Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
00:27:35 (1513): wrapper (7.7.26015): starting
00:27:35 (1513): 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=4446538577
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.18722183._014406.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-17 00:48:11,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722183
2019-08-17 00:48:11,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-17 00:48:11,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-17 00:48:11,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-17 00:48:11,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-17 00:48:11,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-17 00:48:11,525 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-17 00:48:11,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-17 00:48:11,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-17 00:48:11,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 31304 s
2019-08-17 00:48:11,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-17 00:48:11,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-17 00:48:11,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 8230
2019-08-17 00:48:11,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 8230
2019-08-17 00:48:11,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-17 00:48:11,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-17 00:48:11,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-17 00:48:11,526 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-17 00:48:11,526 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4446538577 has completed
2019-08-17 00:48:11,526 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-17 00:48:11,534 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4446538577
2019-08-17 00:48:12,539 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [8230]
2019-08-17 00:48:12,539 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 8230
2019-08-17 00:48:12,539 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-17 00:48:13,542 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-17 00:48:13,542 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=8230
2019-08-17 00:48:13,587 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [8230] (in reverse order)
2019-08-17 00:48:13,629 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-17 00:48:13,630 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-17 00:48:13,630 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-17 00:48:13,630 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-17 00:48:14,142 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-17 00:48:24,191 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-17 00:48:24,191 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-17 00:48:24,226 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35647389696 B)
2019-08-17 00:48:24,226 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-17 00:48:24,227 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-17 00:48:24,228 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-17 00:48:24,229 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-17 00:48:24,249 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-17 00:48:24,249 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-17 00:48:24,251 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-17 00:48:24,311 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-17 00:48:24,311 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140457751365376)>, <ExcThread(job, started 140457535092480)>, <ExcThread(copytool_in, started 140456889407232)>, <ExcThread(queue_monitor, started 140456881014528)>, <ExcThread(payload, started 140457417885440)>, <ExcThread(validate_post, started 140456872621824)>, <ExcThread(copytool_out, started 140457426278144)>, <ExcThread(failed_post, started 140456864229120)>, <ExcThread(job_monitor, started 140456897799936)>, <ExcThread(execute_payloads, started 140456855836416)>, <ExcThread(queue_monitoring, started 140457401100032)>, <ExcThread(validate_pre, started 140456906192640)>, <ExcThread(create_data_payload, started 140457434670848)>]
2019-08-17 00:48:24,395 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-17 00:48:24,613 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-17 00:48:24,613 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140457751365376)>, <ExcThread(job, started 140457535092480)>, <ExcThread(copytool_in, started 140456889407232)>, <ExcThread(queue_monitor, started 140456881014528)>, <ExcThread(payload, started 140457417885440)>, <ExcThread(validate_post, started 140456872621824)>, <ExcThread(copytool_out, started 140457426278144)>, <ExcThread(failed_post, started 140456864229120)>, <ExcThread(job_monitor, started 140456897799936)>, <ExcThread(queue_monitoring, started 140457401100032)>, <ExcThread(validate_pre, started 140456906192640)>, <ExcThread(create_data_payload, started 140457434670848)>]
2019-08-17 00:48:24,637 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-17 00:48:24,915 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-17 00:48:24,915 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140457751365376)>, <ExcThread(job, started 140457535092480)>, <ExcThread(copytool_in, started 140456889407232)>, <ExcThread(queue_monitor, started 140456881014528)>, <ExcThread(payload, started 140457417885440)>, <ExcThread(validate_post, started 140456872621824)>, <ExcThread(copytool_out, started 140457426278144)>, <ExcThread(failed_post, started 140456864229120)>, <ExcThread(job_monitor, started 140456897799936)>, <ExcThread(queue_monitoring, started 140457401100032)>, <ExcThread(create_data_payload, started 140457434670848)>]
2019-08-17 00:48:24,979 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-17 00:48:24,988 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-17 00:48:25,109 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-17 00:48:25,109 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-17 00:48:25,116 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-17 00:48:25,117 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140457751365376)>, <ExcThread(job, started 140457535092480)>, <ExcThread(queue_monitor, started 140456881014528)>, <ExcThread(validate_post, started 140456872621824)>, <ExcThread(copytool_out, started 140457426278144)>, <ExcThread(failed_post, started 140456864229120)>, <ExcThread(job_monitor, started 140456897799936)>, <ExcThread(queue_monitoring, started 140457401100032)>]
2019-08-17 00:48:25,205 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-17 00:48:25,252 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-17 00:48:25,318 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-17 00:48:25,318 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140457751365376)>, <ExcThread(job, started 140457535092480)>, <ExcThread(queue_monitor, started 140456881014528)>, <ExcThread(validate_post, started 140456872621824)>, <ExcThread(job_monitor, started 140456897799936)>, <ExcThread(queue_monitoring, started 140457401100032)>]
2019-08-17 00:48:25,406 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-17 00:48:25,519 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-17 00:48:25,519 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140457751365376)>, <ExcThread(job, started 140457535092480)>, <ExcThread(queue_monitor, started 140456881014528)>, <ExcThread(job_monitor, started 140456897799936)>, <ExcThread(queue_monitoring, started 140457401100032)>]
2019-08-17 00:48:25,575 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-17 00:48:25,575 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-17 00:48:25,620 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-17 00:48:25,620 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140457751365376)>, <ExcThread(queue_monitor, started 140456881014528)>, <ExcThread(job_monitor, started 140456897799936)>, <ExcThread(queue_monitoring, started 140457401100032)>]
2019-08-17 00:48:25,866 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-17 00:48:25,878 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-17 00:48:25,879 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-17 00:48:25,923 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-17 00:48:25,923 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140457751365376)>, <ExcThread(job_monitor, started 140456897799936)>, <ExcThread(queue_monitoring, started 140457401100032)>]
2019-08-17 00:48:28,868 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-17 00:48:28,944 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-17 00:48:28,945 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140457751365376)>, <ExcThread(job_monitor, started 140456897799936)>]
2019-08-17 00:49:08,582 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-17 00:49:08,582 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-17 00:49:08,621 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-17 00:49:08,622 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-17 00:49:08,622 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-17 00:49:08 UTC [wrapper] ==== pilot stdout END ====
2019-08-17 00:49:08 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-17 00:49:08 UTC [wrapper] Pilot exit status: 0
2019-08-17 00:49:08 UTC [wrapper] STATUSCODE: 0
2019-08-17 00:49:08 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 17 00:27 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

2019-08-17 00:49:08 UTC [wrapper] Test setup, not cleaning
2019-08-17 00:49:08 UTC [wrapper] ==== wrapper stdout END ====
2019-08-17 00:49:08 UTC [wrapper] ==== wrapper stderr END ====
2019-08-17 00:49:08 UTC [wrapper] wrapper wrapperexiting ec=0, duration=8491
2019-08-17 00:49:08 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=8491.01s
KernelTime=260.45s
UserTime=31173.85s
CPUUsage=370%
MaxResidentMemory=1945224kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=315995
MinorPageFaults=14246766
Swaps=0
ForcedSwitches=3618151
WaitSwitches=6281488
Inputs=76991808
Outputs=621840
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 252084
drwxrwx--x. 6 grid grid      4096 Aug 17 02:49 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid       516 Aug 17 02:49 9ajLDmJmQIvnShfckohDCDFpABFKDmABFKDm8eSbDmABFKDmVRwRmm.diag
-rw-------. 1 grid grid   7411700 Aug 17 00:27 agis_ddmendpoints.json
-rw-------. 1 grid grid   4399526 Aug 17 00:27 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 17 00:27 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 17 00:27 APPS
-rw-------. 1 grid grid       538 Aug 17 00:27 .asetup
-rw-------. 1 grid grid       826 Aug 17 00:28 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 17 00:27 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 17 02:48 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 17 02:42 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 244213748 Aug 17 00:27 EVNT.18605745._000310.pool.root.1
-rw-------. 1 grid grid     85102 Aug 17 02:48 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 17 00:27 init_data.xml
-rw-rw-r--. 1 grid grid    261617 Aug 17 00:27 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 17 00:27 job.xml
-rw-------. 1 grid grid    505064 Aug 17 02:49 log.18722183._014406.job.log.1
-rw-------. 1 grid grid    834321 Aug 17 02:48 log.18722183._014406.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 17 02:49 output.list
-rw-------. 1 grid grid      2921 Aug 15 10:59 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 15 10:26 pilot2.tar.gz
-rw-------. 1 grid grid     11050 Aug 17 02:49 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 15 10:57 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 17 00:27 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 17 00:27 run_atlas
-rwx------. 1 grid grid     12641 Aug 15 10:59 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 17 02:49 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 17 02:49 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 17 02:49 shared
-rw-rw-r--. 1 grid grid      8688 Aug 17 00:27 start_atlas.sh
-rw-rw-r--. 1 grid grid     18700 Aug 17 02:49 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 17 00:27 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 17 02:48 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
02:49:09 (1513): run_atlas exited; CPU time 31174.225755
02:49:09 (1513): called boinc_finish(0)

</stderr_txt>
]]>

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