Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
13:52:29 (23497): wrapper (7.7.26015): starting
13:52:29 (23497): 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
14:32:55 (11512): wrapper (7.7.26015): starting
14:32:55 (11512): 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
This is not an Event Service job
This is trying to run the run_atlas wrapper for the 2nd time,but it is not an Event Service job,so will restart the job
output.list does not exist...
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=4441386833
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.18605033._051613.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-09 14:02:55,176 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-09 14:02:55,176 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4441386833
2019-08-09 14:02:55,177 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18605033
2019-08-09 14:02:55,177 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-09 14:02:55,177 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-09 14:02:55,177 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-09 14:02:55,177 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-09 14:02:55,177 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-09 14:02:55,177 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-09 14:02:55,177 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-09 14:02:55,177 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-09 14:02:55,177 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 19193 s
2019-08-09 14:02:55,177 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-09 14:02:55,177 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-09 14:02:55,177 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 18286
2019-08-09 14:02:55,177 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 18286
2019-08-09 14:02:55,177 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-09 14:02:55,177 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-09 14:02:55,178 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-09 14:02:55,178 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-09 14:02:55,178 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4441386833 has completed
2019-08-09 14:02:55,178 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-09 14:02:55,192 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4441386833
2019-08-09 14:02:56,197 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [18286]
2019-08-09 14:02:56,197 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 18286
2019-08-09 14:02:56,197 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-09 14:02:57,202 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-09 14:02:57,203 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=18286
2019-08-09 14:02:57,261 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [18286] (in reverse order)
2019-08-09 14:02:57,306 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-09 14:02:57,306 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-09 14:02:57,306 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-09 14:02:57,306 | 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 14:02:57,817 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-09 14:03:07,863 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-09 14:03:07,864 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-09 14:03:07,900 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (36078354432 B)
2019-08-09 14:03:07,901 | 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 14:03:07,901 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-09 14:03:07,942 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-09 14:03:07,978 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 16 threads
2019-08-09 14:03:07,978 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139890076776192)>, <ExcThread(job, started 139889860503296)>, <ExcThread(queue_monitoring, started 139889735612160)>, <ExcThread(job_monitor, started 139889215526656)>, <ExcThread(create_data_payload, started 139889744004864)>, <ExcThread(validate_pre, started 139889718826752)>, <ExcThread(data, started 139889852110592)>, <ExcThread(copytool_in, started 139889223919360)>, <ExcThread(queue_monitor, started 139889198741248)>, <ExcThread(validate, started 139889769182976)>, <ExcThread(monitor, started 139889232312064)>, <ExcThread(failed_post, started 139889190348544)>, <ExcThread(validate_post, started 139889207133952)>, <ExcThread(execute_payloads, started 139889181955840)>, <ExcThread(payload, started 139889752397568)>, <ExcThread(copytool_out, started 139889760790272)>]
2019-08-09 14:03:08,075 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-09 14:03:08,182 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-09 14:03:08,182 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-09 14:03:08,204 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-09 14:03:08,208 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-09 14:03:08,215 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-09 14:03:08,381 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-09 14:03:08,381 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139890076776192)>, <ExcThread(queue_monitoring, started 139889735612160)>, <ExcThread(job_monitor, started 139889215526656)>, <ExcThread(validate_pre, started 139889718826752)>, <ExcThread(data, started 139889852110592)>, <ExcThread(queue_monitor, started 139889198741248)>, <ExcThread(failed_post, started 139889190348544)>, <ExcThread(validate_post, started 139889207133952)>, <ExcThread(execute_payloads, started 139889181955840)>, <ExcThread(payload, started 139889752397568)>, <ExcThread(copytool_out, started 139889760790272)>]
2019-08-09 14:03:08,528 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-09 14:03:08,528 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-09 14:03:08,582 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-09 14:03:08,582 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-09 14:03:08,610 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-09 14:03:08,610 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139890076776192)>, <ExcThread(queue_monitoring, started 139889735612160)>, <ExcThread(job_monitor, started 139889215526656)>, <ExcThread(validate_pre, started 139889718826752)>, <ExcThread(queue_monitor, started 139889198741248)>, <ExcThread(failed_post, started 139889190348544)>, <ExcThread(validate_post, started 139889207133952)>, <ExcThread(execute_payloads, started 139889181955840)>, <ExcThread(copytool_out, started 139889760790272)>]
2019-08-09 14:03:08,627 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-09 14:03:08,693 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-09 14:03:08,711 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-09 14:03:08,711 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139890076776192)>, <ExcThread(queue_monitoring, started 139889735612160)>, <ExcThread(job_monitor, started 139889215526656)>, <ExcThread(validate_pre, started 139889718826752)>, <ExcThread(queue_monitor, started 139889198741248)>, <ExcThread(execute_payloads, started 139889181955840)>, <ExcThread(copytool_out, started 139889760790272)>]
2019-08-09 14:03:08,933 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-09 14:03:09,014 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-09 14:03:09,014 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139890076776192)>, <ExcThread(queue_monitoring, started 139889735612160)>, <ExcThread(job_monitor, started 139889215526656)>, <ExcThread(validate_pre, started 139889718826752)>, <ExcThread(queue_monitor, started 139889198741248)>, <ExcThread(copytool_out, started 139889760790272)>]
2019-08-09 14:03:09,022 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-09 14:03:09,115 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-09 14:03:09,115 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139890076776192)>, <ExcThread(queue_monitoring, started 139889735612160)>, <ExcThread(job_monitor, started 139889215526656)>, <ExcThread(queue_monitor, started 139889198741248)>, <ExcThread(copytool_out, started 139889760790272)>]
2019-08-09 14:03:09,351 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-09 14:03:09,653 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-09 14:03:09,653 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-09 14:03:09,719 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-09 14:03:09,720 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139890076776192)>, <ExcThread(queue_monitoring, started 139889735612160)>, <ExcThread(job_monitor, started 139889215526656)>, <ExcThread(copytool_out, started 139889760790272)>]
2019-08-09 14:03:10,352 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-09 14:03:10,424 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-09 14:03:10,425 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139890076776192)>, <ExcThread(queue_monitoring, started 139889735612160)>, <ExcThread(job_monitor, started 139889215526656)>]
2019-08-09 14:03:10,943 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-09 14:03:11,029 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-09 14:03:11,029 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139890076776192)>, <ExcThread(job_monitor, started 139889215526656)>]
2019-08-09 14:03:48,003 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-09 14:03:48,003 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-09 14:03:48,104 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-09 14:03:48,105 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-09 14:03:48,105 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-09 14:03:48 UTC [wrapper] ==== pilot stdout END ====
2019-08-09 14:03:48 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-09 14:03:48 UTC [wrapper] Pilot exit status: 0
2019-08-09 14:03:48 UTC [wrapper] STATUSCODE: 0
2019-08-09 14:03:48 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 Jul 25 16:38 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 14:03:48 UTC [wrapper] Test setup, not cleaning
2019-08-09 14:03:48 UTC [wrapper] ==== wrapper stdout END ====
2019-08-09 14:03:48 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=5437.32s
KernelTime=190.40s
UserTime=19101.40s
CPUUsage=354%
MaxResidentMemory=1944560kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=255035
MinorPageFaults=12204602
Swaps=0
ForcedSwitches=2252405
WaitSwitches=4960886
Inputs=62016720
Outputs=476160
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 382236
drwxrwx--x. 7 grid grid      4096 Aug  9 16:03 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7409227 Aug  9 13:52 agis_ddmendpoints.json
-rw-------. 1 grid grid   4507284 Aug  9 14:33 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug  9 14:33 .alrb
drwxr-xr-x. 3 grid grid        17 Aug  9 13:52 APPS
drwxr-xr-x. 2 grid grid         6 Aug  9 13:52 .arc
-rw-------. 1 grid grid       538 Aug  9 13:52 .asetup
-rw-------. 1 grid grid       826 Aug  9 14:34 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug  9 13:52 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug  9 16:03 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug  9 15:58 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 377599116 Aug  9 14:33 EVNT.17323852._002122.pool.root.1
-rw-------. 1 grid grid     42999 Aug  9 16:02 heartbeat.json
-rw-rw-r--. 1 grid grid      5869 Aug  9 14:53 init_data.xml
-rw-rw-r--. 1 grid grid    262354 Aug  9 14:33 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug  9 13:52 job.xml
-rw-------. 1 grid grid    355993 Aug  9 16:03 log.18605033._051613.job.log.1
-rw-------. 1 grid grid    807769 Aug  9 16:02 log.18605033._051613.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug  9 16:03 output.list
-rw-------. 1 grid grid      2887 Aug  9 04:01 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug  9 03:26 pilot2.tar.gz
-rw-------. 1 grid grid     11020 Aug  9 16:03 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug  9 04:00 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug  9 14:33 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug  9 13:52 run_atlas
-rwx------. 1 grid grid     15232 Aug  9 04:01 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug  9 16:03 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug  9 16:03 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug  9 16:03 shared
-rw-rw-r--. 1 grid grid      8688 Aug  9 14:33 start_atlas.sh
-rw-rw-r--. 1 grid grid     20354 Aug  9 16:03 stderr.txt
-rw-------. 1 grid grid       570 Aug  9 16:03 vdYLDmVO9FvnShfckohDCDFpABFKDmABFKDm3LkXDmABFKDmD4pPAo.diag
-rw-rw-r--. 1 grid grid       107 Aug  9 13:52 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug  9 16:03 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
16:03:48 (11512): run_atlas exited; CPU time 19101.793545
16:03:48 (11512): called boinc_finish(0)

</stderr_txt>
]]>

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