Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
12:31:39 (18321): wrapper (7.7.26015): starting
12:31:39 (18321): wrapper: running run_atlas (--nthreads 4)
2019-08-17 12:31:39,516: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-17 12:31:39,516: sys.argv = ['run_atlas', '--nthreads', '4']
2019-08-17 12:31:39,517: THREADS=4

2019-08-17 12:31:39,520: Checking for CVMFS
2019-08-17 12:31:41,157: CVMFS is installed
2019-08-17 12:31:41,161: OS:CentOS Linux release 7.6.1810 (Core) 
2019-08-17 12:31:41,161: This is not SLC6, need to run with Singularity....
2019-08-17 12:31:41,161: Checking Singularity...
2019-08-17 12:31:41,164: Singularity is not installed, using version from CVMFS
2019-08-17 12:31:41,164: Testing the function of Singularity...
2019-08-17 12:31:41,164: Checking singularity with cmd:/cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
2019-08-17 12:31:41,453: Singularity Works...
2019-08-17 12:31:41,453: copy /home/grid/slots/0/shared/ATLAS.root_0
2019-08-17 12:31:41,983: copy /home/grid/slots/0/shared/input.tar.gz
2019-08-17 12:31:41,984: copy /home/grid/slots/0/shared/RTE.tar.gz
2019-08-17 12:31:41,984: copy /home/grid/slots/0/shared/start_atlas.sh
2019-08-17 12:31:41,985: export ATHENA_PROC_NUMBER=4;
2019-08-17 12:31:42,006: start atlas job with PandaID=4442992966
2019-08-17 12:31:42,006: cmd = /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec --pwd /home/grid/slots/0 -B /cvmfs,/home /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 sh start_atlas.sh > runtime_log 2> runtime_log.err
2019-08-17 14:52:17,094: running cmd return value is 0
2019-08-17 14:52:17,098: Moving ./HITS.18722398._017714.pool.root.1 to shared/HITS.pool.root.1
2019-08-17 14:52:17,098: *****************The last 100 lines of the pilot log******************
2019-08-17 14:52:17,106: 2019-08-17 12:51:26,870 | DEBUG    | queue_monitor       | pilot.control.job                | send_state                | wrote heartbeat to file /home/grid/slots/0/heartbeat.json
2019-08-17 12:51:26,870 | INFO     | queue_monitor       | pilot.control.job                | queue_monitor             | job 4442992966 was dequeued from the monitored payloads queue
2019-08-17 12:51:27,335 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-17 12:51:27,335 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-17 12:51:27,336 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-17 12:51:27,336 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4442992966
2019-08-17 12:51:27,336 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722398
2019-08-17 12:51:27,336 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-17 12:51:27,336 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-17 12:51:27,336 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-17 12:51:27,336 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-17 12:51:27,336 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-17 12:51:27,336 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-17 12:51:27,336 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-17 12:51:27,336 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-17 12:51:27,336 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 31262 s
2019-08-17 12:51:27,336 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-17 12:51:27,337 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-17 12:51:27,337 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 24999
2019-08-17 12:51:27,337 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 24999
2019-08-17 12:51:27,337 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-17 12:51:27,337 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-17 12:51:27,337 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-17 12:51:27,337 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-17 12:51:27,337 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4442992966 has completed
2019-08-17 12:51:27,337 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-17 12:51:27,345 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4442992966
2019-08-17 12:51:28,350 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [24999]
2019-08-17 12:51:28,351 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 24999
2019-08-17 12:51:28,351 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-17 12:51:29,356 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-17 12:51:29,356 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=24999
2019-08-17 12:51:29,406 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [24999] (in reverse order)
2019-08-17 12:51:29,443 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-17 12:51:29,444 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-17 12:51:29,444 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-17 12:51:29,444 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-17 12:51:29,952 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-17 12:51:39,958 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-17 12:51:39,958 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-17 12:51:39,996 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35000418304 B)
2019-08-17 12:51:39,997 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-17 12:51:39,997 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-17 12:51:40,016 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-17 12:51:40,047 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-17 12:51:40,118 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-17 12:51:40,143 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-17 12:51:40,152 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-17 12:51:40,166 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-17 12:51:40,166 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140542367471360)>, <ExcThread(job, started 140542151198464)>, <ExcThread(monitor, started 140542033770240)>, <ExcThread(queue_monitor, started 140541060708096)>, <ExcThread(job_monitor, started 140541631117056)>, <ExcThread(copytool_out, started 140542042162944)>, <ExcThread(failed_post, started 140541622724352)>, <ExcThread(payload, started 140542050555648)>, <ExcThread(execute_payloads, started 140541614331648)>, <ExcThread(data, started 140542067341056)>, <ExcThread(create_data_payload, started 140542025377536)>, <ExcThread(queue_monitoring, started 140542016984832)>, <ExcThread(validate, started 140542058948352)>]
2019-08-17 12:51:40,554 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-17 12:51:40,554 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-17 12:51:40,588 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-17 12:51:40,669 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-17 12:51:40,669 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140542367471360)>, <ExcThread(job, started 140542151198464)>, <ExcThread(monitor, started 140542033770240)>, <ExcThread(queue_monitor, started 140541060708096)>, <ExcThread(job_monitor, started 140541631117056)>, <ExcThread(copytool_out, started 140542042162944)>, <ExcThread(failed_post, started 140541622724352)>, <ExcThread(payload, started 140542050555648)>, <ExcThread(create_data_payload, started 140542025377536)>, <ExcThread(queue_monitoring, started 140542016984832)>, <ExcThread(validate, started 140542058948352)>]
2019-08-17 12:51:40,878 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-17 12:51:40,937 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-17 12:51:40,970 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-17 12:51:40,971 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140542367471360)>, <ExcThread(job, started 140542151198464)>, <ExcThread(queue_monitor, started 140541060708096)>, <ExcThread(job_monitor, started 140541631117056)>, <ExcThread(copytool_out, started 140542042162944)>, <ExcThread(failed_post, started 140541622724352)>, <ExcThread(payload, started 140542050555648)>, <ExcThread(queue_monitoring, started 140542016984832)>, <ExcThread(validate, started 140542058948352)>]
2019-08-17 12:51:41,017 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-17 12:51:41,049 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-17 12:51:41,049 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-17 12:51:41,104 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-17 12:51:41,104 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-17 12:51:41,104 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-17 12:51:41,135 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-17 12:51:41,136 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140542367471360)>, <ExcThread(queue_monitor, started 140541060708096)>, <ExcThread(job_monitor, started 140541631117056)>, <ExcThread(queue_monitoring, started 140542016984832)>, <ExcThread(validate, started 140542058948352)>]
2019-08-17 12:51:41,250 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-17 12:51:41,337 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-17 12:51:41,337 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140542367471360)>, <ExcThread(queue_monitor, started 140541060708096)>, <ExcThread(job_monitor, started 140541631117056)>, <ExcThread(queue_monitoring, started 140542016984832)>]
2019-08-17 12:51:41,845 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-17 12:51:41,845 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-17 12:51:41,942 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-17 12:51:41,942 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140542367471360)>, <ExcThread(job_monitor, started 140541631117056)>, <ExcThread(queue_monitoring, started 140542016984832)>]
2019-08-17 12:51:43,048 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-17 12:51:43,050 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-17 12:51:43,051 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140542367471360)>, <ExcThread(job_monitor, started 140541631117056)>]
2019-08-17 12:52:16,673 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-17 12:52:16,673 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-17 12:52:16,688 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-17 12:52:16,688 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-17 12:52:16,688 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-17 12:52:16 UTC [wrapper] ==== pilot stdout END ====
2019-08-17 12:52:16 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-17 12:52:16 UTC [wrapper] Pilot exit status: 0
2019-08-17 12:52:16 UTC [wrapper] STATUSCODE: 0
2019-08-17 12:52:16 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
total 44
-rw-------.  1 grid grid 11357 Jul 25 16:38 LICENSE
drwx------. 14 grid grid   216 Aug 17 12:31 pilot
-rwx------.  1 grid grid 20463 Jul 25 16:38 pilot.py
-rw-------.  1 grid grid     8 Aug  7 13:02 PILOTVERSION
-rw-------.  1 grid grid  2251 Jul 25 16:38 README.md
-rw-------.  1 grid grid   221 Jul 25 16:38 TODO.md

2019-08-17 12:52:16 UTC [wrapper] Test setup, not cleaning
2019-08-17 12:52:16 UTC [wrapper] ==== wrapper stdout END ====
2019-08-17 12:52:16 UTC [wrapper] ==== wrapper stderr END ====
2019-08-17 14:52:17,110: ***************diag file************
2019-08-17 14:52:17,111: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=8434.70s
KernelTime=258.21s
UserTime=31133.30s
CPUUsage=372%
MaxResidentMemory=1945276kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=315789
MinorPageFaults=14244004
Swaps=0
ForcedSwitches=3606799
WaitSwitches=6415278
Inputs=76881248
Outputs=622080
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
2019-08-17 14:52:17,120: ******************************WorkDir***********************
2019-08-17 14:52:17,120: total 216660
drwxrwx--x. 7 grid grid      4096 Aug 17 14:52 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7417847 Aug 17 12:31 agis_ddmendpoints.json
-rw-------. 1 grid grid   4400331 Aug 17 12:31 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 17 12:31 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 17 12:31 APPS
drwxr-xr-x. 2 grid grid         6 Aug 17 12:31 .arc
-rw-------. 1 grid grid       538 Aug 17 12:31 .asetup
-rw-------. 1 grid grid       826 Aug 17 12:32 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 17 12:31 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 17 14:52 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 17 14:45 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 207909339 Aug 17 12:31 EVNT.18605775._000348.pool.root.1
-rw-------. 1 grid grid     94471 Aug 17 14:51 heartbeat.json
-rw-------. 1 grid grid       516 Aug 17 14:52 HJrMDmw5sGvnShfckohDCDFpABFKDmABFKDmlcyYDmABFKDmyamcEm.diag
-rw-rw-r--. 1 grid grid      5866 Aug 17 12:31 init_data.xml
-rw-rw-r--. 1 grid grid    262347 Aug 17 12:31 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 17 12:31 job.xml
-rw-------. 1 grid grid    512148 Aug 17 14:52 log.18722398._017714.job.log.1
-rw-------. 1 grid grid    835387 Aug 17 14:51 log.18722398._017714.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 17 14:52 output.list
-rw-------. 1 grid grid      2957 Aug 11 04:49 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 11 04:33 pilot2.tar.gz
-rw-------. 1 grid grid      9570 Aug 17 14:52 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 11 04:49 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 17 12:31 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8466 Aug 17 12:31 run_atlas
-rwx------. 1 grid grid     15232 Aug 11 04:49 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 17 14:52 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 17 14:52 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 17 14:52 shared
-rw-rw-r--. 1 grid grid      8688 Aug 17 12:31 start_atlas.sh
-rw-rw-r--. 1 grid grid     18669 Aug 17 14:52 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 17 12:31 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 17 14:52 wrapper_checkpoint.txt

2019-08-17 14:52:17,120: running start_atlas return value is 0
2019-08-17 14:52:17,120: Parent exit 0
2019-08-17 14:52:17,123: child process exit 0
14:52:17 (18321): run_atlas exited; CPU time 31133.692024
14:52:17 (18321): called boinc_finish(0)

</stderr_txt>
]]>

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