Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
23:47:26 (576): wrapper (7.7.26015): starting
23:47:26 (576): 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=4444737172
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.18722465._009144.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-16 01:39:44,074 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-16 01:39:44,074 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4444737172
2019-08-16 01:39:44,074 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722465
2019-08-16 01:39:44,074 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-16 01:39:44,074 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-16 01:39:44,074 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-16 01:39:44,074 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-16 01:39:44,074 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-16 01:39:44,074 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-16 01:39:44,074 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-16 01:39:44,074 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-16 01:39:44,075 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 52976 s
2019-08-16 01:39:44,075 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-16 01:39:44,075 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-16 01:39:44,075 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 7344
2019-08-16 01:39:44,075 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 7344
2019-08-16 01:39:44,075 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-16 01:39:44,075 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-16 01:39:44,075 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-16 01:39:44,075 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-16 01:39:44,075 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4444737172 has completed
2019-08-16 01:39:44,075 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-16 01:39:44,086 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4444737172
2019-08-16 01:39:45,091 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [7344]
2019-08-16 01:39:45,091 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 7344
2019-08-16 01:39:45,092 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-16 01:39:46,097 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-16 01:39:46,097 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=7344
2019-08-16 01:39:46,143 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [7344] (in reverse order)
2019-08-16 01:39:46,185 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-16 01:39:46,185 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-16 01:39:46,185 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-16 01:39:46,185 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-16 01:39:46,697 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-16 01:39:56,732 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-16 01:39:56,733 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-16 01:39:56,765 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35106324480 B)
2019-08-16 01:39:56,765 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-16 01:39:56,765 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-16 01:39:56,773 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-16 01:39:56,808 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-16 01:39:56,844 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-16 01:39:56,844 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-16 01:39:56,861 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-16 01:39:56,862 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140159981082368)>, <ExcThread(job, started 140159764809472)>, <ExcThread(validate_post, started 140159102199552)>, <ExcThread(payload, started 140159647463168)>, <ExcThread(execute_payloads, started 140158607292160)>, <ExcThread(queue_monitor, started 140159127377664)>, <ExcThread(failed_post, started 140159093806848)>, <ExcThread(create_data_payload, started 140159664248576)>, <ExcThread(validate_pre, started 140159118984960)>, <ExcThread(validate, started 140159681033984)>, <ExcThread(job_monitor, started 140159144163072)>, <ExcThread(queue_monitoring, started 140159639070464)>, <ExcThread(copytool_out, started 140159655855872)>, <ExcThread(copytool_in, started 140159110592256)>]
2019-08-16 01:39:57,036 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-16 01:39:57,051 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-16 01:39:57,163 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-16 01:39:57,163 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140159981082368)>, <ExcThread(job, started 140159764809472)>, <ExcThread(validate_post, started 140159102199552)>, <ExcThread(payload, started 140159647463168)>, <ExcThread(queue_monitor, started 140159127377664)>, <ExcThread(failed_post, started 140159093806848)>, <ExcThread(validate_pre, started 140159118984960)>, <ExcThread(validate, started 140159681033984)>, <ExcThread(job_monitor, started 140159144163072)>, <ExcThread(queue_monitoring, started 140159639070464)>, <ExcThread(copytool_out, started 140159655855872)>, <ExcThread(copytool_in, started 140159110592256)>]
2019-08-16 01:39:57,650 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-16 01:39:57,745 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-16 01:39:57,766 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-16 01:39:57,766 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140159981082368)>, <ExcThread(job, started 140159764809472)>, <ExcThread(validate_post, started 140159102199552)>, <ExcThread(payload, started 140159647463168)>, <ExcThread(queue_monitor, started 140159127377664)>, <ExcThread(failed_post, started 140159093806848)>, <ExcThread(job_monitor, started 140159144163072)>, <ExcThread(queue_monitoring, started 140159639070464)>, <ExcThread(copytool_out, started 140159655855872)>, <ExcThread(copytool_in, started 140159110592256)>]
2019-08-16 01:39:57,776 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-16 01:39:57,776 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-16 01:39:57,809 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-16 01:39:57,967 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-16 01:39:57,968 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-16 01:39:57,968 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140159981082368)>, <ExcThread(job, started 140159764809472)>, <ExcThread(validate_post, started 140159102199552)>, <ExcThread(queue_monitor, started 140159127377664)>, <ExcThread(failed_post, started 140159093806848)>, <ExcThread(job_monitor, started 140159144163072)>, <ExcThread(queue_monitoring, started 140159639070464)>, <ExcThread(copytool_in, started 140159110592256)>]
2019-08-16 01:39:57,968 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-16 01:39:57,970 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-16 01:39:57,991 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-16 01:39:58,069 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-16 01:39:58,070 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140159981082368)>, <ExcThread(validate_post, started 140159102199552)>, <ExcThread(queue_monitor, started 140159127377664)>, <ExcThread(job_monitor, started 140159144163072)>, <ExcThread(queue_monitoring, started 140159639070464)>]
2019-08-16 01:39:58,204 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-16 01:39:58,271 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-16 01:39:58,271 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140159981082368)>, <ExcThread(queue_monitor, started 140159127377664)>, <ExcThread(job_monitor, started 140159144163072)>, <ExcThread(queue_monitoring, started 140159639070464)>]
2019-08-16 01:39:58,573 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-16 01:39:58,574 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-16 01:39:58,575 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-16 01:39:58,675 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-16 01:39:58,675 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140159981082368)>, <ExcThread(job_monitor, started 140159144163072)>, <ExcThread(queue_monitoring, started 140159639070464)>]
2019-08-16 01:40:00,588 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-16 01:40:00,589 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-16 01:40:00,688 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-16 01:40:00,688 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140159981082368)>, <ExcThread(queue_monitoring, started 140159639070464)>]
2019-08-16 01:40:01,575 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-16 01:40:01,594 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-16 01:40:01,595 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-16 01:40:01,595 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-16 01:40:01 UTC [wrapper] ==== pilot stdout END ====
2019-08-16 01:40:01 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-16 01:40:01 UTC [wrapper] Pilot exit status: 0
2019-08-16 01:40:01 UTC [wrapper] STATUSCODE: 0
2019-08-16 01:40:01 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 23:47 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

2019-08-16 01:40:01 UTC [wrapper] Test setup, not cleaning
2019-08-16 01:40:01 UTC [wrapper] ==== wrapper stdout END ====
2019-08-16 01:40:01 UTC [wrapper] ==== wrapper stderr END ====
2019-08-16 01:40:01 UTC [wrapper] wrapper wrapperexiting ec=0, duration=13952
2019-08-16 01:40:01 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=13952.72s
KernelTime=390.57s
UserTime=52766.81s
CPUUsage=380%
MaxResidentMemory=1944584kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=424704
MinorPageFaults=17955387
Swaps=0
ForcedSwitches=6076307
WaitSwitches=9018563
Inputs=102648104
Outputs=879656
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 236320
drwxrwx--x. 6 grid grid      4096 Aug 16 03:40 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7413078 Aug 15 23:47 agis_ddmendpoints.json
-rw-------. 1 grid grid   4438118 Aug 15 23:47 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 15 23:47 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 15 23:47 APPS
-rw-------. 1 grid grid       538 Aug 15 23:47 .asetup
-rw-------. 1 grid grid       826 Aug 15 23:48 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 15 23:47 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 16 03:39 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 16 03:32 boinc_task_state.xml
-rw-------. 1 grid grid       518 Aug 16 03:40 cjbMDmpfnHvnShfckohDCDFpABFKDmABFKDmugSaDmABFKDmb17IVm.diag
-rw-rw-r--. 1 grid grid 227822519 Aug 15 23:47 EVNT.18605785._000160.pool.root.1
-rw-------. 1 grid grid     88705 Aug 16 03:39 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 15 23:47 init_data.xml
-rw-rw-r--. 1 grid grid    261630 Aug 15 23:47 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 15 23:47 job.xml
-rw-------. 1 grid grid    701809 Aug 16 03:40 log.18722465._009144.job.log.1
-rw-------. 1 grid grid    847492 Aug 16 03:39 log.18722465._009144.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 16 03:40 output.list
-rw-------. 1 grid grid      2956 Aug 13 17:13 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 13 16:24 pilot2.tar.gz
-rw-------. 1 grid grid     10448 Aug 16 03:40 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 13 17:13 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 15 23:47 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 15 23:47 run_atlas
-rwx------. 1 grid grid     12641 Aug 13 17:13 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 16 03:40 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 16 03:40 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 16 03:40 shared
-rw-rw-r--. 1 grid grid      8688 Aug 15 23:47 start_atlas.sh
-rw-rw-r--. 1 grid grid     18419 Aug 16 03:40 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 15 23:47 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 16 03:39 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
03:40:02 (576): run_atlas exited; CPU time 52767.184616
03:40:02 (576): called boinc_finish(0)

</stderr_txt>
]]>

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