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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 -ffdx # 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/bmg929/atm/E3SM_clubb_silhs_1c77ed3_20211115_P3^{commit} # timeout=10 Checking out Revision ba623886b19d1bb3e3c061d138f3dc949bdbbb9e (refs/remotes/origin/bmg929/atm/E3SM_clubb_silhs_1c77ed3_20211115_P3) > git config core.sparsecheckout # timeout=10 > git checkout -f ba623886b19d1bb3e3c061d138f3dc949bdbbb9e # timeout=10 Commit message: "Change user namelist name from "user_nl_cam" to "user_nl_eam"." > git rev-list --no-walk 83421cfdc88083ef2e0487e0b8a2b84acd6d72cf # 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 > git rev-parse --resolve-git-dir /home/jenkins/workspace/branch_e3sm_test/.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 -ffdx # 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/bmg929/atm/E3SM_clubb_silhs_1c77ed3_20211115_P3^{commit} # timeout=10 Checking out Revision ba623886b19d1bb3e3c061d138f3dc949bdbbb9e (refs/remotes/origin/bmg929/atm/E3SM_clubb_silhs_1c77ed3_20211115_P3) > git config core.sparsecheckout # timeout=10 > git checkout -f ba623886b19d1bb3e3c061d138f3dc949bdbbb9e # timeout=10 Commit message: "Change user namelist name from "user_nl_cam" to "user_nl_eam"." [Pipeline] } [Pipeline] // stage [Pipeline] withEnv [Pipeline] { [Pipeline] stage [Pipeline] { (Checkout Branch and Submodules) [Pipeline] sh + git submodule init + git submodule update [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 Dec 29 16:51:57 CST 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_EAM%AV1C-L_ELM%SPBC_CICE%PRES_DOCN%DOM_SROF_SGLC_SWAV Compset specification file is /home/jenkins/workspace/branch_e3sm_test/components/eam/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:EAM 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/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_EAM%AV1C-L_ELM%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 setting additional fields from config_pes: {} Compset is: 2000_EAM%AV1C-L_ELM%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: ['eam', 'elm', 'cice', 'docn', 'srof', 'sglc', 'swav', 'siac', 'sesp'] No charge_account info available, using value from PROJECT e3sm model version found: ba62388 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 Successfully cleaned env_mach_specific.xml /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/case_scripts/env_mach_specific.xml already exists, delete to replace Setting Environment NETCDF_C_PATH=/usr/local/NETCDF-C-4.7.0-gfortran Setting Environment NETCDF_FORTRAN_PATH=/usr/local/NETCDF-Fortran-4.4.5-gfortran Setting Environment NETCDF_C_PATH=/usr/local/NETCDF-C-4.7.0-gfortran Setting Environment LIB_NETCDF=/usr/local/NETCDF-Fortran-4.4.5-gfortran/lib Setting Environment INC_NETCDF=/usr/local/NETCDF-Fortran-4.4.5-gfortran/include Creating batch scripts Writing case.run script from input template /home/jenkins/workspace/branch_e3sm_test/cime_config/machines/template.case.run Creating file .case.run Writing case.st_archive script from input template /home/jenkins/workspace/branch_e3sm_test/cime_config/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 2021-12-29 16:52:06 atm Create namelist for component eam Calling /home/jenkins/workspace/branch_e3sm_test/components/eam/cime_config/buildnml 2021-12-29 16:52:06 lnd Create namelist for component elm Calling /home/jenkins/workspace/branch_e3sm_test/components/elm/cime_config/buildnml 2021-12-29 16:52:06 ice Create namelist for component cice Calling /home/jenkins/workspace/branch_e3sm_test/components/cice/cime_config/buildnml 2021-12-29 16:52:07 ocn Create namelist for component docn Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/data_comps_mct/docn/cime_config/buildnml 2021-12-29 16:52:07 rof Create namelist for component srof Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps_mct/srof/cime_config/buildnml 2021-12-29 16:52:07 glc Create namelist for component sglc Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps_mct/sglc/cime_config/buildnml 2021-12-29 16:52:07 wav Create namelist for component swav Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps_mct/swav/cime_config/buildnml 2021-12-29 16:52:07 iac Create namelist for component siac Running /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps_mct/siac/cime_config/buildnml 2021-12-29 16:52:07 esp Create namelist for component sesp Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps_mct/sesp/cime_config/buildnml 2021-12-29 16:52:07 cpl Create namelist for component drv Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/drivers/mct/cime_config/buildnml 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 Setting Environment NETCDF_C_PATH=/usr/local/NETCDF-C-4.7.0-gfortran Setting Environment NETCDF_FORTRAN_PATH=/usr/local/NETCDF-Fortran-4.4.5-gfortran Setting Environment NETCDF_C_PATH=/usr/local/NETCDF-C-4.7.0-gfortran Setting Environment LIB_NETCDF=/usr/local/NETCDF-Fortran-4.4.5-gfortran/lib Setting Environment INC_NETCDF=/usr/local/NETCDF-Fortran-4.4.5-gfortran/include Generating component namelists as part of build 2021-12-29 16:52:08 atm Create namelist for component eam Calling /home/jenkins/workspace/branch_e3sm_test/components/eam/cime_config/buildnml 2021-12-29 16:52:08 lnd Create namelist for component elm Calling /home/jenkins/workspace/branch_e3sm_test/components/elm/cime_config/buildnml 2021-12-29 16:52:08 ice Create namelist for component cice Calling /home/jenkins/workspace/branch_e3sm_test/components/cice/cime_config/buildnml 2021-12-29 16:52:08 ocn Create namelist for component docn Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/data_comps_mct/docn/cime_config/buildnml 2021-12-29 16:52:08 rof Create namelist for component srof Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps_mct/srof/cime_config/buildnml 2021-12-29 16:52:08 glc Create namelist for component sglc Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps_mct/sglc/cime_config/buildnml 2021-12-29 16:52:08 wav Create namelist for component swav Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps_mct/swav/cime_config/buildnml 2021-12-29 16:52:08 iac Create namelist for component siac Running /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps_mct/siac/cime_config/buildnml 2021-12-29 16:52:08 esp Create namelist for component sesp Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/components/stub_comps_mct/sesp/cime_config/buildnml 2021-12-29 16:52:08 cpl Create namelist for component drv Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/drivers/mct/cime_config/buildnml Building gptl with output to file /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/gptl.bldlog.211229-165208 Calling /home/jenkins/workspace/branch_e3sm_test/cime/src/build_scripts/buildlib.gptl ERROR: /home/jenkins/workspace/branch_e3sm_test/cime/src/build_scripts/buildlib.gptl FAILED, cat /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/gptl.bldlog.211229-165208 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] } [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