Stderr output

<core_client_version>8.2.2</core_client_version>
<![CDATA[
<stderr_txt>
09:19:04 (15983): wrapper (7.7.26015): starting
09:19:04 (15983): wrapper: running run_atlas (--nthreads 12)
[2025-11-22 09:19:04] Arguments: --nthreads 12
[2025-11-22 09:19:04] Threads: 12
[2025-11-22 09:19:04] Checking for CVMFS
[2025-11-22 09:19:04] Probing /cvmfs/atlas.cern.ch... OK
[2025-11-22 09:19:04] Probing /cvmfs/atlas-condb.cern.ch... OK
[2025-11-22 09:19:04] Running cvmfs_config stat atlas.cern.ch
[2025-11-22 09:19:08] VERSION PID UPTIME(M) MEM(K) REVISION EXPIRES(M) NOCATALOGS CACHEUSE(K) CACHEMAX(K) NOFDUSE NOFDMAX NOIOERR NOOPEN HITRATE(%) RX(K) SPEED(K/S) HOST PROXY ONLINE
[2025-11-22 09:19:08] 2.13.3.0 5957 951 102820 153166 0 80 4647771 102400000 766 130560 29 4007371 99.995 40625 8 http://cvmfs-stratum-one.cern.ch:8000/cvmfs/atlas.cern.ch DIRECT 1
[2025-11-22 09:19:08] CVMFS is ok
[2025-11-22 09:19:08] Efficiency of ATLAS tasks can be improved by the following measure(s):
[2025-11-22 09:19:08] The CVMFS client on this computer should be configured to use Cloudflare's openhtc.io.
[2025-11-22 09:19:08] Small home clusters do not require a local http proxy but it is suggested if
[2025-11-22 09:19:08] more than 10 cores throughout the same LAN segment are regularly running ATLAS like tasks.
[2025-11-22 09:19:08] Further information can be found at the LHC@home message board.
[2025-11-22 09:19:08] Using apptainer image /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-centos7
[2025-11-22 09:19:08] Checking for apptainer binary...
[2025-11-22 09:19:08] which: no apptainer in (/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin)
[2025-11-22 09:19:08] apptainer is not installed, using version from CVMFS
[2025-11-22 09:19:08] Checking apptainer works with /cvmfs/atlas.cern.ch/repo/containers/sw/apptainer/x86_64-el7/current/bin/apptainer exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-centos7 hostname
[2025-11-22 09:19:08] crocidura-russula
[2025-11-22 09:19:08] apptainer works
[2025-11-22 09:19:08] Set ATHENA_PROC_NUMBER=12
[2025-11-22 09:19:08] Set ATHENA_CORE_NUMBER=12
[2025-11-22 09:19:08] Starting ATLAS job with PandaID=6895328927
[2025-11-22 09:19:08] Running command: /cvmfs/atlas.cern.ch/repo/containers/sw/apptainer/x86_64-el7/current/bin/apptainer exec -B /cvmfs,/virtma/boinc/slots/2 /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-centos7 sh start_atlas.sh
[2025-11-22 13:50:08]  *** The last 200 lines of the pilot log: ***
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | chi2: 40.39920490879337
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | current memory leak: 131.21 B/s (using 246 data points, chi2=40.40)
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | could have reported an average CPU frequency of 3888 MHz (12 samples)
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | ..............................
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . Timing measurements:
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . get job = 0 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . initial setup = 24 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . payload setup = 2 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . stage-in = 0 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . payload execution = 15957 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . stage-out = 12 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . log creation = 0 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | ..............................
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | building log extracts (sent to the server as 'pilotLog')
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | executing command: tail -n 20 /virtma/boinc/slots/2/PanDA_Pilot-6895328927/pilotlog.txt
[2025-11-22 13:50:08] 2025-11-22 13:49:17,369 | WARNING  | detected the following tail of warning/fatal messages in the pilot log:
[2025-11-22 13:50:08] - Log from pilotlog.txt -
[2025-11-22 13:50:08] 2025-11-22 13:49:17,360 | INFO     | sum of square deviations: 4616114457.5
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | sum of deviations: 605676806658.0001
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | mean x: 1763811277.5
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | mean y: 2779962.6341463416
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | intersect: -231425533165.05603
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | chi2: 40.39920490879337
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | current memory leak: 131.21 B/s (using 246 data points, chi2=40.40)
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | could have reported an average CPU frequency of 3888 MHz (12 samples)
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | ..............................
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . Timing measurements:
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . get job = 0 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . initial setup = 24 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . payload setup = 2 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . stage-in = 0 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . payload execution = 15957 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . stage-out = 12 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . log creation = 0 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | ..............................
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | building log extracts (sent to the server as 'pilotLog')
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | executing command: tail -n 20 /virtma/boinc/slots/2/PanDA_Pilot-6895328927/pilotlog.txt
[2025-11-22 13:50:08] 2025-11-22 13:49:17,369 | WARNING  | 
[2025-11-22 13:50:08] [begin log extracts]
[2025-11-22 13:50:08] - Log from pilotlog.txt -
[2025-11-22 13:50:08] 2025-11-22 13:49:17,360 | INFO     | sum of square deviations: 4616114457.5
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | sum of deviations: 605676806658.0001
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | mean x: 1763811277.5
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | mean y: 2779962.6341463416
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | intersect: -231425533165.05603
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | chi2: 40.39920490879337
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | current memory leak: 131.21 B/s (using 246 data points, chi2=40.40)
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | could have reported an average CPU frequency of 3888 MHz (12 samples)
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | ..............................
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . Timing measurements:
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . get job = 0 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . initial setup = 24 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . payload setup = 2 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . stage-in = 0 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . payload execution = 15957 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . stage-out = 12 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | . log creation = 0 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | ..............................
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | building log extracts (sent to the server as 'pilotLog')
[2025-11-22 13:50:08] 2025-11-22 13:49:17,361 | INFO     | executing command: tail -n 20 /virtma/boinc/slots/2/PanDA_Pilot-6895328927/pilotlog.txt
[2025-11-22 13:50:08] [end log extracts]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,369 | WARNING  | pilotErrorCodes = [1305, 1165] (will report primary/first error code)
[2025-11-22 13:50:08] 2025-11-22 13:49:17,369 | WARNING  | pilotErrorDiags = ['Failed to execute payload:PyJobTransforms.transform.execute  CRITICAL Transform executor raised TransformValidationException: Non-zero return c
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | 
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | job summary report
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | --------------------------------------------------
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | PanDA job id: 6895328927
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | task id: 47556137
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | error 1/2: 1305: Failed to execute payload:PyJobTransforms.transform.execute 2025-11-22 13:45:45,821 CRITICAL Transform executor raised TransformValidationExceptio
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | error 2/2: 1165: Local output file is missing
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | status: LOG_TRANSFER = DONE 
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | pilot state: failed 
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | transexitcode: 65
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | exeerrorcode: 65
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | exeerrordiag: Non-zero return code from HITSMergeAthenaMP0 (64); Logfile error in log.HITSMergeAthenaMP0: "Segmentation fault: Event counter: 0; Run: unknown; Evt:
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | exitcode: 65
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | exitmsg: Non-zero return code from HITSMergeAthenaMP0 (64); Logfile error in log.HITSMergeAthenaMP0: "Segmentation fault: Event counter: 0; Run: unknown; Evt: unkn
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | cpuconsumptiontime: 128909 s
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | nevents: 0
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | neventsw: 0
[2025-11-22 13:50:08] 2025-11-22 13:49:17,857 | INFO     | pid: 40188
[2025-11-22 13:50:08] 2025-11-22 13:49:17,858 | INFO     | pgrp: 40188
[2025-11-22 13:50:08] 2025-11-22 13:49:17,858 | INFO     | corecount: 12
[2025-11-22 13:50:08] 2025-11-22 13:49:17,858 | INFO     | event service: False
[2025-11-22 13:50:08] 2025-11-22 13:49:17,858 | INFO     | sizes: {0: 2298751, 2: 2299013, 11: 2299041, 15963: 2333847, 15976: 2338139, 15979: 2338195, 16168: 2338569}
[2025-11-22 13:50:08] 2025-11-22 13:49:17,858 | INFO     | --------------------------------------------------
[2025-11-22 13:50:08] 2025-11-22 13:49:17,858 | INFO     | 
[2025-11-22 13:50:08] 2025-11-22 13:49:17,858 | INFO     | executing command: ls -lF /virtma/boinc/slots/2
[2025-11-22 13:50:08] 2025-11-22 13:49:17,870 | INFO     | queue jobs had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,870 | INFO     | queue payloads had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,870 | INFO     | queue data_in had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,870 | INFO     | queue data_out had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,870 | INFO     | queue current_data_in had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,871 | INFO     | queue validated_jobs had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,871 | INFO     | queue validated_payloads had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,871 | INFO     | queue monitored_payloads had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,871 | INFO     | queue finished_jobs had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,871 | INFO     | queue finished_payloads had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,871 | INFO     | queue finished_data_in had 1 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,871 | INFO     | queue finished_data_out had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,871 | INFO     | queue failed_jobs had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,871 | INFO     | queue failed_payloads had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,871 | INFO     | queue failed_data_in had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,871 | INFO     | queue failed_data_out had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,871 | INFO     | queue completed_jobs had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,871 | INFO     | queue completed_jobids has 1 job(s)
[2025-11-22 13:50:08] 2025-11-22 13:49:17,871 | INFO     | queue realtimelog_payloads had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,871 | INFO     | queue messages had 0 job(s) [purged]
[2025-11-22 13:50:08] 2025-11-22 13:49:17,871 | INFO     | job 6895328927 has completed (purged errors)
[2025-11-22 13:50:08] 2025-11-22 13:49:17,871 | INFO     | overall cleanup function is called
[2025-11-22 13:50:08] 2025-11-22 13:49:18,884 | INFO     | --- collectZombieJob: --- 10, [40188]
[2025-11-22 13:50:08] 2025-11-22 13:49:18,884 | INFO     | zombie collector waiting for pid 40188
[2025-11-22 13:50:08] 2025-11-22 13:49:18,884 | INFO     | harmless exception when collecting zombies: [Errno 10] No child processes
[2025-11-22 13:50:08] 2025-11-22 13:49:18,884 | INFO     | collected zombie processes
[2025-11-22 13:50:08] 2025-11-22 13:49:18,884 | INFO     | will attempt to kill all subprocesses of pid=40188
[2025-11-22 13:50:08] 2025-11-22 13:49:18,963 | INFO     | process IDs to be killed: [40188] (in reverse order)
[2025-11-22 13:50:08] 2025-11-22 13:49:18,996 | WARNING  | found no corresponding commands to process id(s)
[2025-11-22 13:50:08] 2025-11-22 13:49:18,996 | INFO     | Do not look for orphan processes in BOINC jobs
[2025-11-22 13:50:08] 2025-11-22 13:49:18,999 | INFO     | did not find any defunct processes belonging to 40188
[2025-11-22 13:50:08] 2025-11-22 13:49:19,001 | INFO     | did not find any defunct processes belonging to 40188
[2025-11-22 13:50:08] 2025-11-22 13:49:19,002 | WARNING  | condor_chirp not found. condor_config_val not found. | If you're on a worker node/container, HTCondor may not expose configs to your env. Try: export CONDOR_CONFIG
[2025-11-22 13:50:08] 2025-11-22 13:49:19,002 | INFO     | ready for new job
[2025-11-22 13:50:08] 2025-11-22 13:49:19,002 | INFO     | pilot has finished with previous job - re-establishing logging
[2025-11-22 13:50:08] 2025-11-22 13:49:19,003 | INFO     | ***************************************
[2025-11-22 13:50:08] 2025-11-22 13:49:19,003 | INFO     | ***  PanDA Pilot version 3.11.1.15  ***
[2025-11-22 13:50:08] 2025-11-22 13:49:19,003 | INFO     | ***************************************
[2025-11-22 13:50:08] 2025-11-22 13:49:19,003 | INFO     | 
[2025-11-22 13:50:08] 2025-11-22 13:49:19,005 | INFO     | architecture information:
[2025-11-22 13:50:08] 2025-11-22 13:49:19,005 | INFO     | executing command: cat /etc/os-release
[2025-11-22 13:50:08] 2025-11-22 13:49:19,012 | INFO     | cat /etc/os-release:
[2025-11-22 13:50:08] NAME="CentOS Linux"
[2025-11-22 13:50:08] VERSION="7 (Core)"
[2025-11-22 13:50:08] ID="centos"
[2025-11-22 13:50:08] ID_LIKE="rhel fedora"
[2025-11-22 13:50:08] VERSION_ID="7"
[2025-11-22 13:50:08] PRETTY_NAME="CentOS Linux 7 (Core)"
[2025-11-22 13:50:08] ANSI_COLOR="0;31"
[2025-11-22 13:50:08] CPE_NAME="cpe:/o:centos:centos:7"
[2025-11-22 13:50:08] HOME_URL="https://www.centos.org/"
[2025-11-22 13:50:08] BUG_REPORT_URL="https://bugs.centos.org/"
[2025-11-22 13:50:08] 
[2025-11-22 13:50:08] CENTOS_MANTISBT_PROJECT="CentOS-7"
[2025-11-22 13:50:08] CENTOS_MANTISBT_PROJECT_VERSION="7"
[2025-11-22 13:50:08] REDHAT_SUPPORT_PRODUCT="centos"
[2025-11-22 13:50:08] REDHAT_SUPPORT_PRODUCT_VERSION="7"
[2025-11-22 13:50:08] 
[2025-11-22 13:50:08] 2025-11-22 13:49:19,012 | INFO     | ***************************************
[2025-11-22 13:50:08] 2025-11-22 13:49:19,515 | INFO     | executing command: df -mP /virtma/boinc/slots/2
[2025-11-22 13:50:08] 2025-11-22 13:49:19,523 | INFO     | sufficient remaining disk space (957655023616 B)
[2025-11-22 13:50:08] 2025-11-22 13:49:19,524 | WARNING  | since timefloor is set to 0, pilot was only allowed to run one job
[2025-11-22 13:50:08] 2025-11-22 13:49:19,524 | INFO     | current server update state: UPDATING_FINAL
[2025-11-22 13:50:08] 2025-11-22 13:49:19,524 | INFO     | update_server=False
[2025-11-22 13:50:08] 2025-11-22 13:49:19,524 | WARNING  | setting graceful_stop since proceed_with_getjob() returned False (pilot will end)
[2025-11-22 13:50:08] 2025-11-22 13:49:19,524 | WARNING  | data:copytool_out:received graceful stop - abort after this iteration
[2025-11-22 13:50:08] 2025-11-22 13:49:19,524 | WARNING  | data:queue_monitoring:received graceful stop - abort after this iteration
[2025-11-22 13:50:08] 2025-11-22 13:49:19,641 | INFO     | all job control threads have been joined
[2025-11-22 13:50:08] 2025-11-22 13:49:19,790 | INFO     | all payload control threads have been joined
[2025-11-22 13:50:08] 2025-11-22 13:49:20,044 | INFO     | all data control threads have been joined
[2025-11-22 13:50:08] 2025-11-22 13:49:20,422 | WARNING  | job:job_monitor:received graceful stop - abort after this iteration
[2025-11-22 13:50:08] 2025-11-22 13:49:20,422 | INFO     | aborting loop
[2025-11-22 13:50:08] 2025-11-22 13:49:20,529 | INFO     | [job] retrieve thread has finished
[2025-11-22 13:50:08] 2025-11-22 13:49:20,596 | INFO     | [payload] failed_post thread has finished
[2025-11-22 13:50:08] 2025-11-22 13:49:20,646 | INFO     | [job] control thread has finished
[2025-11-22 13:50:08] 2025-11-22 13:49:20,734 | INFO     | [payload] run_realtimelog thread has finished
[2025-11-22 13:50:08] 2025-11-22 13:49:20,796 | INFO     | [payload] control thread has finished
[2025-11-22 13:50:08] 2025-11-22 13:49:21,050 | INFO     | [data] control thread has finished
[2025-11-22 13:50:08] 2025-11-22 13:49:21,155 | INFO     | [payload] execute_payloads thread has finished
[2025-11-22 13:50:08] 2025-11-22 13:49:21,195 | INFO     | [payload] validate_pre thread has finished
[2025-11-22 13:50:08] 2025-11-22 13:49:21,374 | INFO     | [payload] validate_post thread has finished
[2025-11-22 13:50:08] 2025-11-22 13:49:21,427 | INFO     | [job] job monitor thread has finished
[2025-11-22 13:50:08] 2025-11-22 13:49:21,526 | INFO     | [data] copytool_out thread has finished
[2025-11-22 13:50:08] 2025-11-22 13:49:21,577 | INFO     | [job] create_data_payload thread has finished
[2025-11-22 13:50:08] 2025-11-22 13:49:21,738 | INFO     | [job] validate thread has finished
[2025-11-22 13:50:08] 2025-11-22 13:49:21,750 | INFO     | [data] copytool_in thread has finished
[2025-11-22 13:50:08] 2025-11-22 13:49:22,407 | WARNING  | job:queue_monitor:received graceful stop - abort after this iteration
[2025-11-22 13:50:08] 2025-11-22 13:49:23,410 | INFO     | [job] queue monitor thread has finished
[2025-11-22 13:50:08] 2025-11-22 13:49:23,530 | INFO     | [data] queue_monitor thread has finished
[2025-11-22 13:50:08] 2025-11-22 13:49:49,433 | INFO     | PID=20140 has CPU usage=0.7% CMD=/cvmfs/atlas.cern.ch/repo/ATLASLocalRootBase/x86_64/python/3.9.20-x86_64-centos7/bin/python3 pilot3/pilot.py -q BOINC_MCORE -i PR 
[2025-11-22 13:50:08] 2025-11-22 13:49:49,433 | INFO     | .. there are 3 such processes running
[2025-11-22 13:50:08] 2025-11-22 13:49:49,433 | INFO     | found 0 job(s) in 20 queues
[2025-11-22 13:50:08] 2025-11-22 13:49:49,434 | WARNING  | pilot monitor received instruction that args.graceful_stop has been set
[2025-11-22 13:50:08] 2025-11-22 13:49:49,434 | WARNING  | will wait for a maximum of 300 s for threads to finish
[2025-11-22 13:50:08] 2025-11-22 13:50:01,930 | INFO     | [monitor] cgroup control has ended
[2025-11-22 13:50:08] 2025-11-22 13:50:03,587 | INFO     | only monitor.control thread still running - safe to abort: ['<_MainThread(MainThread, started 140437664724800)>', '<ExcThread(monitor, started 140437260048128)>']
[2025-11-22 13:50:08] 2025-11-22 13:50:04,506 | WARNING  | job_aborted has been set - aborting pilot monitoring
[2025-11-22 13:50:08] 2025-11-22 13:50:04,506 | INFO     | [monitor] control thread has ended
[2025-11-22 13:50:08] 2025-11-22 13:50:08,610 | INFO     | all workflow threads have been joined
[2025-11-22 13:50:08] 2025-11-22 13:50:08,610 | INFO     | end of generic workflow (traces error code: 0)
[2025-11-22 13:50:08] 2025-11-22 13:50:08,610 | INFO     | traces error code: 0
[2025-11-22 13:50:08] 2025-11-22 13:50:08,610 | INFO     | pilot has finished (exit code=0, shell exit code=0)
[2025-11-22 13:50:08] 2025-11-22 13:50:08,651 [wrapper] ==== pilot stdout END ====
[2025-11-22 13:50:08] 2025-11-22 13:50:08,652 [wrapper] ==== wrapper stdout RESUME ====
[2025-11-22 13:50:08] 2025-11-22 13:50:08,653 [wrapper] pilotpid: 20140
[2025-11-22 13:50:08] 2025-11-22 13:50:08,655 [wrapper] Pilot exit status: 0
[2025-11-22 13:50:08] 2025-11-22 13:50:08,660 [wrapper] pandaids: 6895328927
[2025-11-22 13:50:08] 2025-11-22 13:50:08,678 [wrapper] cleanup supervisor_pilot  8809 20141
[2025-11-22 13:50:08] 2025-11-22 13:50:08,680 [wrapper] Test setup, not cleaning
[2025-11-22 13:50:08] 2025-11-22 13:50:08,681 [wrapper] apfmon messages muted
[2025-11-22 13:50:08] 2025-11-22 13:50:08,682 [wrapper] ==== wrapper stdout END ====
[2025-11-22 13:50:08] 2025-11-22 13:50:08,683 [wrapper] ==== wrapper stderr END ====
[2025-11-22 13:50:08]  *** Error codes and diagnostics ***
[2025-11-22 13:50:08]     "exeErrorCode": 65,
[2025-11-22 13:50:08]     "exeErrorDiag": "Non-zero return code from HITSMergeAthenaMP0 (64); Logfile error in log.HITSMergeAthenaMP0: \"Segmentation fault: Event counter: 0; Run: unknown; Evt: unknown; Current algorithm: <NONE>; Current Function: unknown\"",
[2025-11-22 13:50:08]     "pilotErrorCode": 1305,
[2025-11-22 13:50:08]     "pilotErrorDiag": "Failed to execute payload:PyJobTransforms.transform.execute  CRITICAL Transform executor raised TransformValidationException: Non-zero return code from HITSMergeAthenaMP0 (64); Logfile error in log.HITSMergeAthenaMP0: \"Segmentation fault: Event counter: 0; Run: unknown; Evt: unknown;",
[2025-11-22 13:50:08]  *** Listing of results directory ***
[2025-11-22 13:50:08] total 413332
[2025-11-22 13:50:08] -rw-r--r-- 1 boinc boinc    576529 Nov 21 18:11 pilot3.tar.gz
[2025-11-22 13:50:08] -rwx------ 1 boinc boinc     36292 Nov 21 18:19 runpilot2-wrapper.sh
[2025-11-22 13:50:08] -rw-r--r-- 1 boinc boinc      5112 Nov 21 18:19 queuedata.json
[2025-11-22 13:50:08] -rw-r--r-- 1 boinc boinc       100 Nov 22 09:19 wrapper_26015_x86_64-pc-linux-gnu
[2025-11-22 13:50:08] -rwxr-xr-x 1 boinc boinc      7986 Nov 22 09:19 run_atlas
[2025-11-22 13:50:08] -rw-r--r-- 1 boinc boinc       105 Nov 22 09:19 job.xml
[2025-11-22 13:50:08] -rw-r--r-- 2 boinc boinc     15847 Nov 22 09:19 start_atlas.sh
[2025-11-22 13:50:08] drwxrwx--x 2 boinc boinc        68 Nov 22 09:19 shared
[2025-11-22 13:50:08] -rw-r--r-- 2 boinc boinc    590097 Nov 22 09:19 input.tar.gz
[2025-11-22 13:50:08] -rw-r--r-- 1 boinc boinc      8919 Nov 22 09:19 init_data.xml
[2025-11-22 13:50:08] -rw-r--r-- 2 boinc boinc 410880241 Nov 22 09:19 EVNT.47483658._000095.pool.root.1
[2025-11-22 13:50:08] -rw-r--r-- 1 boinc boinc         0 Nov 22 09:19 boinc_setup_complete
[2025-11-22 13:50:08] -rw-r--r-- 1 boinc boinc         0 Nov 22 09:19 boinc_lockfile
[2025-11-22 13:50:08] -rw-r--r-- 1 boinc boinc      2783 Nov 22 09:19 pandaJob.out
[2025-11-22 13:50:08] -rw------- 1 boinc boinc    989768 Nov 22 09:19 agis_schedconf.cvmfs.json
[2025-11-22 13:50:08] drwx------ 5 boinc boinc      4096 Nov 22 09:19 pilot3
[2025-11-22 13:50:08] -rw-r--r-- 1 boinc boinc       532 Nov 22 13:22 boinc_task_state.xml
[2025-11-22 13:50:08] -rw------- 1 boinc boinc      1039 Nov 22 13:45 memory_monitor_summary.json
[2025-11-22 13:50:08] -rw------- 1 boinc boinc   1949634 Nov 22 13:45 log.47556137._000946.job.log.tgz.1
[2025-11-22 13:50:08] -rw------- 1 boinc boinc   1526164 Nov 22 13:46 agis_ddmendpoints.agis.ALL.json
[2025-11-22 13:50:08] -rw------- 1 boinc boinc        95 Nov 22 13:48 pilot_heartbeat.json
[2025-11-22 13:50:08] -rw------- 1 boinc boinc     11385 Nov 22 13:49 heartbeat.json
[2025-11-22 13:50:08] -rw-r--r-- 1 boinc boinc      8192 Nov 22 13:50 boinc_mmap_file
[2025-11-22 13:50:08] -rw-r--r-- 1 boinc boinc        29 Nov 22 13:50 wrapper_checkpoint.txt
[2025-11-22 13:50:08] -rw------- 1 boinc boinc      4821 Nov 22 13:50 pilotlog.txt
[2025-11-22 13:50:08] -rw------- 1 boinc boinc   2282422 Nov 22 13:50 log.47556137._000946.job.log.1
[2025-11-22 13:50:08] -rw------- 1 boinc boinc       186 Nov 22 13:50 output.list
[2025-11-22 13:50:08] -rw-r--r-- 1 boinc boinc       620 Nov 22 13:50 runtime_log
[2025-11-22 13:50:08] -rw------- 1 boinc boinc   4249600 Nov 22 13:50 result.tar.gz
[2025-11-22 13:50:08] -rw-r--r-- 1 boinc boinc      8662 Nov 22 13:50 runtime_log.err
[2025-11-22 13:50:08] -rw------- 1 boinc boinc       663 Nov 22 13:50 AYfLDmoukg8n9Rq4apOajLDm4fhM0noT9bVo0NGKDmnlHKDmGhjwhm.diag
[2025-11-22 13:50:08] -rw-r--r-- 1 boinc boinc     22400 Nov 22 13:50 stderr.txt
[2025-11-22 13:50:08] No HITS result produced
[2025-11-22 13:50:08]  *** Contents of shared directory: ***
[2025-11-22 13:50:08] total 406000
[2025-11-22 13:50:08] -rw-r--r-- 2 boinc boinc     15847 Nov 22 09:19 start_atlas.sh
[2025-11-22 13:50:08] -rw-r--r-- 2 boinc boinc    590097 Nov 22 09:19 input.tar.gz
[2025-11-22 13:50:08] -rw-r--r-- 2 boinc boinc 410880241 Nov 22 09:19 ATLAS.root_0
[2025-11-22 13:50:08] -rw------- 1 boinc boinc   4249600 Nov 22 13:50 result.tar.gz
13:50:10 (15983): run_atlas exited; CPU time 128952.974077
13:50:10 (15983): called boinc_finish(0)

</stderr_txt>
]]>

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