Started by an SCM change Obtained jenkins_tests/e3sm_ne4_silhs_run_gfortran_test/Jenkinsfile from git https://github.com/larson-group/e3sm.git Running in Durability level: MAX_SURVIVABILITY [Pipeline] Start of Pipeline [Pipeline] node Running on Jenkins in /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test [Pipeline] { [Pipeline] stage [Pipeline] { (Declarative: Checkout SCM) [Pipeline] checkout The recommended git tool is: git Cloning the remote Git repository Cloning repository https://github.com/larson-group/e3sm.git > git init /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test # timeout=10 Fetching upstream changes from https://github.com/larson-group/e3sm.git > git --version # timeout=10 > git --version # 'git version 1.8.3.1' using GIT_ASKPASS to set credentials A token based key used by Jenkins to preform Github actions, created 6/21/2021 > git fetch --tags --progress https://github.com/larson-group/e3sm.git +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/larson-group/e3sm.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/clubb_silhs_devel^{commit} # timeout=10 Checking out Revision 9af53143676f1f868706d65621089805e201becc (refs/remotes/origin/clubb_silhs_devel) > git config core.sparsecheckout # timeout=10 > git checkout -f 9af53143676f1f868706d65621089805e201becc # timeout=10 Commit message: "Applying the fix for the new CLUBB code to the developmental branch of clubb_silhs_devel." > git rev-list --no-walk 9651b2f0422d94bb8e670d908658cef73918becf # timeout=10 [Pipeline] } [Pipeline] // stage [Pipeline] withEnv [Pipeline] { [Pipeline] stage [Pipeline] { (Checkout Branch and Submodules) [Pipeline] sh + git submodule init Submodule 'components/cam/src/physics/rrtmgp/external' (https://github.com/RobertPincus/rte-rrtmgp.git) registered for path 'components/cam/src/physics/rrtmgp/external' Submodule 'components/clm/src/external_models/fates' (https://github.com/NGEET/fates.git) registered for path 'components/clm/src/external_models/fates' Submodule 'alm-mpp' (https://github.com/MPP-LSM/MPP.git) registered for path 'components/clm/src/external_models/mpp' Submodule 'sbetr' (https://github.com/BeTR-biogeochemistry-modeling/sbetr.git) registered for path 'components/clm/src/external_models/sbetr' Submodule 'components/mpas-source' (https://github.com/MPAS-Dev/MPAS-Model.git) registered for path 'components/mpas-source' Submodule 'externals/scorpio_classic' (https://github.com/E3SM-Project/scorpio.git) registered for path 'externals/scorpio_classic' + git submodule update Cloning into 'components/cam/src/physics/rrtmgp/external'... Submodule path 'components/cam/src/physics/rrtmgp/external': checked out '0b1cffdd51a35045c28aae314e2b29e2a663b5e6' Cloning into 'components/clm/src/external_models/fates'... Submodule path 'components/clm/src/external_models/fates': checked out '1ad93c311ed1a5d45df656b9031c8714a7071e64' Cloning into 'components/clm/src/external_models/mpp'... Submodule path 'components/clm/src/external_models/mpp': checked out '82ef0c1a37ffd469e9a6ce84dbf487c6ef8762b2' Cloning into 'components/clm/src/external_models/sbetr'... Submodule path 'components/clm/src/external_models/sbetr': checked out 'd71fb2df928099bacc4e9a3a9f4b8a1f2a6e37a1' Cloning into 'components/mpas-source'... Submodule path 'components/mpas-source': checked out 'bb1ea15299544e2b25144c06c621ff40fa482760' Cloning into 'externals/scorpio_classic'... Submodule path 'externals/scorpio_classic': checked out '1e538b56fa7cfa209c119e866a95669875eb200d' [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (Remove Old Output) [Pipeline] sh + rm -rf /home/jenkins/E3SM_simulations [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (Run) [Pipeline] sh + csh nightly_test/nightly_e3sm_ne4_silhs.csh run_e3sm: ++++++++ run_e3sm starting (Wed Nov 3 03:36:50 CDT 2021), version 3.0.22 ++++++++ run_e3sm: $case_name = nelson.mg2_def.ne4_ne4 run_e3sm: -------- Starting create_newcase -------- run_e3sm: /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test//cime/scripts/create_newcase --case nelson.mg2_def.ne4_ne4 --compset FC5AV1C-L --script-root /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/case_scripts --res ne4_ne4 --pecount M --handle-preexisting-dirs u --mach nelson --output-root /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4 --project condo Compset longname is 2000_CAM5%AV1C-L_CLM45%SPBC_CICE%PRES_DOCN%DOM_SROF_SGLC_SWAV Compset specification file is /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/components/cam/cime_config/config_compsets.xml Automatically adding SIAC to compset Automatically adding SESP to compset Compset forcing is Com forcing is present day: ATM component is cam5 physics:CAM with complete set of E3SM atmospheric mods for V1 (72 layers model) and ACES4BGC SOAG emissions- v04p2: LND component is clm4.5 physics:clm4.5 Satellite phenology:clm4.5 Satellite phenology with black carbon deposition: ICE component is prescribed cice: OCN component is DOCN prescribed ocean mode ROF component is Stub river component GLC component is Stub glacier (land ice) component WAV component is Stub wave component IAC component is Stub iac component ESP component is Stub external system processing (ESP) component Pes specification file is /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/config/e3sm/allactive/config_pesall.xml Machine is nelson Pes setting: grid is a%ne4np4_l%ne4np4_oi%ne4np4_r%null_g%null_w%null_z%null_m%oQU240 Pes setting: compset is 2000_CAM5%AV1C-L_CLM45%SPBC_CICE%PRES_DOCN%DOM_SROF_SGLC_SWAV_SIAC_SESP Pes setting: tasks is {'NTASKS_ATM': 16, 'NTASKS_ICE': 16, 'NTASKS_CPL': 16, 'NTASKS_LND': 16, 'NTASKS_WAV': 16, 'NTASKS_ROF': 16, 'NTASKS_OCN': 16, 'NTASKS_GLC': 16} Pes setting: threads is {'NTHRDS_ICE': 1, 'NTHRDS_ATM': 1, 'NTHRDS_ROF': 1, 'NTHRDS_LND': 1, 'NTHRDS_WAV': 1, 'NTHRDS_OCN': 1, 'NTHRDS_CPL': 1, 'NTHRDS_GLC': 1} Pes setting: rootpe is {'ROOTPE_OCN': 0, 'ROOTPE_LND': 0, 'ROOTPE_ATM': 0, 'ROOTPE_ICE': 0, 'ROOTPE_WAV': 0, 'ROOTPE_CPL': 0, 'ROOTPE_ROF': 0, 'ROOTPE_GLC': 0} Pes setting: pstrid is {} Pes other settings: {} Pes comments: none Compset is: 2000_CAM5%AV1C-L_CLM45%SPBC_CICE%PRES_DOCN%DOM_SROF_SGLC_SWAV_SIAC_SESP Grid is: a%ne4np4_l%ne4np4_oi%ne4np4_r%null_g%null_w%null_z%null_m%oQU240 Components in compset are: ['cam', 'clm', 'cice', 'docn', 'srof', 'sglc', 'swav', 'siac', 'sesp', 'drv'] No charge_account info available, using value from PROJECT e3sm model version found: 9af5314 Batch_system_type is none Creating Case directory /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/case_scripts run_e3sm: -------- Finished create_newcase -------- run_e3sm: Project used for submission: condo run_e3sm: Configuring E3SM to use the COSP simulator. run_e3sm: -------- Starting case.setup -------- run_e3sm: /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/case_scripts/case.setup /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/case_scripts/env_mach_specific.xml already exists, delete to replace /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/case_scripts/env_mach_specific.xml already exists, delete to replace Creating batch scripts Writing case.run script from input template /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/config/e3sm/machines/template.case.run Creating file .case.run Writing case.st_archive script from input template /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/config/e3sm/machines/template.st_archive Creating file case.st_archive Creating file .case.run.sh Creating user_nl_xxx files for components and cpl If an old case build already exists, might want to run 'case.build --clean' before building Generating component namelists as part of setup Creating component namelists 2021-11-03 03:36:59 atm Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/components/cam/cime_config/buildnml 2021-11-03 03:37:00 lnd Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/components/clm/cime_config/buildnml 2021-11-03 03:37:00 ice Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/components/cice/cime_config/buildnml 2021-11-03 03:37:00 ocn Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/data_comps/docn/cime_config/buildnml 2021-11-03 03:37:00 rof Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps/srof/cime_config/buildnml 2021-11-03 03:37:00 glc Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps/sglc/cime_config/buildnml 2021-11-03 03:37:00 wav Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps/swav/cime_config/buildnml 2021-11-03 03:37:00 iac Running /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps/siac/cime_config/buildnml 2021-11-03 03:37:00 esp Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps/sesp/cime_config/buildnml 2021-11-03 03:37:00 cpl Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/drivers/mct/cime_config/buildnml Finished creating component namelists You can now run './preview_run' to get more info on how your case will be run run_e3sm: -------- Finished case.setup -------- run_e3sm: Creating logical links to make navigating easier. run_e3sm: Note: Beware of using ".." with the links, since the behavior of shell commands can vary. run_e3sm: /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/nightly_test/nightly_e3sm_ne4_silhs.csh=a_run_link run_e3sm: run_root /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4 run_e3sm: run_dir /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/nightly_test/nightly_e3sm_ne4_silhs.csh=a_run_link setting case file to env_run.xml run_e3sm: -------- Starting Build -------- run_e3sm: WARNING: Make sure there are no double-slashes (//) in the build command below: => Will cause a build error run_e3sm: /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/case_scripts/case.build Building case in directory /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/case_scripts sharedlib_only is False model_only is False Generating component namelists as part of build Creating component namelists 2021-11-03 03:37:01 atm Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/components/cam/cime_config/buildnml 2021-11-03 03:37:02 lnd Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/components/clm/cime_config/buildnml 2021-11-03 03:37:02 ice Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/components/cice/cime_config/buildnml 2021-11-03 03:37:02 ocn Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/data_comps/docn/cime_config/buildnml 2021-11-03 03:37:02 rof Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps/srof/cime_config/buildnml 2021-11-03 03:37:02 glc Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps/sglc/cime_config/buildnml 2021-11-03 03:37:02 wav Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps/swav/cime_config/buildnml 2021-11-03 03:37:02 iac Running /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps/siac/cime_config/buildnml 2021-11-03 03:37:02 esp Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps/sesp/cime_config/buildnml 2021-11-03 03:37:02 cpl Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/drivers/mct/cime_config/buildnml Finished creating component namelists Building gptl with output to file /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/gptl.bldlog.211103-033701 Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/build_scripts/buildlib.gptl Component gptl build complete with 1 warnings Building mct with output to file /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/mct.bldlog.211103-033701 Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/build_scripts/buildlib.mct Building pio with output to file /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/pio.bldlog.211103-033701 Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/build_scripts/buildlib.pio Building csm_share with output to file /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/csm_share.bldlog.211103-033701 Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/build_scripts/buildlib.csm_share Component csm_share build complete with 4 warnings - Building atm Library Building atm with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/atm.bldlog.211103-033701 - Building lnd Library Building lnd with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/lnd.bldlog.211103-033701 - Building ice Library Building ice with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/ice.bldlog.211103-033701 - Building ocn Library - Building rof Library Building ocn with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/ocn.bldlog.211103-033701 Building rof with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/rof.bldlog.211103-033701 - Building glc Library Building glc with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/glc.bldlog.211103-033701 - Building wav Library Building wav with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/wav.bldlog.211103-033701 - Building iac Library - Building esp Library Building iac with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/iac.bldlog.211103-033701 Building esp with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/esp.bldlog.211103-033701 srof built in 0.514774 seconds swav built in 0.509041 seconds sglc built in 0.535657 seconds sesp built in 0.556721 seconds siac built in 0.612631 seconds docn built in 1.360679 seconds Component ice build complete with 9 warnings Component ice build complete with 9 warnings cice built in 23.947393 seconds Error: Explicit shaped array with nonconstant bounds at (1) Error: Unclassifiable statement at (1) Error: Unclassifiable statement at (1) Error: Symbol ‘mu’ referenced at (1) not found in module ‘clubb_api_module’ Error: Symbol ‘mu’ referenced at (1) not found in module ‘parameters_tunable’ Error: Symbol ‘mu’ at (1) has no IMPLICIT type Error: Symbol ‘clubb_params’ at (1) has no IMPLICIT type; did you mean ‘nparams’? Error: Function ‘clubb_params’ at (1) has no IMPLICIT type Error: Explicit shaped array with nonconstant bounds at (1) Error: Unclassifiable statement at (1) Error: Unclassifiable statement at (1) Error: Symbol mu referenced at (1) not found in module clubb_api_module Error: Symbol mu referenced at (1) not found in module parameters_tunable Error: Symbol mu at (1) has no IMPLICIT type Error: Symbol clubb_params at (1) has no IMPLICIT type; did you mean nparams ? Error: Function clubb_params at (1) has no IMPLICIT type Component atm build complete with 22 warnings Error: Explicit shaped array with nonconstant bounds at (1) Error: Unclassifiable statement at (1) Error: Unclassifiable statement at (1) Error: Symbol ‘mu’ referenced at (1) not found in module ‘clubb_api_module’ Error: Symbol ‘mu’ referenced at (1) not found in module ‘parameters_tunable’ Error: Symbol ‘mu’ at (1) has no IMPLICIT type Error: Symbol ‘clubb_params’ at (1) has no IMPLICIT type; did you mean ‘nparams’? Error: Function ‘clubb_params’ at (1) has no IMPLICIT type Error: Explicit shaped array with nonconstant bounds at (1) Error: Unclassifiable statement at (1) Error: Unclassifiable statement at (1) Error: Symbol mu referenced at (1) not found in module clubb_api_module Error: Symbol mu referenced at (1) not found in module parameters_tunable Error: Symbol mu at (1) has no IMPLICIT type Error: Symbol clubb_params at (1) has no IMPLICIT type; did you mean nparams ? Error: Function clubb_params at (1) has no IMPLICIT type Component atm build complete with 22 warnings cam built in 112.438139 seconds Component lnd build complete with 6 warnings Component lnd build complete with 6 warnings clm built in 118.068349 seconds ERROR: BUILD FAIL: cam.buildlib failed, cat /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/atm.bldlog.211103-033701 The case.build step failed. [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (Display log files) Stage "Display log files" skipped due to earlier failure(s) [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] script [Pipeline] { [Pipeline] emailext Sending email to: messnermet@uwm.edu [Pipeline] } [Pipeline] // script [Pipeline] } [Pipeline] // stage [Pipeline] } [Pipeline] // withEnv [Pipeline] } [Pipeline] // node [Pipeline] End of Pipeline ERROR: script returned exit code 1 Finished: FAILURE