/run_test.py -c /home/pub/jenkins_BFB_test_configs/clubb_BFB_gfortran_test_config
Directory 1 is 0da744a4b04f078044dcee08c614ad2a47916751
Directory 2 is 61aa970643913037e2766554210e4527bb5e8171
Using reporting threshold:  0.0 


The following cases will be compared: ['arm', 'arm_97', 'atex', 'bomex', 'dycoms2_rf01', 'dycoms2_rf02_ds', 'gabls3_night', 'lba', 'rico', 'twp_ice', 'wangara']

###DIFFING arm netCDF (*.nc) files###
>No differences detected by the linux diff in arm_zm.nc<
>No differences detected by the linux diff in arm_zt.nc<
>No differences detected by the linux diff in arm_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case arm.<<<
**********************************************************************************************************
###DIFFING arm_97 netCDF (*.nc) files###
>No differences detected by the linux diff in arm_97_zm.nc<
>No differences detected by the linux diff in arm_97_zt.nc<
>No differences detected by the linux diff in arm_97_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case arm_97.<<<
**********************************************************************************************************
###DIFFING atex netCDF (*.nc) files###
>No differences detected by the linux diff in atex_zm.nc<
>No differences detected by the linux diff in atex_zt.nc<
>No differences detected by the linux diff in atex_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case atex.<<<
**********************************************************************************************************
###DIFFING bomex netCDF (*.nc) files###
>No differences detected by the linux diff in bomex_zm.nc<
>No differences detected by the linux diff in bomex_zt.nc<
>No differences detected by the linux diff in bomex_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case bomex.<<<
**********************************************************************************************************
###DIFFING dycoms2_rf01 netCDF (*.nc) files###
>No differences detected by the linux diff in dycoms2_rf01_zm.nc<
>No differences detected by the linux diff in dycoms2_rf01_zt.nc<
>No differences detected by the linux diff in dycoms2_rf01_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case dycoms2_rf01.<<<
**********************************************************************************************************
###DIFFING dycoms2_rf02_ds netCDF (*.nc) files###
>No differences detected by the linux diff in dycoms2_rf02_ds_zm.nc<
>No differences detected by the linux diff in dycoms2_rf02_ds_zt.nc<
>No differences detected by the linux diff in dycoms2_rf02_ds_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case dycoms2_rf02_ds.<<<
**********************************************************************************************************
###DIFFING gabls3_night netCDF (*.nc) files###
>No differences detected by the linux diff in gabls3_night_zm.nc<
>No differences detected by the linux diff in gabls3_night_zt.nc<
>No differences detected by the linux diff in gabls3_night_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case gabls3_night.<<<
**********************************************************************************************************
###DIFFING lba netCDF (*.nc) files###
>No differences detected by the linux diff in lba_zm.nc<
>No differences detected by the linux diff in lba_zt.nc<
>No differences detected by the linux diff in lba_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case lba.<<<
**********************************************************************************************************
###DIFFING rico netCDF (*.nc) files###
>No differences detected by the linux diff in rico_zm.nc<
>No differences detected by the linux diff in rico_zt.nc<
>No differences detected by the linux diff in rico_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case rico.<<<
**********************************************************************************************************
###DIFFING twp_ice netCDF (*.nc) files###
>No differences detected by the linux diff in twp_ice_zm.nc<
>No differences detected by the linux diff in twp_ice_zt.nc<
>No differences detected by the linux diff in twp_ice_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case twp_ice.<<<
**********************************************************************************************************
###DIFFING wangara netCDF (*.nc) files###
>No differences detected by the linux diff in wangara_zm.nc<
>No differences detected by the linux diff in wangara_zt.nc<
>No differences detected by the linux diff in wangara_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case wangara.<<<
**********************************************************************************************************
SUMMARY:
Linux diff did not detect any differences in the compared files.
Directory 1 is 040e9961b5b422803a0aa816c5921be9576aa4a8
Directory 2 is 0da744a4b04f078044dcee08c614ad2a47916751
Using reporting threshold:  0.0 


The following cases will be compared: ['arm', 'arm_97', 'atex', 'bomex', 'dycoms2_rf01', 'dycoms2_rf02_ds', 'gabls3_night', 'lba', 'rico', 'twp_ice', 'wangara']

###DIFFING arm netCDF (*.nc) files###
>No differences detected by the linux diff in arm_zm.nc<
>No differences detected by the linux diff in arm_zt.nc<
>No differences detected by the linux diff in arm_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case arm.<<<
**********************************************************************************************************
###DIFFING arm_97 netCDF (*.nc) files###
>No differences detected by the linux diff in arm_97_zm.nc<
>No differences detected by the linux diff in arm_97_zt.nc<
>No differences detected by the linux diff in arm_97_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case arm_97.<<<
**********************************************************************************************************
###DIFFING atex netCDF (*.nc) files###
>No differences detected by the linux diff in atex_zm.nc<
>No differences detected by the linux diff in atex_zt.nc<
>No differences detected by the linux diff in atex_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case atex.<<<
**********************************************************************************************************
###DIFFING bomex netCDF (*.nc) files###
>No differences detected by the linux diff in bomex_zm.nc<
>No differences detected by the linux diff in bomex_zt.nc<
>No differences detected by the linux diff in bomex_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case bomex.<<<
**********************************************************************************************************
###DIFFING dycoms2_rf01 netCDF (*.nc) files###
>No differences detected by the linux diff in dycoms2_rf01_zm.nc<
>No differences detected by the linux diff in dycoms2_rf01_zt.nc<
>No differences detected by the linux diff in dycoms2_rf01_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case dycoms2_rf01.<<<
**********************************************************************************************************
###DIFFING dycoms2_rf02_ds netCDF (*.nc) files###
>No differences detected by the linux diff in dycoms2_rf02_ds_zm.nc<
>No differences detected by the linux diff in dycoms2_rf02_ds_zt.nc<
>No differences detected by the linux diff in dycoms2_rf02_ds_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case dycoms2_rf02_ds.<<<
**********************************************************************************************************
###DIFFING gabls3_night netCDF (*.nc) files###
>No differences detected by the linux diff in gabls3_night_zm.nc<
>No differences detected by the linux diff in gabls3_night_zt.nc<
>No differences detected by the linux diff in gabls3_night_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case gabls3_night.<<<
**********************************************************************************************************
###DIFFING lba netCDF (*.nc) files###
>No differences detected by the linux diff in lba_zm.nc<
>No differences detected by the linux diff in lba_zt.nc<
>No differences detected by the linux diff in lba_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case lba.<<<
**********************************************************************************************************
###DIFFING rico netCDF (*.nc) files###
>No differences detected by the linux diff in rico_zm.nc<
>No differences detected by the linux diff in rico_zt.nc<
>No differences detected by the linux diff in rico_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case rico.<<<
**********************************************************************************************************
###DIFFING twp_ice netCDF (*.nc) files###
>No differences detected by the linux diff in twp_ice_zm.nc<
>No differences detected by the linux diff in twp_ice_zt.nc<
>No differences detected by the linux diff in twp_ice_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case twp_ice.<<<
**********************************************************************************************************
###DIFFING wangara netCDF (*.nc) files###
>No differences detected by the linux diff in wangara_zm.nc<
>No differences detected by the linux diff in wangara_zt.nc<
>No differences detected by the linux diff in wangara_sfc.nc<
>>>The linux diff could not detect any differences in the file pairs for case wangara.<<<
**********************************************************************************************************
SUMMARY:
Linux diff did not detect any differences in the compared files.

=============================== Configuring Test ===============================


Working directory set to: /home/jenkins/workspace/clubb_BFB_gfortran_test
Checking specified repo: /home/jenkins/workspace/clubb_BFB_gfortran_test

Using /home/jenkins/workspace/clubb_BFB_gfortran_test with origin https://github.com/larson-group/clubb.git

Output Save Mode: none

Using branch: master

Making list from 'UnresolvedCommits':

CheckRange = True: Getting commit range

Run Output Path: output

Run commands: ['python compile.py -debug', '\nrm -rf output', '\nmkdir output', '\npython run_scripts/run_scm_all.py -min_cases']

Diffing command: run_scripts/run_bindiff_all.py

=============================== Running Test ===============================

Parsing message from commit: d5703f0d199f44b4fb66df14b4ebfcdb14b57c19
Parsing message from commit: 0da744a4b04f078044dcee08c614ad2a47916751
Parsing message from commit: 040e9961b5b422803a0aa816c5921be9576aa4a8
	Found: BIT_CHANGING

Checking Commit: d5703f0d199f44b4fb66df14b4ebfcdb14b57c19
	Skipping: not final commit and not labelled BIT_CHANGING

Checking Commit: 0da744a4b04f078044dcee08c614ad2a47916751
	Skipping: not final commit and not labelled BIT_CHANGING

Checking Commit: 040e9961b5b422803a0aa816c5921be9576aa4a8
	Checking out 0da744a4b04f078044dcee08c614ad2a47916751
	Running: 'python compile.py -debug'
	Running: 'rm -rf output'
	Running: 'mkdir output'
	Running: 'python run_scripts/run_scm_all.py -min_cases'
	Checking out 61aa970643913037e2766554210e4527bb5e8171
	Running: 'python compile.py -debug'
	Running: 'rm -rf output'
	Running: 'mkdir output'
	Running: 'python run_scripts/run_scm_all.py -min_cases'
	Diffing: 'run_scripts/run_bindiff_all.py 0da744a4b04f078044dcee08c614ad2a47916751 61aa970643913037e2766554210e4527bb5e8171'
	Checking out 040e9961b5b422803a0aa816c5921be9576aa4a8
	Running: 'python compile.py -debug'
	Running: 'rm -rf output'
	Running: 'mkdir output'
	Running: 'python run_scripts/run_scm_all.py -min_cases'
	Output from 0da744a4b04f078044dcee08c614ad2a47916751 already saved
	Diffing: 'run_scripts/run_bindiff_all.py 040e9961b5b422803a0aa816c5921be9576aa4a8 0da744a4b04f078044dcee08c614ad2a47916751'
	WARNING: commit '040e9961b5b422803a0aa816c5921be9576aa4a8' was supposed to be BIT_CHANGING, but is not.

=============================== Test Results ===============================

Commit Range Checked = 61aa970643913037e2766554210e4527bb5e8171...040e9961b5b422803a0aa816c5921be9576aa4a8

No new Unresolved commits found.

Fake BIT_CHANGING Commits:
	040e9961b5b422803a0aa816c5921be9576aa4a8

No remaining Unresolved Commits.

=============================== Updating Config File ===============================


Saving into UnresolvedCommits: 

Saving into BaselineCommit: 040e9961b5b422803a0aa816c5921be9576aa4a8

=============================== Cleanup ===============================

Removing all generated output
	REMOVING: 61aa970643913037e2766554210e4527bb5e8171
	REMOVING: 0da744a4b04f078044dcee08c614ad2a47916751
	REMOVING: 040e9961b5b422803a0aa816c5921be9576aa4a8

================== Unresolved Commit Status ==================

No remaining Unresolved Commits.

Exiting with code: 0
[Pipeline] }
[Pipeline] // stage
[Pipeline] }
[Pipeline] // withEnv
[Pipeline] }
[Pipeline] // node
[Pipeline] End of Pipeline
Finished: SUCCESS