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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 1f572936bf191bb31671a41f8fe9daedc98bdfb4 (refs/remotes/origin/clubb_silhs_devel) > git config core.sparsecheckout # timeout=10 > git checkout -f 1f572936bf191bb31671a41f8fe9daedc98bdfb4 # timeout=10 Commit message: "Raw-copy updating components/eam/src/physics/clubb" > git rev-list --no-walk c9092a6e71199123e696048843bcf416605ae0b0 # timeout=10 [Pipeline] } [Pipeline] // stage [Pipeline] withEnv [Pipeline] { [Pipeline] stage [Pipeline] { (Checkout Branch and Submodules) [Pipeline] sh + git submodule init Submodule 'cime' (https://github.com/ESMCI/cime.git) registered for path 'cime' Submodule 'cosp2' (git@github.com:CFMIP/COSPv2.0.git) registered for path 'components/eam/src/physics/cosp2/external' Submodule 'rrtmgp' (git@github.com:RobertPincus/rte-rrtmgp.git) registered for path 'components/eam/src/physics/rrtmgp/external' Submodule 'fates' (git@github.com:NGEET/fates.git) registered for path 'components/elm/src/external_models/fates' Submodule 'alm-mpp' (git@github.com:MPP-LSM/MPP.git) registered for path 'components/elm/src/external_models/mpp' Submodule 'sbetr' (git@github.com:BeTR-biogeochemistry-modeling/sbetr.git) registered for path 'components/elm/src/external_models/sbetr' Submodule 'components/mpas-source' (https://github.com/MPAS-Dev/MPAS-Model.git) registered for path 'components/mpas-source' Submodule 'externals/YAKL' (git@github.com:mrnorman/YAKL.git) registered for path 'externals/YAKL' Submodule 'externals/cub' (git@github.com:NVlabs/cub.git) registered for path 'externals/cub' Submodule 'externals/kokkos' (https://github.com/E3SM-Project/kokkos.git) registered for path 'externals/kokkos' Submodule 'externals/scorpio' (https://github.com/E3SM-Project/scorpio.git) registered for path 'externals/scorpio' Submodule 'externals/scorpio_classic' (https://github.com/E3SM-Project/scorpio.git) registered for path 'externals/scorpio_classic' + git submodule update Cloning into 'cime'... Submodule path 'cime': checked out '2b49cf54f1fb0a53832762dc29f19fc31c491d31' Cloning into 'components/eam/src/physics/cosp2/external'... Submodule path 'components/eam/src/physics/cosp2/external': checked out '34d8eef3d231a87c0f73e565f6b5d548876b294a' Cloning into 'components/eam/src/physics/rrtmgp/external'... Submodule path 'components/eam/src/physics/rrtmgp/external': checked out 'fdb714ea58e0fcbb23c81e0c6bf93840e5516c27' Cloning into 'components/elm/src/external_models/fates'... Submodule path 'components/elm/src/external_models/fates': checked out '5534a9405bbc5d9b825bf37bd0d65147bc0fda41' Cloning into 'components/elm/src/external_models/mpp'... Submodule path 'components/elm/src/external_models/mpp': checked out 'c0c903e675e31e6b9ab447b0cc51ccd8a36fa7a7' Cloning into 'components/elm/src/external_models/sbetr'... Submodule path 'components/elm/src/external_models/sbetr': checked out 'f3636700b35441dbd30bf2921310a66f238d8e9e' Cloning into 'components/mpas-source'... Submodule path 'components/mpas-source': checked out 'bb1ea15299544e2b25144c06c621ff40fa482760' Cloning into 'externals/YAKL'... Submodule path 'externals/YAKL': checked out '7a5777e5d0afd3dae948462f2cb769043b06d073' Cloning into 'externals/cub'... Submodule path 'externals/cub': checked out 'c3cceac115c072fb63df1836ff46d8c60d9eb304' Cloning into 'externals/kokkos'... Submodule path 'externals/kokkos': checked out '8d62288677f9f7ed20d0e6a15009f0d9087e3170' Cloning into 'externals/scorpio'... Submodule path 'externals/scorpio': checked out '205e1e16d04aa2d449053af26204bc641d9feebf' Cloning into 'externals/scorpio_classic'... Submodule path 'externals/scorpio_classic': checked out '154b0320ed99395ee7e790ed1122ca8bfac3bbc0' [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 (Sat Feb 26 03:37:01 CST 2022), 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_EAM%AV1C-L_ELM%SPBC_CICE%PRES_DOCN%DOM_SROF_SGLC_SWAV Compset specification file is /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_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/e3sm_ne4_silhs_run_gfortran_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: 1f57293 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/e3sm_ne4_silhs_run_gfortran_test/cime_config/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/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 2022-02-26 03:37:11 atm Create namelist for component eam Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/components/eam/cime_config/buildnml 2022-02-26 03:37:11 lnd Create namelist for component elm Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/components/elm/cime_config/buildnml 2022-02-26 03:37:11 ice Create namelist for component cice Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/components/cice/cime_config/buildnml 2022-02-26 03:37:11 ocn Create namelist for component docn Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/data_comps_mct/docn/cime_config/buildnml 2022-02-26 03:37:11 rof Create namelist for component srof Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps_mct/srof/cime_config/buildnml 2022-02-26 03:37:11 glc Create namelist for component sglc Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps_mct/sglc/cime_config/buildnml 2022-02-26 03:37:11 wav Create namelist for component swav Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps_mct/swav/cime_config/buildnml 2022-02-26 03:37:11 iac Create namelist for component siac Running /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps_mct/siac/cime_config/buildnml 2022-02-26 03:37:11 esp Create namelist for component sesp Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps_mct/sesp/cime_config/buildnml 2022-02-26 03:37:11 cpl Create namelist for component drv Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_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/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 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 2022-02-26 03:37:12 atm Create namelist for component eam Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/components/eam/cime_config/buildnml 2022-02-26 03:37:13 lnd Create namelist for component elm Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/components/elm/cime_config/buildnml 2022-02-26 03:37:13 ice Create namelist for component cice Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/components/cice/cime_config/buildnml 2022-02-26 03:37:13 ocn Create namelist for component docn Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/data_comps_mct/docn/cime_config/buildnml 2022-02-26 03:37:13 rof Create namelist for component srof Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps_mct/srof/cime_config/buildnml 2022-02-26 03:37:13 glc Create namelist for component sglc Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps_mct/sglc/cime_config/buildnml 2022-02-26 03:37:13 wav Create namelist for component swav Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps_mct/swav/cime_config/buildnml 2022-02-26 03:37:13 iac Create namelist for component siac Running /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps_mct/siac/cime_config/buildnml 2022-02-26 03:37:13 esp Create namelist for component sesp Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/components/stub_comps_mct/sesp/cime_config/buildnml 2022-02-26 03:37:13 cpl Create namelist for component drv Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_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.220226-033712 Calling /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/build_scripts/buildlib.gptl ERROR: /home/jenkins/workspace/e3sm_ne4_silhs_run_gfortran_test/cime/src/build_scripts/buildlib.gptl FAILED, cat /home/jenkins/E3SM_simulations/nelson.mg2_def.ne4_ne4/build/gptl.bldlog.220226-033712 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 Not sent to the following valid addresses: 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