Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
03:35:56 (10639): wrapper (7.7.26015): starting
03:35:56 (10639): wrapper: running run_atlas (--nthreads 4)
2019-08-23 03:35:56,796: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-23 03:35:56,796: sys.argv = ['run_atlas', '--nthreads', '4']
2019-08-23 03:35:56,797: THREADS=4

2019-08-23 03:35:56,799: Checking for CVMFS
2019-08-23 03:35:58,421: CVMFS is installed
2019-08-23 03:35:58,424: OS:CentOS Linux release 7.6.1810 (Core) 
2019-08-23 03:35:58,424: This is not SLC6, need to run with Singularity....
2019-08-23 03:35:58,424: Checking Singularity...
2019-08-23 03:35:58,427: Singularity is not installed, using version from CVMFS
2019-08-23 03:35:58,428: Testing the function of Singularity...
2019-08-23 03:35:58,428: 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
2019-08-23 03:35:58,666: Singularity Works...
2019-08-23 03:35:58,666: copy /home/grid/slots/0/shared/ATLAS.root_0
2019-08-23 03:35:59,089: copy /home/grid/slots/0/shared/input.tar.gz
2019-08-23 03:35:59,090: copy /home/grid/slots/0/shared/RTE.tar.gz
2019-08-23 03:35:59,091: copy /home/grid/slots/0/shared/start_atlas.sh
2019-08-23 03:35:59,091: export ATHENA_PROC_NUMBER=4;
2019-08-23 03:35:59,114: start atlas job with PandaID=4452275828
2019-08-23 03:35:59,114: 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
2019-08-23 05:24:46,914: running cmd return value is 0
2019-08-23 05:24:46,917: Moving ./HITS.18722144._020189.pool.root.1 to shared/HITS.pool.root.1
2019-08-23 05:24:46,917: *****************The last 100 lines of the pilot log******************
2019-08-23 05:24:46,926: 2019-08-23 03:23:45,101 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722144
2019-08-23 03:23:45,101 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-23 03:23:45,101 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-23 03:23:45,101 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-23 03:23:45,101 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-23 03:23:45,101 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-23 03:23:45,101 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-23 03:23:45,101 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-23 03:23:45,101 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-23 03:23:45,101 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 23519 s
2019-08-23 03:23:45,101 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-23 03:23:45,102 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-23 03:23:45,102 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 17439
2019-08-23 03:23:45,102 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 17439
2019-08-23 03:23:45,102 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-23 03:23:45,102 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-23 03:23:45,102 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-23 03:23:45,102 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-23 03:23:45,102 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4452275828 has completed
2019-08-23 03:23:45,102 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-23 03:23:45,112 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4452275828
2019-08-23 03:23:46,116 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [17439]
2019-08-23 03:23:46,116 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 17439
2019-08-23 03:23:46,116 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-23 03:23:47,120 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-23 03:23:47,120 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=17439
2019-08-23 03:23:47,173 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [17439] (in reverse order)
2019-08-23 03:23:47,213 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-23 03:23:47,213 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-23 03:23:47,213 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-23 03:23:47,213 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-23 03:23:47,723 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-23 03:23:57,765 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-23 03:23:57,766 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-23 03:23:57,797 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (36249272320 B)
2019-08-23 03:23:57,798 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-23 03:23:57,798 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-23 03:23:57,826 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 16 threads
2019-08-23 03:23:57,827 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140236230792960)>, <ExcThread(job, started 140236014520064)>, <ExcThread(queue_monitoring, started 140235748914944)>, <ExcThread(validate_post, started 140235220436736)>, <ExcThread(payload, started 140235757307648)>, <ExcThread(monitor, started 140235245614848)>, <ExcThread(validate, started 140236006127360)>, <ExcThread(copytool_out, started 140235774093056)>, <ExcThread(copytool_in, started 140235228829440)>, <ExcThread(create_data_payload, started 140235782485760)>, <ExcThread(job_monitor, started 140235740522240)>, <ExcThread(failed_post, started 140235212044032)>, <ExcThread(validate_pre, started 140235732129536)>, <ExcThread(queue_monitor, started 140235237222144)>, <ExcThread(data, started 140235997734656)>, <ExcThread(execute_payloads, started 140235203651328)>]
2019-08-23 03:23:57,855 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-23 03:23:57,855 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-23 03:23:57,908 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-23 03:23:57,977 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-23 03:23:58,036 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-23 03:23:58,134 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-23 03:23:58,194 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-23 03:23:58,229 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-23 03:23:58,229 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140236230792960)>, <ExcThread(queue_monitoring, started 140235748914944)>, <ExcThread(payload, started 140235757307648)>, <ExcThread(copytool_out, started 140235774093056)>, <ExcThread(copytool_in, started 140235228829440)>, <ExcThread(job_monitor, started 140235740522240)>, <ExcThread(failed_post, started 140235212044032)>, <ExcThread(validate_pre, started 140235732129536)>, <ExcThread(queue_monitor, started 140235237222144)>, <ExcThread(data, started 140235997734656)>]
2019-08-23 03:23:58,300 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-23 03:23:58,300 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-23 03:23:58,349 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-23 03:23:58,430 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-23 03:23:58,430 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140236230792960)>, <ExcThread(queue_monitoring, started 140235748914944)>, <ExcThread(copytool_out, started 140235774093056)>, <ExcThread(job_monitor, started 140235740522240)>, <ExcThread(failed_post, started 140235212044032)>, <ExcThread(validate_pre, started 140235732129536)>, <ExcThread(queue_monitor, started 140235237222144)>, <ExcThread(data, started 140235997734656)>]
2019-08-23 03:23:58,619 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-23 03:23:58,619 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-23 03:23:58,631 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-23 03:23:58,632 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140236230792960)>, <ExcThread(queue_monitoring, started 140235748914944)>, <ExcThread(copytool_out, started 140235774093056)>, <ExcThread(job_monitor, started 140235740522240)>, <ExcThread(failed_post, started 140235212044032)>, <ExcThread(validate_pre, started 140235732129536)>, <ExcThread(queue_monitor, started 140235237222144)>]
2019-08-23 03:23:58,727 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-23 03:23:58,730 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-23 03:23:58,924 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-23 03:23:58,933 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-23 03:23:58,934 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140236230792960)>, <ExcThread(queue_monitoring, started 140235748914944)>, <ExcThread(copytool_out, started 140235774093056)>, <ExcThread(job_monitor, started 140235740522240)>, <ExcThread(validate_pre, started 140235732129536)>, <ExcThread(queue_monitor, started 140235237222144)>]
2019-08-23 03:23:59,078 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-23 03:23:59,135 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-23 03:23:59,135 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140236230792960)>, <ExcThread(queue_monitoring, started 140235748914944)>, <ExcThread(copytool_out, started 140235774093056)>, <ExcThread(job_monitor, started 140235740522240)>, <ExcThread(queue_monitor, started 140235237222144)>]
2019-08-23 03:23:59,608 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-23 03:23:59,608 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-23 03:23:59,639 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-23 03:23:59,639 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140236230792960)>, <ExcThread(queue_monitoring, started 140235748914944)>, <ExcThread(copytool_out, started 140235774093056)>, <ExcThread(job_monitor, started 140235740522240)>]
2019-08-23 03:23:59,728 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-23 03:23:59,740 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-23 03:23:59,740 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140236230792960)>, <ExcThread(queue_monitoring, started 140235748914944)>, <ExcThread(job_monitor, started 140235740522240)>]
2019-08-23 03:24:01,731 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-23 03:24:01,754 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-23 03:24:01,755 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140236230792960)>, <ExcThread(job_monitor, started 140235740522240)>]
2019-08-23 03:24:46,436 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 123 s)
2019-08-23 03:24:46,437 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-23 03:24:46,480 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-23 03:24:46,481 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-23 03:24:46,481 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-23 03:24:46 UTC [wrapper] ==== pilot stdout END ====
2019-08-23 03:24:46 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-23 03:24:46 UTC [wrapper] Pilot exit status: 0
2019-08-23 03:24:46 UTC [wrapper] STATUSCODE: 0
2019-08-23 03:24:46 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 23 03:36 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

2019-08-23 03:24:46 UTC [wrapper] Test setup, not cleaning
2019-08-23 03:24:46 UTC [wrapper] ==== wrapper stdout END ====
2019-08-23 03:24:46 UTC [wrapper] ==== wrapper stderr END ====
2019-08-23 03:24:46 UTC [wrapper] wrapper wrapperexiting ec=0, duration=6527
2019-08-23 03:24:46 UTC [wrapper] apfmon messages muted
2019-08-23 05:24:46,930: ***************diag file************
2019-08-23 05:24:46,930: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=6527.44s
KernelTime=219.56s
UserTime=23408.05s
CPUUsage=361%
MaxResidentMemory=1945280kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=282112
MinorPageFaults=13133584
Swaps=0
ForcedSwitches=2763279
WaitSwitches=5460255
Inputs=68809680
Outputs=578168
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
2019-08-23 05:24:46,939: ******************************WorkDir***********************
2019-08-23 05:24:46,939: total 247580
drwxrwx--x. 6 grid grid      4096 Aug 23 05:24 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid       516 Aug 23 05:24 5WaMDmb4kJvnShfckohDCDFpABFKDmABFKDmz31LDmABFKDmLswMpm.diag
-rw-------. 1 grid grid   7460931 Aug 23 03:36 agis_ddmendpoints.json
-rw-------. 1 grid grid   4339162 Aug 23 03:36 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 23 03:35 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 23 03:35 APPS
-rw-------. 1 grid grid       538 Aug 23 03:36 .asetup
-rw-------. 1 grid grid       826 Aug 23 03:36 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 23 03:35 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 23 05:24 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 23 05:18 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 239721728 Aug 23 03:35 EVNT.18605742._000392.pool.root.1
-rw-------. 1 grid grid     72259 Aug 23 05:23 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 23 03:35 init_data.xml
-rw-rw-r--. 1 grid grid    261623 Aug 23 03:35 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 23 03:35 job.xml
-rw-------. 1 grid grid    422054 Aug 23 05:24 log.18722144._020189.job.log.1
-rw-------. 1 grid grid    820471 Aug 23 05:23 log.18722144._020189.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 23 05:24 output.list
-rw-------. 1 grid grid      2921 Aug 19 02:51 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 19 02:27 pilot2.tar.gz
-rw-------. 1 grid grid     10893 Aug 23 05:24 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 19 02:51 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 23 03:35 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8466 Aug 23 03:35 run_atlas
-rwx------. 1 grid grid     12641 Aug 19 02:51 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 23 05:24 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 23 05:24 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 23 05:24 shared
-rw-rw-r--. 1 grid grid      8688 Aug 23 03:35 start_atlas.sh
-rw-rw-r--. 1 grid grid     19177 Aug 23 05:24 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 23 03:35 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 23 05:24 wrapper_checkpoint.txt

2019-08-23 05:24:46,939: running start_atlas return value is 0
2019-08-23 05:24:46,939: Parent exit 0
2019-08-23 05:24:46,941: child process exit 0
05:24:47 (10639): run_atlas exited; CPU time 23408.433197
05:24:47 (10639): called boinc_finish(0)

</stderr_txt>
]]>

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