Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
22:44:43 (27871): wrapper (7.7.26015): starting
22:44:43 (27871): 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 grep: pandaJobData.out: No such file or directory
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.18722355._008324.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-09 22:24:37,254 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722355
2019-08-09 22:24:37,254 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-09 22:24:37,254 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-09 22:24:37,254 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-09 22:24:37,255 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-09 22:24:37,255 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-09 22:24:37,255 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-09 22:24:37,255 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-09 22:24:37,255 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-09 22:24:37,255 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 21606 s
2019-08-09 22:24:37,255 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-09 22:24:37,255 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-09 22:24:37,255 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 2130
2019-08-09 22:24:37,255 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 2130
2019-08-09 22:24:37,255 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-09 22:24:37,255 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-09 22:24:37,255 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-09 22:24:37,255 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-09 22:24:37,255 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4441973726 has completed
2019-08-09 22:24:37,255 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-09 22:24:37,264 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4441973726
2019-08-09 22:24:38,270 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [2130]
2019-08-09 22:24:38,270 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 2130
2019-08-09 22:24:38,270 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-09 22:24:39,275 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-09 22:24:39,275 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=2130
2019-08-09 22:24:39,323 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [2130] (in reverse order)
2019-08-09 22:24:39,367 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-09 22:24:39,367 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-09 22:24:39,367 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-09 22:24:39,367 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-09 22:24:39,876 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-09 22:24:49,908 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-09 22:24:49,908 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-09 22:24:49,945 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35640049664 B)
2019-08-09 22:24:49,946 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-09 22:24:49,946 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-09 22:24:49,948 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-09 22:24:50,035 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-09 22:24:50,035 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139799385167616)>, <ExcThread(job, started 139799168894720)>, <ExcThread(validate, started 139799160502016)>, <ExcThread(job_monitor, started 139798601774848)>, <ExcThread(copytool_in, started 139798626952960)>, <ExcThread(validate_pre, started 139798610167552)>, <ExcThread(validate_post, started 139798593382144)>, <ExcThread(queue_monitor, started 139798584989440)>, <ExcThread(payload, started 139799118538496)>, <ExcThread(execute_payloads, started 139798090082048)>, <ExcThread(queue_monitoring, started 139799126931200)>, <ExcThread(copytool_out, started 139799135323904)>, <ExcThread(failed_post, started 139798098474752)>, <ExcThread(create_data_payload, started 139799143716608)>, <ExcThread(data, started 139799152109312)>]
2019-08-09 22:24:50,193 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-09 22:24:50,193 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-09 22:24:50,274 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-09 22:24:50,401 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-09 22:24:50,402 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139799385167616)>, <ExcThread(job_monitor, started 139798601774848)>, <ExcThread(copytool_in, started 139798626952960)>, <ExcThread(validate_pre, started 139798610167552)>, <ExcThread(validate_post, started 139798593382144)>, <ExcThread(queue_monitor, started 139798584989440)>, <ExcThread(payload, started 139799118538496)>, <ExcThread(execute_payloads, started 139798090082048)>, <ExcThread(queue_monitoring, started 139799126931200)>, <ExcThread(copytool_out, started 139799135323904)>, <ExcThread(failed_post, started 139798098474752)>, <ExcThread(create_data_payload, started 139799143716608)>, <ExcThread(data, started 139799152109312)>]
2019-08-09 22:24:50,466 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-09 22:24:50,638 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-09 22:24:50,638 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-09 22:24:50,667 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-09 22:24:50,667 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139799385167616)>, <ExcThread(job_monitor, started 139798601774848)>, <ExcThread(copytool_in, started 139798626952960)>, <ExcThread(validate_pre, started 139798610167552)>, <ExcThread(validate_post, started 139798593382144)>, <ExcThread(queue_monitor, started 139798584989440)>, <ExcThread(queue_monitoring, started 139799126931200)>, <ExcThread(copytool_out, started 139799135323904)>, <ExcThread(failed_post, started 139798098474752)>, <ExcThread(create_data_payload, started 139799143716608)>, <ExcThread(data, started 139799152109312)>]
2019-08-09 22:24:50,876 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-09 22:24:51,040 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-09 22:24:51,040 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-09 22:24:51,070 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-09 22:24:51,071 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139799385167616)>, <ExcThread(job_monitor, started 139798601774848)>, <ExcThread(validate_pre, started 139798610167552)>, <ExcThread(validate_post, started 139798593382144)>, <ExcThread(queue_monitor, started 139798584989440)>, <ExcThread(queue_monitoring, started 139799126931200)>, <ExcThread(copytool_out, started 139799135323904)>, <ExcThread(failed_post, started 139798098474752)>, <ExcThread(create_data_payload, started 139799143716608)>]
2019-08-09 22:24:51,119 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-09 22:24:51,141 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-09 22:24:51,142 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-09 22:24:51,172 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-09 22:24:51,172 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139799385167616)>, <ExcThread(job_monitor, started 139798601774848)>, <ExcThread(validate_post, started 139798593382144)>, <ExcThread(queue_monitor, started 139798584989440)>, <ExcThread(queue_monitoring, started 139799126931200)>, <ExcThread(copytool_out, started 139799135323904)>, <ExcThread(create_data_payload, started 139799143716608)>]
2019-08-09 22:24:51,230 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-09 22:24:51,273 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-09 22:24:51,274 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139799385167616)>, <ExcThread(job_monitor, started 139798601774848)>, <ExcThread(validate_post, started 139798593382144)>, <ExcThread(queue_monitor, started 139798584989440)>, <ExcThread(queue_monitoring, started 139799126931200)>, <ExcThread(copytool_out, started 139799135323904)>]
2019-08-09 22:24:51,471 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-09 22:24:51,476 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-09 22:24:51,476 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139799385167616)>, <ExcThread(job_monitor, started 139798601774848)>, <ExcThread(queue_monitor, started 139798584989440)>, <ExcThread(queue_monitoring, started 139799126931200)>, <ExcThread(copytool_out, started 139799135323904)>]
2019-08-09 22:24:51,737 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-09 22:24:51,737 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-09 22:24:51,745 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-09 22:24:51,778 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-09 22:24:51,779 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139799385167616)>, <ExcThread(job_monitor, started 139798601774848)>, <ExcThread(queue_monitoring, started 139799126931200)>, <ExcThread(copytool_out, started 139799135323904)>]
2019-08-09 22:24:52,143 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-09 22:24:52,182 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-09 22:24:52,182 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139799385167616)>, <ExcThread(job_monitor, started 139798601774848)>, <ExcThread(queue_monitoring, started 139799126931200)>]
2019-08-09 22:24:54,664 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-09 22:24:54,664 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-09 22:24:54,699 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-09 22:24:54,700 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139799385167616)>, <ExcThread(queue_monitoring, started 139799126931200)>]
2019-08-09 22:24:54,747 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-09 22:24:54,800 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-09 22:24:54,801 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-09 22:24:54,802 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-09 22:24:55 UTC [wrapper] ==== pilot stdout END ====
2019-08-09 22:24:55 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-09 22:24:55 UTC [wrapper] Pilot exit status: 0
2019-08-09 22:24:55 UTC [wrapper] STATUSCODE: 0
2019-08-09 22:24:55 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  9 22:44 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

2019-08-09 22:24:55 UTC [wrapper] Test setup, not cleaning
2019-08-09 22:24:55 UTC [wrapper] ==== wrapper stdout END ====
2019-08-09 22:24:55 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=6009.62s
KernelTime=209.75s
UserTime=21507.62s
CPUUsage=361%
MaxResidentMemory=1944992kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=270470
MinorPageFaults=12706653
Swaps=0
ForcedSwitches=2572637
WaitSwitches=5291148
Inputs=65781200
Outputs=530784
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 209540
drwxrwx--x. 7 grid grid      4096 Aug 10 00:24 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7408903 Aug  9 22:45 agis_ddmendpoints.json
-rw-------. 1 grid grid   4506889 Aug  9 22:44 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug  9 22:44 .alrb
drwxr-xr-x. 3 grid grid        17 Aug  9 22:44 APPS
drwxr-xr-x. 2 grid grid         6 Aug  9 22:44 .arc
-rw-------. 1 grid grid       538 Aug  9 22:44 .asetup
-rw-------. 1 grid grid       826 Aug  9 22:45 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug  9 22:44 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 10 00:24 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 10 00:18 boinc_task_state.xml
-rw-------. 1 grid grid       516 Aug 10 00:24 c2ANDmATIGvnShfckohDCDFpABFKDmABFKDmnIzXDmABFKDmH4K6In.diag
-rw-rw-r--. 1 grid grid 200686329 Aug  9 22:44 EVNT.18605773._000169.pool.root.1
-rw-------. 1 grid grid     61221 Aug 10 00:24 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug  9 22:44 init_data.xml
-rw-rw-r--. 1 grid grid    262350 Aug  9 22:44 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug  9 22:44 job.xml
-rw-------. 1 grid grid    399472 Aug 10 00:24 log.18722355._008324.job.log.1
-rw-------. 1 grid grid    821347 Aug 10 00:24 log.18722355._008324.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 10 00:24 output.list
-rw-------. 1 grid grid      2956 Aug  9 13:42 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug  9 13:29 pilot2.tar.gz
-rw-------. 1 grid grid     11957 Aug 10 00:24 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug  9 13:40 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug  9 22:44 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug  9 22:44 run_atlas
-rwx------. 1 grid grid     15232 Aug  9 13:42 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 10 00:24 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 10 00:24 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 10 00:24 shared
-rw-rw-r--. 1 grid grid      8688 Aug  9 22:44 start_atlas.sh
-rw-rw-r--. 1 grid grid     19507 Aug 10 00:24 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug  9 22:44 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 10 00:24 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
00:24:55 (27871): run_atlas exited; CPU time 21508.005882
00:24:55 (27871): called boinc_finish(0)

</stderr_txt>
]]>

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