Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
14:02:35 (27795): wrapper (7.7.26015): starting
14:02:35 (27795): wrapper: running run_atlas (--nthreads 4)
2019-09-25 14:02:35,936: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-09-25 14:02:35,936: sys.argv = ['run_atlas', '--nthreads', '4']
2019-09-25 14:02:35,937: THREADS=4

2019-09-25 14:02:35,951: Checking for CVMFS
2019-09-25 14:02:37,297: CVMFS is installed
2019-09-25 14:02:37,303: OS:CentOS Linux release 7.6.1810 (Core) 
2019-09-25 14:02:37,303: This is not SLC6, need to run with Singularity....
2019-09-25 14:02:37,304: Checking Singularity...
2019-09-25 14:02:37,954: Singularity is installed, version singularity version 3.2.1-1
2019-09-25 14:02:37,954: Testing the function of Singularity...
2019-09-25 14:02:37,954: Checking singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
2019-09-25 14:02:40,680: Singularity Works...
2019-09-25 14:02:40,680: copy /home/grid/slots/0/shared/ATLAS.root_0
2019-09-25 14:02:42,643: copy /home/grid/slots/0/shared/input.tar.gz
2019-09-25 14:02:42,644: copy /home/grid/slots/0/shared/RTE.tar.gz
2019-09-25 14:02:42,644: copy /home/grid/slots/0/shared/start_atlas.sh
2019-09-25 14:02:42,644: export ATHENA_PROC_NUMBER=4;
2019-09-25 14:02:43,925: start atlas job with PandaID=4486252265
2019-09-25 14:02:43,926: cmd = 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
2019-09-25 15:50:52,051: running cmd return value is 0
2019-09-25 15:50:52,055: *****************The last 100 lines of the pilot log******************
2019-09-25 15:50:52,092: 2019-09-25 13:50:37,041 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-09-25 13:50:37,041 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4486252265 has completed
2019-09-25 13:50:37,041 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-09-25 13:50:37,050 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4486252265
2019-09-25 13:50:38,054 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [11049]
2019-09-25 13:50:38,055 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 11049
2019-09-25 13:50:38,055 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-09-25 13:50:39,058 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-09-25 13:50:39,059 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=11049
2019-09-25 13:50:39,156 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [11049] (in reverse order)
2019-09-25 13:50:39,211 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-09-25 13:50:39,211 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-09-25 13:50:39,211 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-09-25 13:50:39,212 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-09-25 13:50:39,235 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-25 13:50:39,235 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | ***  PanDA Pilot version 2.1.25 (11)  ***
2019-09-25 13:50:39,235 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-25 13:50:39,235 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | 
2019-09-25 13:50:39,235 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | pilot is running in a VM
2019-09-25 13:50:39,235 | INFO     | retrieve            | pilot.util.auxiliary             | display_architecture_info | architecture information:
2019-09-25 13:50:39,413 | INFO     | retrieve            | pilot.util.auxiliary             | display_architecture_info | 
LSB Version:	:base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch
Distributor ID:	ScientificCERNSLC
Description:	Scientific Linux CERN SLC release 6.10 (Carbon)
Release:	6.10
Codename:	Carbon
2019-09-25 13:50:39,414 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | *****************************************
2019-09-25 13:50:39,917 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-09-25 13:50:39,952 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (20146290688 B)
2019-09-25 13:50:39,952 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-09-25 13:50:39,953 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-09-25 13:50:39,999 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-09-25 13:50:40,013 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-09-25 13:50:40,013 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140522231465728)>, <ExcThread(job, started 140522015192832)>, <ExcThread(validate_pre, started 140521884325632)>, <ExcThread(payload, started 140521901111040)>, <ExcThread(copytool_out, started 140521909503744)>, <ExcThread(job_monitor, started 140521381025536)>, <ExcThread(create_data_payload, started 140521917896448)>, <ExcThread(queue_monitor, started 140521364240128)>, <ExcThread(validate_post, started 140521355847424)>, <ExcThread(queue_monitoring, started 140521389418240)>, <ExcThread(failed_post, started 140521347454720)>, <ExcThread(validate, started 140521934681856)>, <ExcThread(execute_payloads, started 140520860940032)>, <ExcThread(data, started 140521926289152)>, <ExcThread(copytool_in, started 140521372632832)>]
2019-09-25 13:50:40,194 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-09-25 13:50:40,195 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-09-25 13:50:40,405 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-09-25 13:50:40,415 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-09-25 13:50:40,416 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140522231465728)>, <ExcThread(validate_pre, started 140521884325632)>, <ExcThread(payload, started 140521901111040)>, <ExcThread(copytool_out, started 140521909503744)>, <ExcThread(job_monitor, started 140521381025536)>, <ExcThread(create_data_payload, started 140521917896448)>, <ExcThread(queue_monitor, started 140521364240128)>, <ExcThread(validate_post, started 140521355847424)>, <ExcThread(queue_monitoring, started 140521389418240)>, <ExcThread(failed_post, started 140521347454720)>, <ExcThread(validate, started 140521934681856)>, <ExcThread(data, started 140521926289152)>, <ExcThread(copytool_in, started 140521372632832)>]
2019-09-25 13:50:40,528 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-09-25 13:50:40,717 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-09-25 13:50:40,718 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140522231465728)>, <ExcThread(validate_pre, started 140521884325632)>, <ExcThread(payload, started 140521901111040)>, <ExcThread(copytool_out, started 140521909503744)>, <ExcThread(job_monitor, started 140521381025536)>, <ExcThread(create_data_payload, started 140521917896448)>, <ExcThread(queue_monitor, started 140521364240128)>, <ExcThread(validate_post, started 140521355847424)>, <ExcThread(queue_monitoring, started 140521389418240)>, <ExcThread(failed_post, started 140521347454720)>, <ExcThread(data, started 140521926289152)>, <ExcThread(copytool_in, started 140521372632832)>]
2019-09-25 13:50:40,793 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-09-25 13:50:40,845 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-09-25 13:50:40,977 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-09-25 13:50:40,977 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-09-25 13:50:41,017 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-09-25 13:50:41,019 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-09-25 13:50:41,019 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140522231465728)>, <ExcThread(payload, started 140521901111040)>, <ExcThread(copytool_out, started 140521909503744)>, <ExcThread(job_monitor, started 140521381025536)>, <ExcThread(create_data_payload, started 140521917896448)>, <ExcThread(validate_post, started 140521355847424)>, <ExcThread(queue_monitoring, started 140521389418240)>, <ExcThread(data, started 140521926289152)>, <ExcThread(copytool_in, started 140521372632832)>]
2019-09-25 13:50:41,026 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-09-25 13:50:41,037 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-09-25 13:50:41,054 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-09-25 13:50:41,055 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-09-25 13:50:41,106 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-09-25 13:50:41,106 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-09-25 13:50:41,120 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-09-25 13:50:41,120 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140522231465728)>, <ExcThread(copytool_out, started 140521909503744)>, <ExcThread(job_monitor, started 140521381025536)>, <ExcThread(validate_post, started 140521355847424)>, <ExcThread(queue_monitoring, started 140521389418240)>]
2019-09-25 13:50:41,377 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-09-25 13:50:41,423 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-09-25 13:50:41,423 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140522231465728)>, <ExcThread(copytool_out, started 140521909503744)>, <ExcThread(job_monitor, started 140521381025536)>, <ExcThread(queue_monitoring, started 140521389418240)>]
2019-09-25 13:50:41,794 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-09-25 13:50:41,826 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-09-25 13:50:41,826 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140522231465728)>, <ExcThread(job_monitor, started 140521381025536)>, <ExcThread(queue_monitoring, started 140521389418240)>]
2019-09-25 13:50:42,409 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-09-25 13:50:45,411 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-09-25 13:50:45,444 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-09-25 13:50:45,445 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140522231465728)>, <ExcThread(job_monitor, started 140521381025536)>]
2019-09-25 13:50:51,444 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-09-25 13:50:51,445 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-09-25 13:50:51,487 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-09-25 13:50:51,488 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-09-25 13:50:51,488 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-09-25 13:50:51 UTC [wrapper] ==== pilot stdout END ====
2019-09-25 13:50:51 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-09-25 13:50:51 UTC [wrapper] Pilot exit status: 0
2019-09-25 13:50:51 UTC [wrapper] STATUSCODE: 0
2019-09-25 13:50:51 UTC [wrapper] apfmon messages muted
---- find pandaIDs.out ----
total 56
-rw-------.  1 grid grid 11357 Jul 25 16:38 LICENSE
-rw-------.  1 grid grid    20 Sep  9 13:04 MANIFEST.IN
-rw-------.  1 grid grid    11 Sep 25 14:03 pandaIDs.out
drwx------. 14 grid grid   216 Sep 25 14:03 pilot
-rwx------.  1 grid grid 20136 Sep  9 13:04 pilot.py
-rw-------.  1 grid grid     9 Sep  9 13:04 PILOTVERSION
-rw-------.  1 grid grid  2251 Jul 25 16:38 README.md
-rw-------.  1 grid grid   760 Aug 22 11:01 setup.py
-rw-------.  1 grid grid   221 Jul 25 16:38 TODO.md

2019-09-25 13:50:51 UTC [wrapper] pandaIDs.out files:
-rw-------. 1 grid grid 11 Sep 25 14:03 /home/grid/slots/0/pilot2/pandaIDs.out
2019-09-25 13:50:51 UTC [wrapper] pandaIDs.out content:
4486252265

2019-09-25 13:50:51 UTC [wrapper] Test setup, not cleaning
2019-09-25 13:50:51 UTC [wrapper] ==== wrapper stdout END ====
2019-09-25 13:50:51 UTC [wrapper] ==== wrapper stderr END ====
2019-09-25 13:50:51 UTC [wrapper] wrapper wrapperexiting ec=0, duration=6483
2019-09-25 13:50:51 UTC [wrapper] apfmon messages muted
2019-09-25 15:50:52,099: ***************diag file************
2019-09-25 15:50:52,099: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=6483.97s
KernelTime=231.88s
UserTime=5963.63s
CPUUsage=95%
MaxResidentMemory=1945096kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=258815
MinorPageFaults=10828877
Swaps=0
ForcedSwitches=946573
WaitSwitches=4689864
Inputs=62286634
Outputs=71648
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
2019-09-25 15:50:52,172: ******************************WorkDir***********************
2019-09-25 15:50:52,172: total 232796
drwxrwx--x. 7 grid grid      4096 Sep 25 15:50 .
drwxr-x--x. 7 grid grid        51 Sep 25 15:02 ..
-rw-------. 1 grid grid   7579510 Sep 25 14:03 agis_ddmendpoints.json
-rw-------. 1 grid grid   4045335 Sep 25 14:03 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Sep 25 14:02 .alrb
drwxr-xr-x. 3 grid grid        17 Sep 25 14:02 APPS
-rw-------. 1 grid grid       538 Sep 25 14:03 .asetup
-rw-------. 1 grid grid       826 Sep 25 14:04 .asetup.save
drwx------. 2 grid grid         6 Sep 25 14:04 .asetup-sysbin_8239
-rw-r--r--. 1 grid grid         0 Sep 25 14:02 boinc_lockfile
-rw-r--r--. 1 grid grid      8192 Sep 25 15:50 boinc_mmap_file
-rw-r--r--. 1 grid grid       536 Sep 25 15:48 boinc_task_state.xml
-rw-r--r--. 1 grid grid 225282256 Sep 25 14:02 EVNT.18605806._000054.pool.root.1
-rw-------. 1 grid grid     23573 Sep 25 15:50 heartbeat.json
-rw-r--r--. 1 grid grid      5865 Sep 25 14:02 init_data.xml
-rw-r--r--. 1 grid grid    267503 Sep 25 14:02 input.tar.gz
-rw-r--r--. 1 grid grid       112 Sep 25 14:02 job.xml
-rw-------. 1 grid grid    372927 Sep 25 15:50 log.19056345._002550.job.log.1
-rw-------. 1 grid grid    378664 Sep 25 15:50 log.19056345._002550.job.log.tgz.1
-rw-------. 1 grid grid       241 Sep 25 15:50 output.list
-rw-------. 1 grid grid      2865 Sep 24 21:48 pandaJobData.out
drwx------. 3 grid grid       229 Sep 25 14:03 pilot2
-rw-r--r--. 1 grid grid    259319 Sep 24 21:34 pilot2.tar.gz
-rw-------. 1 grid grid     11799 Sep 25 15:50 pilotlog.txt
-rw-r--r--. 1 grid grid      4480 Sep 24 21:48 queuedata.json
-rw-------. 1 grid grid       512 Sep 25 15:50 rMZNDmBy5WvnShfckohDCDFpABFKDmABFKDm1VqPDmABFKDmGMN6Lm.diag
-rw-r--r--. 1 grid grid       815 Sep 25 14:02 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8466 Sep 25 14:02 run_atlas
-rwx------. 1 grid grid     12762 Sep 24 21:48 runpilot2-wrapper.sh
-rw-r--r--. 1 grid grid       692 Sep 25 15:50 runtime_log
-rw-r--r--. 1 grid grid      6655 Sep 25 15:50 runtime_log.err
drwxrwx--x. 2 grid grid       107 Sep 25 15:50 shared
-rw-r--r--. 1 grid grid      8688 Sep 25 14:02 start_atlas.sh
-rw-r--r--. 1 grid grid     17817 Sep 25 15:50 stderr.txt
-rw-r--r--. 1 grid grid       107 Sep 25 14:02 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--. 1 grid grid        27 Sep 25 15:50 wrapper_checkpoint.txt

2019-09-25 15:50:52,173: running start_atlas return value is 0
2019-09-25 15:50:52,173: Parent exit 0
2019-09-25 15:50:52,176: child process exit 0
15:50:52 (27795): run_atlas exited; CPU time 5964.106254
15:50:52 (27795): called boinc_finish(0)

</stderr_txt>
]]>

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