Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
18:56:17 (31691): wrapper (7.7.26015): starting
18:56:17 (31691): wrapper: running run_atlas (--nthreads 4)
singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
sys.argv = ['run_atlas', '--nthreads', '4']
THREADS=4
Checking for CVMFS
CVMFS is installed
OS:CentOS Linux release 7.6.1810 (Core) 

This is not SLC6, need to run with Singularity....
Checking Singularity...
Singularity is not installed, using version from CVMFS
Testing the function of Singularity...
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
Singularity Works...

copy /home/grid/slots/0/shared/ATLAS.root_0
copy /home/grid/slots/0/shared/input.tar.gz
copy /home/grid/slots/0/shared/RTE.tar.gz
copy /home/grid/slots/0/shared/start_atlas.sh
export ATHENA_PROC_NUMBER=4;start atlas job with PandaID=4442774483
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
running cmd return value is 0
Moving ./HITS.18722298._014322.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-15 21:46:13,743 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-15 21:46:13,744 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-15 21:46:13,744 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4442774483
2019-08-15 21:46:13,744 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722298
2019-08-15 21:46:13,744 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-15 21:46:13,744 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-15 21:46:13,744 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-15 21:46:13,744 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-15 21:46:13,744 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-15 21:46:13,744 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-15 21:46:13,744 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-15 21:46:13,744 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-15 21:46:13,744 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 66441 s
2019-08-15 21:46:13,744 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-15 21:46:13,745 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-15 21:46:13,745 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 5986
2019-08-15 21:46:13,745 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 5986
2019-08-15 21:46:13,745 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-15 21:46:13,745 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-15 21:46:13,745 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-15 21:46:13,745 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-15 21:46:13,745 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4442774483 has completed
2019-08-15 21:46:13,745 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-15 21:46:13,754 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4442774483
2019-08-15 21:46:14,759 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [5986]
2019-08-15 21:46:14,759 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 5986
2019-08-15 21:46:14,760 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-15 21:46:15,765 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-15 21:46:15,765 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=5986
2019-08-15 21:46:15,814 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [5986] (in reverse order)
2019-08-15 21:46:15,860 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-15 21:46:15,860 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-15 21:46:15,860 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-15 21:46:15,860 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-15 21:46:16,371 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-15 21:46:19,842 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-15 21:46:26,421 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-15 21:46:26,422 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-15 21:46:26,463 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35190210560 B)
2019-08-15 21:46:26,463 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-15 21:46:26,463 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-15 21:46:26,606 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-15 21:46:26,606 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-15 21:46:26,737 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-15 21:46:26,834 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-15 21:46:26,834 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140036008122112)>, <ExcThread(job, started 140035791849216)>, <ExcThread(validate_pre, started 140035741492992)>, <ExcThread(failed_post, started 140035361847040)>, <ExcThread(create_data_payload, started 140035758278400)>, <ExcThread(copytool_out, started 140035387025152)>, <ExcThread(validate, started 140035783456512)>, <ExcThread(monitor, started 140035749885696)>, <ExcThread(job_monitor, started 140035370239744)>, <ExcThread(queue_monitoring, started 140035353454336)>, <ExcThread(copytool_in, started 140034783045376)>, <ExcThread(validate_post, started 140035378632448)>, <ExcThread(data, started 140035775063808)>, <ExcThread(queue_monitor, started 140035345061632)>]
2019-08-15 21:46:26,934 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-15 21:46:26,934 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-15 21:46:26,978 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-15 21:46:26,979 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-15 21:46:27,013 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-15 21:46:27,015 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-15 21:46:27,015 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140036008122112)>, <ExcThread(validate_pre, started 140035741492992)>, <ExcThread(failed_post, started 140035361847040)>, <ExcThread(create_data_payload, started 140035758278400)>, <ExcThread(copytool_out, started 140035387025152)>, <ExcThread(validate, started 140035783456512)>, <ExcThread(job_monitor, started 140035370239744)>, <ExcThread(queue_monitoring, started 140035353454336)>, <ExcThread(copytool_in, started 140034783045376)>, <ExcThread(validate_post, started 140035378632448)>, <ExcThread(queue_monitor, started 140035345061632)>]
2019-08-15 21:46:27,072 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-15 21:46:27,116 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-15 21:46:27,116 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140036008122112)>, <ExcThread(validate_pre, started 140035741492992)>, <ExcThread(failed_post, started 140035361847040)>, <ExcThread(create_data_payload, started 140035758278400)>, <ExcThread(copytool_out, started 140035387025152)>, <ExcThread(validate, started 140035783456512)>, <ExcThread(job_monitor, started 140035370239744)>, <ExcThread(queue_monitoring, started 140035353454336)>, <ExcThread(validate_post, started 140035378632448)>, <ExcThread(queue_monitor, started 140035345061632)>]
2019-08-15 21:46:27,522 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-15 21:46:27,633 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-15 21:46:27,636 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-15 21:46:27,676 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-15 21:46:27,720 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-15 21:46:27,720 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140036008122112)>, <ExcThread(validate_pre, started 140035741492992)>, <ExcThread(create_data_payload, started 140035758278400)>, <ExcThread(copytool_out, started 140035387025152)>, <ExcThread(job_monitor, started 140035370239744)>, <ExcThread(queue_monitoring, started 140035353454336)>, <ExcThread(queue_monitor, started 140035345061632)>]
2019-08-15 21:46:27,833 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-15 21:46:27,923 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-15 21:46:27,950 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-15 21:46:28,022 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-15 21:46:28,023 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140036008122112)>, <ExcThread(copytool_out, started 140035387025152)>, <ExcThread(job_monitor, started 140035370239744)>, <ExcThread(queue_monitoring, started 140035353454336)>, <ExcThread(queue_monitor, started 140035345061632)>]
2019-08-15 21:46:28,109 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-15 21:46:28,110 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-15 21:46:28,123 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-15 21:46:28,124 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140036008122112)>, <ExcThread(copytool_out, started 140035387025152)>, <ExcThread(job_monitor, started 140035370239744)>, <ExcThread(queue_monitoring, started 140035353454336)>]
2019-08-15 21:46:28,522 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-15 21:46:28,526 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-15 21:46:28,526 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140036008122112)>, <ExcThread(job_monitor, started 140035370239744)>, <ExcThread(queue_monitoring, started 140035353454336)>]
2019-08-15 21:46:30,834 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-15 21:46:30,842 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-15 21:46:30,842 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140036008122112)>, <ExcThread(job_monitor, started 140035370239744)>]
2019-08-15 21:47:21,429 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 123 s)
2019-08-15 21:47:21,430 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-15 21:47:21,495 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-15 21:47:21,495 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-15 21:47:21,495 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-15 21:47:21 UTC [wrapper] ==== pilot stdout END ====
2019-08-15 21:47:21 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-15 21:47:21 UTC [wrapper] Pilot exit status: 0
2019-08-15 21:47:21 UTC [wrapper] STATUSCODE: 0
2019-08-15 21:47:21 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 15 18:56 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

2019-08-15 21:47:21 UTC [wrapper] Test setup, not cleaning
2019-08-15 21:47:21 UTC [wrapper] ==== wrapper stdout END ====
2019-08-15 21:47:21 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=17462.06s
KernelTime=481.95s
UserTime=66173.19s
CPUUsage=381%
MaxResidentMemory=1945296kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=491676
MinorPageFaults=19939622
Swaps=0
ForcedSwitches=7711513
WaitSwitches=10404291
Inputs=118494136
Outputs=963616
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 286488
drwxrwx--x. 7 grid grid      4096 Aug 15 23:47 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7409162 Aug 15 18:56 agis_ddmendpoints.json
-rw-------. 1 grid grid   4438071 Aug 15 18:56 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 15 18:56 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 15 18:56 APPS
drwxr-xr-x. 2 grid grid         6 Aug 15 18:56 .arc
-rw-------. 1 grid grid       538 Aug 15 18:56 .asetup
-rw-------. 1 grid grid       826 Aug 15 18:57 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 15 18:56 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 15 23:46 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 15 23:36 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 279103754 Aug 15 18:56 EVNT.18605754._000276.pool.root.1
-rw-------. 1 grid grid       519 Aug 15 23:47 g5DODmbLeGvnShfckohDCDFpABFKDmABFKDmPcaYDmABFKDms9y9Un.diag
-rw-------. 1 grid grid     73279 Aug 15 23:46 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 15 18:56 init_data.xml
-rw-rw-r--. 1 grid grid    262346 Aug 15 18:56 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 15 18:56 job.xml
-rw-------. 1 grid grid    805198 Aug 15 23:47 log.18722298._014322.job.log.1
-rw-------. 1 grid grid    851496 Aug 15 23:46 log.18722298._014322.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 15 23:47 output.list
-rw-------. 1 grid grid      2915 Aug 10 13:04 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 10 12:40 pilot2.tar.gz
-rw-------. 1 grid grid     10563 Aug 15 23:47 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 10 13:03 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 15 18:56 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 15 18:56 run_atlas
-rwx------. 1 grid grid     15232 Aug 10 13:04 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 15 23:47 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 15 23:47 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 15 23:47 shared
-rw-rw-r--. 1 grid grid      8688 Aug 15 18:56 start_atlas.sh
-rw-rw-r--. 1 grid grid     18546 Aug 15 23:47 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 15 18:56 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 15 23:46 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
23:47:22 (31691): run_atlas exited; CPU time 66173.584075
23:47:22 (31691): called boinc_finish(0)

</stderr_txt>
]]>

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