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Started by user Peter Roels Checking out git https://github.com/larson-group/e3sm.git into /home/jenkins/workspace/branch_e3sm_test@script to read jenkins_tests/e3sm_ne4_silhs_run_gfortran_test/Jenkinsfile The recommended git tool is: git > git rev-parse --resolve-git-dir /home/jenkins/workspace/branch_e3sm_test@script/.git # timeout=10 Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/larson-group/e3sm.git # timeout=10 Cleaning workspace > git rev-parse --verify HEAD # timeout=10 Resetting working tree > git reset --hard # timeout=10 > git clean -fdx # 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 rev-parse refs/remotes/origin/clubb_silhs_devel^{commit} # timeout=10 Checking out Revision eb4cdd98a18cb717d699273363e808b85bf268e7 (refs/remotes/origin/clubb_silhs_devel) > git config core.sparsecheckout # timeout=10 > git checkout -f eb4cdd98a18cb717d699273363e808b85bf268e7 # timeout=10 Commit message: "Reverting changes to clubb and silhs" > git rev-list --no-walk 03251deb52bd67a26da2af86195c3626e2d9d917 # timeout=10 Running in Durability level: MAX_SURVIVABILITY [Pipeline] Start of Pipeline [Pipeline] node Running on Jenkins in /home/jenkins/workspace/branch_e3sm_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/branch_e3sm_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 eb4cdd98a18cb717d699273363e808b85bf268e7 (refs/remotes/origin/clubb_silhs_devel) > git config core.sparsecheckout # timeout=10 > git checkout -f eb4cdd98a18cb717d699273363e808b85bf268e7 # timeout=10 Commit message: "Reverting changes to clubb and silhs" [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 (Mon Aug 16 13:29:36 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/branch_e3sm_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/branch_e3sm_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/branch_e3sm_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: eb4cdd9 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/branch_e3sm_test/cime/config/e3sm/machines/template.case.run Creating file .case.run Writing case.st_archive script from input template /home/jenkins/workspace/branch_e3sm_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 2021-08-16 13:29:44 atm Calling /home/jenkins/workspace/branch_e3sm_test/components/cam/cime_config/buildnml 2021-08-16 13:29:44 lnd Calling /home/jenkins/workspace/branch_e3sm_test/components/clm/cime_config/buildnml 2021-08-16 13:29:44 ice Calling /home/jenkins/workspace/branch_e3sm_test/components/cice/cime_config/buildnml 2021-08-16 13:29:44 ocn Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/data_comps/docn/cime_config/buildnml 2021-08-16 13:29:44 rof Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps/srof/cime_config/buildnml 2021-08-16 13:29:44 glc Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps/sglc/cime_config/buildnml 2021-08-16 13:29:44 wav Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps/swav/cime_config/buildnml 2021-08-16 13:29:44 iac Running /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps/siac/cime_config/buildnml 2021-08-16 13:29:44 esp Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps/sesp/cime_config/buildnml 2021-08-16 13:29:44 cpl Calling /home/jenkins/workspace/branch_e3sm_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/branch_e3sm_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/branch_e3sm_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 2021-08-16 13:29:45 atm Calling /home/jenkins/workspace/branch_e3sm_test/components/cam/cime_config/buildnml 2021-08-16 13:29:46 lnd Calling /home/jenkins/workspace/branch_e3sm_test/components/clm/cime_config/buildnml 2021-08-16 13:29:46 ice Calling /home/jenkins/workspace/branch_e3sm_test/components/cice/cime_config/buildnml 2021-08-16 13:29:46 ocn Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/data_comps/docn/cime_config/buildnml 2021-08-16 13:29:46 rof Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps/srof/cime_config/buildnml 2021-08-16 13:29:46 glc Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps/sglc/cime_config/buildnml 2021-08-16 13:29:46 wav Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps/swav/cime_config/buildnml 2021-08-16 13:29:46 iac Running /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps/siac/cime_config/buildnml 2021-08-16 13:29:46 esp Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps/sesp/cime_config/buildnml 2021-08-16 13:29:46 cpl Calling /home/jenkins/workspace/branch_e3sm_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.210816-132945 Calling /home/jenkins/workspace/branch_e3sm_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.210816-132945 Calling /home/jenkins/workspace/branch_e3sm_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.210816-132945 Calling /home/jenkins/workspace/branch_e3sm_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.210816-132945 Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/build_scripts/buildlib.csm_share Component csm_share build complete with 4 warnings - Building atm Library - Building lnd Library Building atm with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/atm.bldlog.210816-132945 Building lnd with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/lnd.bldlog.210816-132945 - Building ice Library Building ice with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/ice.bldlog.210816-132945 - Building ocn Library - Building rof Library Building ocn with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/ocn.bldlog.210816-132945 - Building glc Library Building rof with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/rof.bldlog.210816-132945 Building glc with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/glc.bldlog.210816-132945 - Building wav Library Building wav with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/wav.bldlog.210816-132945 - Building iac Library Building iac with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/iac.bldlog.210816-132945 - Building esp Library Building esp with output to /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/esp.bldlog.210816-132945 sesp built in 0.576660 seconds srof built in 0.721459 seconds siac built in 0.716203 seconds swav built in 0.780718 seconds sglc built in 0.811692 seconds docn built in 1.808709 seconds Component ice build complete with 9 warnings Component ice build complete with 9 warnings cice built in 27.183325 seconds Error: Missing actual argument for argument ‘l_use_tke_in_wp3_pr_turb_term’ at (1) Error: Type mismatch in argument ‘l_use_tke_in_wp3_pr_turb_term’ at (1); passed TYPE(clubb_config_flags_type) to LOGICAL(4) Error: Missing actual argument for argument l_use_tke_in_wp3_pr_turb_term at (1) Error: Type mismatch in argument l_use_tke_in_wp3_pr_turb_term at (1); passed TYPE(clubb_config_flags_type) to LOGICAL(4) Component atm build complete with 20 warnings Error: Missing actual argument for argument ‘l_use_tke_in_wp3_pr_turb_term’ at (1) Error: Type mismatch in argument ‘l_use_tke_in_wp3_pr_turb_term’ at (1); passed TYPE(clubb_config_flags_type) to LOGICAL(4) Error: Missing actual argument for argument l_use_tke_in_wp3_pr_turb_term at (1) Error: Type mismatch in argument l_use_tke_in_wp3_pr_turb_term at (1); passed TYPE(clubb_config_flags_type) to LOGICAL(4) Component atm build complete with 20 warnings cam built in 150.733797 seconds Component lnd build complete with 6 warnings Component lnd build complete with 6 warnings clm built in 154.531535 seconds ERROR: BUILD FAIL: cam.buildlib failed, cat /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/atm.bldlog.210816-132945 The case.build step failed. [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (Declarative: Post Actions) [Pipeline] script [Pipeline] { [Pipeline] } [Pipeline] // script [Pipeline] script [Pipeline] { [Pipeline] } [Pipeline] // script [Pipeline] } [Pipeline] // stage [Pipeline] } [Pipeline] // withEnv [Pipeline] } [Pipeline] // node [Pipeline] End of Pipeline ERROR: script returned exit code 1 Finished: FAILURE