Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
01:03:07 (32312): wrapper (7.7.26015): starting
01:03:07 (32312): wrapper: running run_atlas (--nthreads 4)
2019-08-20 01:03:07,560: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-20 01:03:07,560: sys.argv = ['run_atlas', '--nthreads', '4']
2019-08-20 01:03:07,561: THREADS=4

2019-08-20 01:03:07,563: Checking for CVMFS
2019-08-20 01:03:09,250: CVMFS is installed
2019-08-20 01:03:09,253: OS:CentOS Linux release 7.6.1810 (Core) 
2019-08-20 01:03:09,254: This is not SLC6, need to run with Singularity....
2019-08-20 01:03:09,254: Checking Singularity...
2019-08-20 01:03:09,257: Singularity is not installed, using version from CVMFS
2019-08-20 01:03:09,257: Testing the function of Singularity...
2019-08-20 01:03:09,257: 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
2019-08-20 01:03:09,486: Singularity Works...
2019-08-20 01:03:09,486: copy /home/grid/slots/0/shared/ATLAS.root_0
2019-08-20 01:03:09,787: copy /home/grid/slots/0/shared/input.tar.gz
2019-08-20 01:03:09,788: copy /home/grid/slots/0/shared/RTE.tar.gz
2019-08-20 01:03:09,788: copy /home/grid/slots/0/shared/start_atlas.sh
2019-08-20 01:03:09,789: export ATHENA_PROC_NUMBER=4;
2019-08-20 01:03:09,813: start atlas job with PandaID=4452212861
2019-08-20 01:03:09,813: 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
2019-08-20 02:49:39,953: running cmd return value is 0
2019-08-20 02:49:39,956: Moving ./HITS.18722355._012816.pool.root.1 to shared/HITS.pool.root.1
2019-08-20 02:49:39,957: *****************The last 100 lines of the pilot log******************
2019-08-20 02:49:39,964: 2019-08-20 00:48:34,207 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-20 00:48:34,207 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-20 00:48:34,207 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-20 00:48:34,207 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 22975 s
2019-08-20 00:48:34,207 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-20 00:48:34,207 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-20 00:48:34,207 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 6610
2019-08-20 00:48:34,208 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 6610
2019-08-20 00:48:34,208 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-20 00:48:34,208 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-20 00:48:34,208 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-20 00:48:34,208 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-20 00:48:34,208 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4452212861 has completed
2019-08-20 00:48:34,208 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-20 00:48:34,215 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4452212861
2019-08-20 00:48:35,031 | INFO     | monitor             | pilot.control.monitor            | control                   | 6311 s have passed since pilot start
2019-08-20 00:48:35,217 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [6610]
2019-08-20 00:48:35,218 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 6610
2019-08-20 00:48:35,218 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-20 00:48:36,223 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-20 00:48:36,223 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=6610
2019-08-20 00:48:36,280 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [6610] (in reverse order)
2019-08-20 00:48:36,322 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-20 00:48:36,322 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-20 00:48:36,322 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-20 00:48:36,323 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-20 00:48:36,833 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-20 00:48:37,913 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-20 00:48:46,883 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-20 00:48:46,883 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-20 00:48:46,923 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (34706817024 B)
2019-08-20 00:48:46,924 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-20 00:48:46,924 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-20 00:48:46,933 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-20 00:48:46,971 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-20 00:48:47,180 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-20 00:48:47,180 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139794602231552)>, <ExcThread(job, started 139794385958656)>, <ExcThread(payload, started 139794352387840)>, <ExcThread(copytool_out, started 139794360780544)>, <ExcThread(validate, started 139794369173248)>, <ExcThread(execute_payloads, started 139793862223616)>, <ExcThread(data, started 139794377565952)>, <ExcThread(validate_pre, started 139794004834048)>, <ExcThread(queue_monitor, started 139793845438208)>, <ExcThread(failed_post, started 139793962870528)>, <ExcThread(validate_post, started 139793979655936)>, <ExcThread(job_monitor, started 139793853830912)>, <ExcThread(copytool_in, started 139793988048640)>, <ExcThread(create_data_payload, started 139793971263232)>, <ExcThread(queue_monitoring, started 139793870616320)>]
2019-08-20 00:48:47,393 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-20 00:48:47,393 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-20 00:48:47,457 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-20 00:48:47,457 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-20 00:48:47,468 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-20 00:48:47,482 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-20 00:48:47,482 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139794602231552)>, <ExcThread(copytool_out, started 139794360780544)>, <ExcThread(validate, started 139794369173248)>, <ExcThread(execute_payloads, started 139793862223616)>, <ExcThread(data, started 139794377565952)>, <ExcThread(validate_pre, started 139794004834048)>, <ExcThread(queue_monitor, started 139793845438208)>, <ExcThread(failed_post, started 139793962870528)>, <ExcThread(validate_post, started 139793979655936)>, <ExcThread(job_monitor, started 139793853830912)>, <ExcThread(create_data_payload, started 139793971263232)>, <ExcThread(queue_monitoring, started 139793870616320)>]
2019-08-20 00:48:47,546 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-20 00:48:47,546 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-20 00:48:47,583 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-20 00:48:47,583 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139794602231552)>, <ExcThread(copytool_out, started 139794360780544)>, <ExcThread(validate, started 139794369173248)>, <ExcThread(execute_payloads, started 139793862223616)>, <ExcThread(validate_pre, started 139794004834048)>, <ExcThread(queue_monitor, started 139793845438208)>, <ExcThread(failed_post, started 139793962870528)>, <ExcThread(validate_post, started 139793979655936)>, <ExcThread(job_monitor, started 139793853830912)>, <ExcThread(create_data_payload, started 139793971263232)>, <ExcThread(queue_monitoring, started 139793870616320)>]
2019-08-20 00:48:47,619 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-20 00:48:47,684 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-20 00:48:47,685 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139794602231552)>, <ExcThread(copytool_out, started 139794360780544)>, <ExcThread(validate, started 139794369173248)>, <ExcThread(execute_payloads, started 139793862223616)>, <ExcThread(validate_pre, started 139794004834048)>, <ExcThread(queue_monitor, started 139793845438208)>, <ExcThread(failed_post, started 139793962870528)>, <ExcThread(job_monitor, started 139793853830912)>, <ExcThread(create_data_payload, started 139793971263232)>, <ExcThread(queue_monitoring, started 139793870616320)>]
2019-08-20 00:48:47,740 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-20 00:48:47,785 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-20 00:48:47,786 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139794602231552)>, <ExcThread(copytool_out, started 139794360780544)>, <ExcThread(validate, started 139794369173248)>, <ExcThread(execute_payloads, started 139793862223616)>, <ExcThread(validate_pre, started 139794004834048)>, <ExcThread(queue_monitor, started 139793845438208)>, <ExcThread(job_monitor, started 139793853830912)>, <ExcThread(create_data_payload, started 139793971263232)>, <ExcThread(queue_monitoring, started 139793870616320)>]
2019-08-20 00:48:47,867 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-20 00:48:47,887 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-20 00:48:47,887 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139794602231552)>, <ExcThread(copytool_out, started 139794360780544)>, <ExcThread(execute_payloads, started 139793862223616)>, <ExcThread(validate_pre, started 139794004834048)>, <ExcThread(queue_monitor, started 139793845438208)>, <ExcThread(job_monitor, started 139793853830912)>, <ExcThread(create_data_payload, started 139793971263232)>, <ExcThread(queue_monitoring, started 139793870616320)>]
2019-08-20 00:48:47,972 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-20 00:48:47,988 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-20 00:48:47,988 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139794602231552)>, <ExcThread(execute_payloads, started 139793862223616)>, <ExcThread(validate_pre, started 139794004834048)>, <ExcThread(queue_monitor, started 139793845438208)>, <ExcThread(job_monitor, started 139793853830912)>, <ExcThread(create_data_payload, started 139793971263232)>, <ExcThread(queue_monitoring, started 139793870616320)>]
2019-08-20 00:48:48,026 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-20 00:48:48,077 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-20 00:48:48,089 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-20 00:48:48,089 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139794602231552)>, <ExcThread(queue_monitor, started 139793845438208)>, <ExcThread(job_monitor, started 139793853830912)>, <ExcThread(create_data_payload, started 139793971263232)>, <ExcThread(queue_monitoring, started 139793870616320)>]
2019-08-20 00:48:48,109 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-20 00:48:48,190 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-20 00:48:48,190 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139794602231552)>, <ExcThread(queue_monitor, started 139793845438208)>, <ExcThread(job_monitor, started 139793853830912)>, <ExcThread(queue_monitoring, started 139793870616320)>]
2019-08-20 00:48:48,685 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-20 00:48:48,694 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-20 00:48:48,695 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-20 00:48:48,794 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-20 00:48:48,795 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139794602231552)>, <ExcThread(job_monitor, started 139793853830912)>, <ExcThread(queue_monitoring, started 139793870616320)>]
2019-08-20 00:48:51,686 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-20 00:48:51,714 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-20 00:48:51,714 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139794602231552)>, <ExcThread(job_monitor, started 139793853830912)>]
2019-08-20 00:49:39,499 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 123 s)
2019-08-20 00:49:39,499 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-20 00:49:39,544 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-20 00:49:39,544 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-20 00:49:39,544 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-20 00:49:39 UTC [wrapper] ==== pilot stdout END ====
2019-08-20 00:49:39 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-20 00:49:39 UTC [wrapper] Pilot exit status: 0
2019-08-20 00:49:39 UTC [wrapper] STATUSCODE: 0
2019-08-20 00:49:39 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 20 01:03 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

2019-08-20 00:49:39 UTC [wrapper] Test setup, not cleaning
2019-08-20 00:49:39 UTC [wrapper] ==== wrapper stdout END ====
2019-08-20 00:49:39 UTC [wrapper] ==== wrapper stderr END ====
2019-08-20 00:49:39 UTC [wrapper] wrapper wrapperexiting ec=0, duration=6389
2019-08-20 00:49:39 UTC [wrapper] apfmon messages muted
2019-08-20 02:49:39,968: ***************diag file************
2019-08-20 02:49:39,968: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=6389.78s
KernelTime=196.69s
UserTime=22884.47s
CPUUsage=361%
MaxResidentMemory=1944960kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=273430
MinorPageFaults=12844739
Swaps=0
ForcedSwitches=2675231
WaitSwitches=5578868
Inputs=66704464
Outputs=543888
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
2019-08-20 02:49:39,977: ******************************WorkDir***********************
2019-08-20 02:49:39,977: total 210508
drwxrwx--x. 6 grid grid      4096 Aug 20 02:49 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid       516 Aug 20 02:49 20DMDmYGiJvnShfckohDCDFpABFKDmABFKDmJUxLDmABFKDm7wPg0n.diag
-rw-------. 1 grid grid   7442625 Aug 20 01:03 agis_ddmendpoints.json
-rw-------. 1 grid grid   4371574 Aug 20 01:03 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 20 01:03 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 20 01:03 APPS
-rw-------. 1 grid grid       538 Aug 20 01:03 .asetup
-rw-------. 1 grid grid       826 Aug 20 01:04 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 20 01:03 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 20 02:49 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 20 02:43 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 201747578 Aug 20 01:03 EVNT.18605773._000256.pool.root.1
-rw-------. 1 grid grid     68208 Aug 20 02:48 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 20 01:03 init_data.xml
-rw-rw-r--. 1 grid grid    261614 Aug 20 01:03 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 20 01:03 job.xml
-rw-------. 1 grid grid    416884 Aug 20 02:49 log.18722355._012816.job.log.1
-rw-------. 1 grid grid    821863 Aug 20 02:48 log.18722355._012816.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 20 02:49 output.list
-rw-------. 1 grid grid      2955 Aug 18 23:51 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 18 23:24 pilot2.tar.gz
-rw-------. 1 grid grid     13035 Aug 20 02:49 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 18 23:51 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 20 01:03 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8466 Aug 20 01:03 run_atlas
-rwx------. 1 grid grid     12641 Aug 18 23:51 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 20 02:49 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 20 02:49 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 20 02:49 shared
-rw-rw-r--. 1 grid grid      8688 Aug 20 01:03 start_atlas.sh
-rw-rw-r--. 1 grid grid     20622 Aug 20 02:49 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 20 01:03 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 20 02:49 wrapper_checkpoint.txt

2019-08-20 02:49:39,977: running start_atlas return value is 0
2019-08-20 02:49:39,977: Parent exit 0
2019-08-20 02:49:39,979: child process exit 0
02:49:40 (32312): run_atlas exited; CPU time 22884.854638
02:49:40 (32312): called boinc_finish(0)

</stderr_txt>
]]>

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