Stderr output

<core_client_version>8.2.2</core_client_version>
<![CDATA[
<stderr_txt>
13:38:45 (37427): wrapper (7.7.26015): starting
13:38:45 (37427): wrapper: running run_atlas (--nthreads 12)
[2025-11-22 13:38:45] Arguments: --nthreads 12
[2025-11-22 13:38:45] Threads: 12
[2025-11-22 13:38:45] Checking for CVMFS
[2025-11-22 13:38:45] Probing /cvmfs/atlas.cern.ch... OK
[2025-11-22 13:38:45] Probing /cvmfs/atlas-condb.cern.ch... OK
[2025-11-22 13:38:45] Running cvmfs_config stat atlas.cern.ch
[2025-11-22 13:38:52] 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 13:38:52] 2.13.3.0 5957 1211 105916 153173 3 81 4694140 102400001 1717 130560 29 4421010 99.995 51230 9 http://cvmfs-stratum-one.cern.ch:8000/cvmfs/atlas.cern.ch DIRECT 1
[2025-11-22 13:38:52] CVMFS is ok
[2025-11-22 13:38:52] Efficiency of ATLAS tasks can be improved by the following measure(s):
[2025-11-22 13:38:52] The CVMFS client on this computer should be configured to use Cloudflare's openhtc.io.
[2025-11-22 13:38:52] Small home clusters do not require a local http proxy but it is suggested if
[2025-11-22 13:38:52] more than 10 cores throughout the same LAN segment are regularly running ATLAS like tasks.
[2025-11-22 13:38:52] Further information can be found at the LHC@home message board.
[2025-11-22 13:38:52] Using apptainer image /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-centos7
[2025-11-22 13:38:52] Checking for apptainer binary...
[2025-11-22 13:38:52] which: no apptainer in (/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin)
[2025-11-22 13:38:52] apptainer is not installed, using version from CVMFS
[2025-11-22 13:38:52] 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 13:38:52] crocidura-russula
[2025-11-22 13:38:52] apptainer works
[2025-11-22 13:38:52] Set ATHENA_PROC_NUMBER=12
[2025-11-22 13:38:52] Set ATHENA_CORE_NUMBER=12
[2025-11-22 13:38:52] Starting ATLAS job with PandaID=6894287367
[2025-11-22 13:38:52] Running command: /cvmfs/atlas.cern.ch/repo/containers/sw/apptainer/x86_64-el7/current/bin/apptainer exec -B /cvmfs,/virtma/boinc/slots/1 /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-centos7 sh start_atlas.sh
[2025-11-22 17:51:04]  *** The last 200 lines of the pilot log: ***
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | chi2: 66.6681600844044
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | current memory leak: 7.32 B/s (using 229 data points, chi2=66.67)
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | could have reported an average CPU frequency of 4034 MHz (12 samples)
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | ..............................
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . Timing measurements:
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . get job = 0 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . initial setup = 17 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . payload setup = 10 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . stage-in = 0 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . payload execution = 14907 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . stage-out = 14 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . log creation = 0 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | ..............................
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | building log extracts (sent to the server as 'pilotLog')
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | executing command: tail -n 20 /virtma/boinc/slots/1/PanDA_Pilot-6894287367/pilotlog.txt
[2025-11-22 17:51:04] 2025-11-22 17:50:31,803 | WARNING  | detected the following tail of warning/fatal messages in the pilot log:
[2025-11-22 17:51:04] - Log from pilotlog.txt -
[2025-11-22 17:51:04] 2025-11-22 17:50:31,794 | INFO     | sum of square deviations: 3723716330.0
[2025-11-22 17:51:04] 2025-11-22 17:50:31,794 | INFO     | sum of deviations: 27269400472.00009
[2025-11-22 17:51:04] 2025-11-22 17:50:31,794 | INFO     | mean x: 1763826358.0
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | mean y: 2533867.7030567685
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | intersect: -12914262970.946411
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | chi2: 66.6681600844044
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | current memory leak: 7.32 B/s (using 229 data points, chi2=66.67)
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | could have reported an average CPU frequency of 4034 MHz (12 samples)
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | ..............................
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . Timing measurements:
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . get job = 0 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . initial setup = 17 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . payload setup = 10 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . stage-in = 0 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . payload execution = 14907 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . stage-out = 14 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . log creation = 0 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | ..............................
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | building log extracts (sent to the server as 'pilotLog')
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | executing command: tail -n 20 /virtma/boinc/slots/1/PanDA_Pilot-6894287367/pilotlog.txt
[2025-11-22 17:51:04] 2025-11-22 17:50:31,803 | WARNING  | 
[2025-11-22 17:51:04] [begin log extracts]
[2025-11-22 17:51:04] - Log from pilotlog.txt -
[2025-11-22 17:51:04] 2025-11-22 17:50:31,794 | INFO     | sum of square deviations: 3723716330.0
[2025-11-22 17:51:04] 2025-11-22 17:50:31,794 | INFO     | sum of deviations: 27269400472.00009
[2025-11-22 17:51:04] 2025-11-22 17:50:31,794 | INFO     | mean x: 1763826358.0
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | mean y: 2533867.7030567685
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | intersect: -12914262970.946411
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | chi2: 66.6681600844044
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | current memory leak: 7.32 B/s (using 229 data points, chi2=66.67)
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | could have reported an average CPU frequency of 4034 MHz (12 samples)
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | ..............................
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . Timing measurements:
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . get job = 0 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . initial setup = 17 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . payload setup = 10 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . stage-in = 0 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . payload execution = 14907 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . stage-out = 14 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | . log creation = 0 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | ..............................
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | building log extracts (sent to the server as 'pilotLog')
[2025-11-22 17:51:04] 2025-11-22 17:50:31,795 | INFO     | executing command: tail -n 20 /virtma/boinc/slots/1/PanDA_Pilot-6894287367/pilotlog.txt
[2025-11-22 17:51:04] [end log extracts]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,803 | WARNING  | pilotErrorCodes = [1305, 1165] (will report primary/first error code)
[2025-11-22 17:51:04] 2025-11-22 17:50:31,804 | WARNING  | pilotErrorDiags = ['Failed to execute payload:PyJobTransforms.transform.execute  CRITICAL Transform executor raised TransformValidationException: HITSMergeAthenaMP
[2025-11-22 17:51:04] 2025-11-22 17:50:31,834 | INFO     | 
[2025-11-22 17:51:04] 2025-11-22 17:50:31,834 | INFO     | job summary report
[2025-11-22 17:51:04] 2025-11-22 17:50:31,834 | INFO     | --------------------------------------------------
[2025-11-22 17:51:04] 2025-11-22 17:50:31,834 | INFO     | PanDA job id: 6894287367
[2025-11-22 17:51:04] 2025-11-22 17:50:31,834 | INFO     | task id: 47533967
[2025-11-22 17:51:04] 2025-11-22 17:50:31,834 | INFO     | error 1/2: 1305: Failed to execute payload:PyJobTransforms.transform.execute 2025-11-22 17:48:09,652 CRITICAL Transform executor raised TransformValidationExceptio
[2025-11-22 17:51:04] 2025-11-22 17:50:31,834 | INFO     | error 2/2: 1165: Local output file is missing
[2025-11-22 17:51:04] 2025-11-22 17:50:31,834 | INFO     | status: LOG_TRANSFER = DONE 
[2025-11-22 17:51:04] 2025-11-22 17:50:31,834 | INFO     | pilot state: failed 
[2025-11-22 17:51:04] 2025-11-22 17:50:31,834 | INFO     | transexitcode: 65
[2025-11-22 17:51:04] 2025-11-22 17:50:31,834 | INFO     | exeerrorcode: 65
[2025-11-22 17:51:04] 2025-11-22 17:50:31,834 | INFO     | exeerrordiag: HITSMergeAthenaMP0 got a SIGABRT signal (exit code 134); Logfile error in log.HITSMergeAthenaMP0: "Segmentation fault: Event counter: 0; Run: unknown
[2025-11-22 17:51:04] 2025-11-22 17:50:31,834 | INFO     | exitcode: 65
[2025-11-22 17:51:04] 2025-11-22 17:50:31,835 | INFO     | exitmsg: HITSMergeAthenaMP0 got a SIGABRT signal (exit code 134); Logfile error in log.HITSMergeAthenaMP0: "Segmentation fault: Event counter: 0; Run: unknown; Evt
[2025-11-22 17:51:04] 2025-11-22 17:50:31,835 | INFO     | cpuconsumptiontime: 105528 s
[2025-11-22 17:51:04] 2025-11-22 17:50:31,835 | INFO     | nevents: 0
[2025-11-22 17:51:04] 2025-11-22 17:50:31,835 | INFO     | neventsw: 0
[2025-11-22 17:51:04] 2025-11-22 17:50:31,835 | INFO     | pid: 48135
[2025-11-22 17:51:04] 2025-11-22 17:50:31,835 | INFO     | pgrp: 48135
[2025-11-22 17:51:04] 2025-11-22 17:50:31,835 | INFO     | corecount: 12
[2025-11-22 17:51:04] 2025-11-22 17:50:31,835 | INFO     | event service: False
[2025-11-22 17:51:04] 2025-11-22 17:50:31,835 | INFO     | sizes: {0: 2298628, 1: 2298827, 3: 2299089, 11: 2299117, 14922: 2333732, 14936: 2338024, 14938: 2338208, 15057: 2338454}
[2025-11-22 17:51:04] 2025-11-22 17:50:31,835 | INFO     | --------------------------------------------------
[2025-11-22 17:51:04] 2025-11-22 17:50:31,835 | INFO     | 
[2025-11-22 17:51:04] 2025-11-22 17:50:31,835 | INFO     | executing command: ls -lF /virtma/boinc/slots/1
[2025-11-22 17:51:04] 2025-11-22 17:50:31,848 | INFO     | queue jobs had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue payloads had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue data_in had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue data_out had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue current_data_in had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue validated_jobs had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue validated_payloads had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue monitored_payloads had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue finished_jobs had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue finished_payloads had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue finished_data_in had 1 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue finished_data_out had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue failed_jobs had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue failed_payloads had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue failed_data_in had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue failed_data_out had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue completed_jobs had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue completed_jobids has 1 job(s)
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue realtimelog_payloads had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | queue messages had 0 job(s) [purged]
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | job 6894287367 has completed (purged errors)
[2025-11-22 17:51:04] 2025-11-22 17:50:31,849 | INFO     | overall cleanup function is called
[2025-11-22 17:51:04] 2025-11-22 17:50:32,862 | INFO     | --- collectZombieJob: --- 10, [48135]
[2025-11-22 17:51:04] 2025-11-22 17:50:32,862 | INFO     | zombie collector waiting for pid 48135
[2025-11-22 17:51:04] 2025-11-22 17:50:32,862 | INFO     | harmless exception when collecting zombies: [Errno 10] No child processes
[2025-11-22 17:51:04] 2025-11-22 17:50:32,862 | INFO     | collected zombie processes
[2025-11-22 17:51:04] 2025-11-22 17:50:32,862 | INFO     | will attempt to kill all subprocesses of pid=48135
[2025-11-22 17:51:04] 2025-11-22 17:50:32,971 | INFO     | process IDs to be killed: [48135] (in reverse order)
[2025-11-22 17:51:04] 2025-11-22 17:50:33,008 | WARNING  | found no corresponding commands to process id(s)
[2025-11-22 17:51:04] 2025-11-22 17:50:33,008 | INFO     | Do not look for orphan processes in BOINC jobs
[2025-11-22 17:51:04] 2025-11-22 17:50:33,012 | INFO     | did not find any defunct processes belonging to 48135
[2025-11-22 17:51:04] 2025-11-22 17:50:33,016 | INFO     | did not find any defunct processes belonging to 48135
[2025-11-22 17:51:04] 2025-11-22 17:50:33,017 | 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 17:51:04] 2025-11-22 17:50:33,017 | INFO     | ready for new job
[2025-11-22 17:51:04] 2025-11-22 17:50:33,017 | INFO     | pilot has finished with previous job - re-establishing logging
[2025-11-22 17:51:04] 2025-11-22 17:50:33,019 | INFO     | ***************************************
[2025-11-22 17:51:04] 2025-11-22 17:50:33,019 | INFO     | ***  PanDA Pilot version 3.11.1.15  ***
[2025-11-22 17:51:04] 2025-11-22 17:50:33,019 | INFO     | ***************************************
[2025-11-22 17:51:04] 2025-11-22 17:50:33,019 | INFO     | 
[2025-11-22 17:51:04] 2025-11-22 17:50:33,021 | INFO     | architecture information:
[2025-11-22 17:51:04] 2025-11-22 17:50:33,021 | INFO     | executing command: cat /etc/os-release
[2025-11-22 17:51:04] 2025-11-22 17:50:33,030 | INFO     | cat /etc/os-release:
[2025-11-22 17:51:04] NAME="CentOS Linux"
[2025-11-22 17:51:04] VERSION="7 (Core)"
[2025-11-22 17:51:04] ID="centos"
[2025-11-22 17:51:04] ID_LIKE="rhel fedora"
[2025-11-22 17:51:04] VERSION_ID="7"
[2025-11-22 17:51:04] PRETTY_NAME="CentOS Linux 7 (Core)"
[2025-11-22 17:51:04] ANSI_COLOR="0;31"
[2025-11-22 17:51:04] CPE_NAME="cpe:/o:centos:centos:7"
[2025-11-22 17:51:04] HOME_URL="https://www.centos.org/"
[2025-11-22 17:51:04] BUG_REPORT_URL="https://bugs.centos.org/"
[2025-11-22 17:51:04] 
[2025-11-22 17:51:04] CENTOS_MANTISBT_PROJECT="CentOS-7"
[2025-11-22 17:51:04] CENTOS_MANTISBT_PROJECT_VERSION="7"
[2025-11-22 17:51:04] REDHAT_SUPPORT_PRODUCT="centos"
[2025-11-22 17:51:04] REDHAT_SUPPORT_PRODUCT_VERSION="7"
[2025-11-22 17:51:04] 
[2025-11-22 17:51:04] 2025-11-22 17:50:33,030 | INFO     | ***************************************
[2025-11-22 17:51:04] 2025-11-22 17:50:33,532 | INFO     | executing command: df -mP /virtma/boinc/slots/1
[2025-11-22 17:51:04] 2025-11-22 17:50:33,542 | INFO     | sufficient remaining disk space (961020952576 B)
[2025-11-22 17:51:04] 2025-11-22 17:50:33,542 | WARNING  | since timefloor is set to 0, pilot was only allowed to run one job
[2025-11-22 17:51:04] 2025-11-22 17:50:33,542 | INFO     | current server update state: UPDATING_FINAL
[2025-11-22 17:51:04] 2025-11-22 17:50:33,542 | INFO     | update_server=False
[2025-11-22 17:51:04] 2025-11-22 17:50:33,542 | WARNING  | setting graceful_stop since proceed_with_getjob() returned False (pilot will end)
[2025-11-22 17:51:04] 2025-11-22 17:50:33,543 | WARNING  | job:job_monitor:received graceful stop - abort after this iteration
[2025-11-22 17:51:04] 2025-11-22 17:50:33,543 | WARNING  | job:queue_monitor:received graceful stop - abort after this iteration
[2025-11-22 17:51:04] 2025-11-22 17:50:33,543 | INFO     | aborting loop
[2025-11-22 17:51:04] 2025-11-22 17:50:33,749 | INFO     | all job control threads have been joined
[2025-11-22 17:51:04] 2025-11-22 17:50:34,267 | WARNING  | data:copytool_out:received graceful stop - abort after this iteration
[2025-11-22 17:51:04] 2025-11-22 17:50:34,491 | INFO     | all data control threads have been joined
[2025-11-22 17:51:04] 2025-11-22 17:50:34,546 | INFO     | [job] retrieve thread has finished
[2025-11-22 17:51:04] 2025-11-22 17:50:34,548 | INFO     | [job] queue monitor thread has finished
[2025-11-22 17:51:04] 2025-11-22 17:50:34,549 | INFO     | [job] job monitor thread has finished
[2025-11-22 17:51:04] 2025-11-22 17:50:34,630 | INFO     | all payload control threads have been joined
[2025-11-22 17:51:04] 2025-11-22 17:50:34,754 | INFO     | [job] control thread has finished
[2025-11-22 17:51:04] 2025-11-22 17:50:34,777 | INFO     | [payload] run_realtimelog thread has finished
[2025-11-22 17:51:04] 2025-11-22 17:50:34,977 | INFO     | [payload] validate_post thread has finished
[2025-11-22 17:51:04] 2025-11-22 17:50:35,076 | INFO     | [payload] validate_pre thread has finished
[2025-11-22 17:51:04] 2025-11-22 17:50:35,376 | INFO     | [job] validate thread has finished
[2025-11-22 17:51:04] 2025-11-22 17:50:35,414 | INFO     | [job] create_data_payload thread has finished
[2025-11-22 17:51:04] 2025-11-22 17:50:35,435 | INFO     | [payload] failed_post thread has finished
[2025-11-22 17:51:04] 2025-11-22 17:50:35,494 | INFO     | [data] control thread has finished
[2025-11-22 17:51:04] 2025-11-22 17:50:35,636 | INFO     | [payload] control thread has finished
[2025-11-22 17:51:04] 2025-11-22 17:50:35,641 | WARNING  | data:queue_monitoring:received graceful stop - abort after this iteration
[2025-11-22 17:51:04] 2025-11-22 17:50:35,773 | INFO     | [payload] execute_payloads thread has finished
[2025-11-22 17:51:04] 2025-11-22 17:50:35,990 | INFO     | [data] copytool_in thread has finished
[2025-11-22 17:51:04] 2025-11-22 17:50:36,273 | INFO     | [data] copytool_out thread has finished
[2025-11-22 17:51:04] 2025-11-22 17:50:39,647 | INFO     | [data] queue_monitor thread has finished
[2025-11-22 17:51:04] 2025-11-22 17:50:43,354 | INFO     | [monitor] cgroup control has ended
[2025-11-22 17:51:04] 2025-11-22 17:50:45,430 | INFO     | only monitor.control thread still running - safe to abort: ['<_MainThread(MainThread, started 140657722074944)>', '<ExcThread(monitor, started 140657318405888)>']
[2025-11-22 17:51:04] 2025-11-22 17:50:50,454 | INFO     | all workflow threads have been joined
[2025-11-22 17:51:04] 2025-11-22 17:50:50,454 | INFO     | end of generic workflow (traces error code: 0)
[2025-11-22 17:51:04] 2025-11-22 17:50:50,454 | INFO     | traces error code: 0
[2025-11-22 17:51:04] 2025-11-22 17:50:50,454 | INFO     | pilot has finished (exit code=0, shell exit code=0)
[2025-11-22 17:51:04] 2025-11-22 17:51:04,329 | INFO     | PID=41355 has CPU usage=0.8% 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 17:51:04] 2025-11-22 17:51:04,329 | INFO     | .. there are 3 such processes running
[2025-11-22 17:51:04] 2025-11-22 17:51:04,329 | INFO     | found 0 job(s) in 20 queues
[2025-11-22 17:51:04] 2025-11-22 17:51:04,329 | WARNING  | pilot monitor received instruction that args.graceful_stop has been set
[2025-11-22 17:51:04] 2025-11-22 17:51:04,329 | WARNING  | will wait for a maximum of 300 s for threads to finish
[2025-11-22 17:51:04] 2025-11-22 17:51:04,329 | WARNING  | job_aborted has been set - aborting pilot monitoring
[2025-11-22 17:51:04] 2025-11-22 17:51:04,329 | INFO     | [monitor] control thread has ended
[2025-11-22 17:51:04] 2025-11-22 17:51:04,385 [wrapper] ==== pilot stdout END ====
[2025-11-22 17:51:04] 2025-11-22 17:51:04,387 [wrapper] ==== wrapper stdout RESUME ====
[2025-11-22 17:51:04] 2025-11-22 17:51:04,389 [wrapper] pilotpid: 41355
[2025-11-22 17:51:04] 2025-11-22 17:51:04,390 [wrapper] Pilot exit status: 0
[2025-11-22 17:51:04] 2025-11-22 17:51:04,396 [wrapper] pandaids: 6894287367
[2025-11-22 17:51:04] 2025-11-22 17:51:04,420 [wrapper] cleanup supervisor_pilot 31032 41356
[2025-11-22 17:51:04] 2025-11-22 17:51:04,422 [wrapper] Test setup, not cleaning
[2025-11-22 17:51:04] 2025-11-22 17:51:04,424 [wrapper] apfmon messages muted
[2025-11-22 17:51:04] 2025-11-22 17:51:04,425 [wrapper] ==== wrapper stdout END ====
[2025-11-22 17:51:04] 2025-11-22 17:51:04,427 [wrapper] ==== wrapper stderr END ====
[2025-11-22 17:51:04]  *** Error codes and diagnostics ***
[2025-11-22 17:51:04]     "exeErrorCode": 65,
[2025-11-22 17:51:04]     "exeErrorDiag": "HITSMergeAthenaMP0 got a SIGABRT signal (exit code 134); Logfile error in log.HITSMergeAthenaMP0: \"Segmentation fault: Event counter: 0; Run: unknown; Evt: unknown; Current algorithm: <NONE>; Current Function: unknown\"",
[2025-11-22 17:51:04]     "pilotErrorCode": 1305,
[2025-11-22 17:51:04]     "pilotErrorDiag": "Failed to execute payload:PyJobTransforms.transform.execute  CRITICAL Transform executor raised TransformValidationException: HITSMergeAthenaMP0 got a SIGABRT signal (exit code 134); Logfile error in log.HITSMergeAthenaMP0: \"Segmentation fault: Event counter: 0; Run: unknown; Evt: unk",
[2025-11-22 17:51:04]  *** Listing of results directory ***
[2025-11-22 17:51:04] total 412880
[2025-11-22 17:51:04] -rw-r--r-- 1 boinc boinc    576529 Nov 21 10:34 pilot3.tar.gz
[2025-11-22 17:51:04] -rwx------ 1 boinc boinc     36292 Nov 21 10:45 runpilot2-wrapper.sh
[2025-11-22 17:51:04] -rw-r--r-- 1 boinc boinc      5112 Nov 21 10:45 queuedata.json
[2025-11-22 17:51:04] -rw-r--r-- 1 boinc boinc       100 Nov 22 13:38 wrapper_26015_x86_64-pc-linux-gnu
[2025-11-22 17:51:04] -rwxr-xr-x 1 boinc boinc      7986 Nov 22 13:38 run_atlas
[2025-11-22 17:51:04] -rw-r--r-- 1 boinc boinc       105 Nov 22 13:38 job.xml
[2025-11-22 17:51:04] -rw-r--r-- 2 boinc boinc     15847 Nov 22 13:38 start_atlas.sh
[2025-11-22 17:51:04] drwxrwx--x 2 boinc boinc        68 Nov 22 13:38 shared
[2025-11-22 17:51:04] -rw-r--r-- 2 boinc boinc    590098 Nov 22 13:38 input.tar.gz
[2025-11-22 17:51:04] -rw-r--r-- 1 boinc boinc      8919 Nov 22 13:38 init_data.xml
[2025-11-22 17:51:04] -rw-r--r-- 2 boinc boinc 410690537 Nov 22 13:38 EVNT.47493127._002377.pool.root.1
[2025-11-22 17:51:04] -rw-r--r-- 1 boinc boinc         0 Nov 22 13:38 boinc_setup_complete
[2025-11-22 17:51:04] -rw-r--r-- 1 boinc boinc         0 Nov 22 13:38 boinc_lockfile
[2025-11-22 17:51:04] -rw-r--r-- 1 boinc boinc      2782 Nov 22 13:38 pandaJob.out
[2025-11-22 17:51:04] -rw------- 1 boinc boinc    989768 Nov 22 13:39 agis_schedconf.cvmfs.json
[2025-11-22 17:51:04] drwx------ 5 boinc boinc      4096 Nov 22 13:39 pilot3
[2025-11-22 17:51:04] -rw-r--r-- 1 boinc boinc       532 Nov 22 17:00 boinc_task_state.xml
[2025-11-22 17:51:04] -rw------- 1 boinc boinc      1036 Nov 22 17:48 memory_monitor_summary.json
[2025-11-22 17:51:04] -rw------- 1 boinc boinc   1924802 Nov 22 17:48 log.47533967._003481.job.log.tgz.1
[2025-11-22 17:51:04] -rw------- 1 boinc boinc   1526164 Nov 22 17:48 agis_ddmendpoints.agis.ALL.json
[2025-11-22 17:51:04] -rw------- 1 boinc boinc        95 Nov 22 17:50 pilot_heartbeat.json
[2025-11-22 17:51:04] -rw------- 1 boinc boinc     11393 Nov 22 17:50 heartbeat.json
[2025-11-22 17:51:04] -rw-r--r-- 1 boinc boinc        29 Nov 22 17:51 wrapper_checkpoint.txt
[2025-11-22 17:51:04] -rw-r--r-- 1 boinc boinc      8192 Nov 22 17:51 boinc_mmap_file
[2025-11-22 17:51:04] -rw------- 1 boinc boinc       820 Nov 22 17:51 pilotlog.txt
[2025-11-22 17:51:04] -rw------- 1 boinc boinc   2169695 Nov 22 17:51 log.47533967._003481.job.log.1
[2025-11-22 17:51:04] -rw------- 1 boinc boinc       186 Nov 22 17:51 output.list
[2025-11-22 17:51:04] -rw-r--r-- 1 boinc boinc       620 Nov 22 17:51 runtime_log
[2025-11-22 17:51:04] -rw------- 1 boinc boinc   4116480 Nov 22 17:51 result.tar.gz
[2025-11-22 17:51:04] -rw-r--r-- 1 boinc boinc      8662 Nov 22 17:51 runtime_log.err
[2025-11-22 17:51:04] -rw------- 1 boinc boinc       662 Nov 22 17:51 fUWLDm4odg8nsSi4ap6QjLDmwznN0nGgGQJmNLGKDmTIJKDmrXyATm.diag
[2025-11-22 17:51:04] -rw-r--r-- 1 boinc boinc     22415 Nov 22 17:51 stderr.txt
[2025-11-22 17:51:04] No HITS result produced
[2025-11-22 17:51:04]  *** Contents of shared directory: ***
[2025-11-22 17:51:04] total 405684
[2025-11-22 17:51:04] -rw-r--r-- 2 boinc boinc     15847 Nov 22 13:38 start_atlas.sh
[2025-11-22 17:51:04] -rw-r--r-- 2 boinc boinc    590098 Nov 22 13:38 input.tar.gz
[2025-11-22 17:51:04] -rw-r--r-- 2 boinc boinc 410690537 Nov 22 13:38 ATLAS.root_0
[2025-11-22 17:51:04] -rw------- 1 boinc boinc   4116480 Nov 22 17:51 result.tar.gz
17:51:06 (37427): run_atlas exited; CPU time 105597.439986
17:51:06 (37427): called boinc_finish(0)

</stderr_txt>
]]>

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