Stderr output

<core_client_version>7.6.31</core_client_version>
<![CDATA[
<stderr_txt>
13:19:42 (25149): wrapper (7.7.26015): starting
13:19:42 (25149): wrapper: running run_atlas (--nthreads 12)
2019-09-05 13:19:42,276: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-09-05 13:19:42,276: sys.argv = ['run_atlas', '--nthreads', '12']
2019-09-05 13:19:42,277: THREADS=12

2019-09-05 13:19:42,292: Checking for CVMFS
2019-09-05 13:19:45,515: CVMFS is installed
2019-09-05 13:19:45,540: OS:cat: /etc/redhat-release: No such file or directory
2019-09-05 13:19:45,540: This is not SLC6, need to run with Singularity....
2019-09-05 13:19:45,540: Checking Singularity...
2019-09-05 13:19:45,558: Singularity is installed, version 2.4.2-dist
2019-09-05 13:19:45,558: Testing the function of Singularity...
2019-09-05 13:19:45,558: Checking singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
2019-09-05 13:19:45,732: Singularity Works...
2019-09-05 13:19:45,732: copy /var/lib/boinc2/slots/6/shared/RTE.tar.gz
2019-09-05 13:19:45,733: copy /var/lib/boinc2/slots/6/shared/ATLAS.root_0
2019-09-05 13:19:46,078: copy /var/lib/boinc2/slots/6/shared/input.tar.gz
2019-09-05 13:19:46,079: copy /var/lib/boinc2/slots/6/shared/start_atlas.sh
2019-09-05 13:19:46,079: export ATHENA_PROC_NUMBER=12;
2019-09-05 13:19:46,159: start atlas job with PandaID=4002876565
2019-09-05 13:19:46,159: cmd = singularity exec --pwd /var/lib/boinc2/slots/6 -B /cvmfs,/var /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 sh start_atlas.sh > runtime_log 2> runtime_log.err
2019-09-05 14:27:54,146: running cmd return value is 0
2019-09-05 14:27:54,147: Moving ./HITS.000649-3282993-30533._078090.pool.root.1 to shared/HITS.pool.root.1
2019-09-05 14:27:54,147: *****************The last 100 lines of the pilot log******************
2019-09-05 14:27:54,171: 2019-09-05 20:27:19,996 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-09-05 20:27:19,996 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-09-05 20:27:19,996 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-09-05 20:27:19,996 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-09-05 20:27:19,996 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-09-05 20:27:19,996 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-09-05 20:27:19,996 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 1854 s
2019-09-05 20:27:19,996 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 10
2019-09-05 20:27:19,996 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-09-05 20:27:19,997 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 27090
2019-09-05 20:27:19,997 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 27090
2019-09-05 20:27:19,997 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 12
2019-09-05 20:27:19,997 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-09-05 20:27:19,997 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-09-05 20:27:19,997 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-09-05 20:27:19,997 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4002876565 has completed
2019-09-05 20:27:19,997 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-09-05 20:27:19,999 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /var/lib/boinc2/slots/6/PanDA_Pilot-4002876565
2019-09-05 20:27:21,008 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [27090]
2019-09-05 20:27:21,008 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 27090
2019-09-05 20:27:21,008 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-09-05 20:27:22,011 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-09-05 20:27:22,012 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=27090
2019-09-05 20:27:22,388 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [27090] (in reverse order)
2019-09-05 20:27:22,791 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-09-05 20:27:22,791 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-09-05 20:27:22,791 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-09-05 20:27:22,791 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-09-05 20:27:22,829 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | ****************************************
2019-09-05 20:27:22,829 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | ***  PanDA Pilot version 2.1.24 (1)  ***
2019-09-05 20:27:22,830 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | ****************************************
2019-09-05 20:27:22,830 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | 
2019-09-05 20:27:22,830 | INFO     | retrieve            | pilot.util.auxiliary             | display_architecture_info | architecture information:
2019-09-05 20:27:24,064 | 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
2019-09-05 20:27:24,067 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | ****************************************
2019-09-05 20:27:34,619 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /var/lib/boinc2/slots/6
2019-09-05 20:27:34,828 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (292156342272 B)
2019-09-05 20:27:34,829 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-09-05 20:27:34,829 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-09-05 20:27:34,843 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-09-05 20:27:34,863 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-09-05 20:27:34,864 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-09-05 20:27:34,867 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-09-05 20:27:34,975 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-09-05 20:27:34,975 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-09-05 20:27:35,123 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-09-05 20:27:35,124 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139966743070464)>, <ExcThread(copytool_out, started 139966488950528)>, <ExcThread(validate_pre, started 139966264895232)>, <ExcThread(queue_monitoring, started 139966239717120)>, <ExcThread(data, started 139966505735936)>, <ExcThread(copytool_in, started 139965803525888)>, <ExcThread(validate, started 139966514128640)>, <ExcThread(execute_payloads, started 139965795133184)>, <ExcThread(failed_post, started 139966222931712)>, <ExcThread(payload, started 139966273287936)>, <ExcThread(job_monitor, started 139965786740480)>, <ExcThread(validate_post, started 139966248109824)>, <ExcThread(create_data_payload, started 139966497343232)>]
2019-09-05 20:27:35,227 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-09-05 20:27:35,340 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-09-05 20:27:35,347 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-09-05 20:27:35,431 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-09-05 20:27:35,432 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139966743070464)>, <ExcThread(copytool_out, started 139966488950528)>, <ExcThread(queue_monitoring, started 139966239717120)>, <ExcThread(data, started 139966505735936)>, <ExcThread(validate, started 139966514128640)>, <ExcThread(failed_post, started 139966222931712)>, <ExcThread(payload, started 139966273287936)>, <ExcThread(job_monitor, started 139965786740480)>, <ExcThread(validate_post, started 139966248109824)>, <ExcThread(create_data_payload, started 139966497343232)>]
2019-09-05 20:27:35,839 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-09-05 20:27:35,847 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-09-05 20:27:35,875 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-09-05 20:27:35,877 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-09-05 20:27:35,911 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-09-05 20:27:35,955 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-09-05 20:27:35,991 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-09-05 20:27:35,992 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-09-05 20:27:35,992 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139966743070464)>, <ExcThread(queue_monitoring, started 139966239717120)>, <ExcThread(payload, started 139966273287936)>, <ExcThread(job_monitor, started 139965786740480)>]
2019-09-05 20:27:36,011 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-09-05 20:27:36,012 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-09-05 20:27:36,095 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-09-05 20:27:36,096 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139966743070464)>, <ExcThread(queue_monitoring, started 139966239717120)>, <ExcThread(job_monitor, started 139965786740480)>]
2019-09-05 20:27:38,331 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-09-05 20:27:41,340 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-09-05 20:27:41,403 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-09-05 20:27:41,404 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139966743070464)>, <ExcThread(job_monitor, started 139965786740480)>]
2019-09-05 20:27:51,924 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-09-05 20:27:51,924 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-09-05 20:27:52,003 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-09-05 20:27:52,004 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-09-05 20:27:52,004 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-09-05 20:27:52 UTC [wrapper] ==== pilot stdout END ====
2019-09-05 20:27:52 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-09-05 20:27:52 UTC [wrapper] Pilot exit status: 0
2019-09-05 20:27:52 UTC [wrapper] STATUSCODE: 0
2019-09-05 20:27:52 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
total 52
-rw-rw-r--  1 320 320 11357 Jul 25 08:38 LICENSE
drwxrwxr-x 14 320 320  4096 Sep  5 13:20 pilot
-rwxr-xr-x  1 320 320 20098 Aug 22 03:01 pilot.py
-rw-r--r--  1 320 320     8 Aug 23 07:01 PILOTVERSION
-rw-rw-r--  1 320 320  2251 Jul 25 08:38 README.md
-rw-r--r--  1 320 320   760 Aug 22 03:01 setup.py
-rw-rw-r--  1 320 320   221 Jul 25 08:38 TODO.md

2019-09-05 20:27:53 UTC [wrapper] Test setup, not cleaning
2019-09-05 20:27:53 UTC [wrapper] ==== wrapper stdout END ====
2019-09-05 20:27:53 UTC [wrapper] ==== wrapper stderr END ====
2019-09-05 20:27:53 UTC [wrapper] wrapper wrapperexiting ec=0, duration=4087
2019-09-05 20:27:53 UTC [wrapper] apfmon messages muted
2019-09-05 14:27:54,195: ***************diag file************
2019-09-05 14:27:54,196: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=4086.63s
KernelTime=66.19s
UserTime=1847.44s
CPUUsage=46%
MaxResidentMemory=1977900kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=214038
MinorPageFaults=25945630
Swaps=0
ForcedSwitches=886785
WaitSwitches=2915239
Inputs=52043928
Outputs=57264
SocketReceived=0
SocketSent=0
Signals=0

nodename=wHewitt@d8
exitcode=0
2019-09-05 14:27:54,211: ******************************WorkDir***********************
2019-09-05 14:27:54,212: total 369268
drwxrwx--x 7 root root      4096 Sep  5 14:27 .
drwxrwxrwx 9 root root      4096 Sep  5 10:29 ..
-rw------- 1 root root   7513978 Sep  5 13:20 agis_ddmendpoints.json
-rw------- 1 root root   4149845 Sep  5 13:20 agis_schedconf.cvmfs.json
drwx------ 2 root root      4096 Sep  5 13:19 .alrb
drwxr-xr-x 3 root root      4096 Sep  5 13:19 APPS
-rw------- 1 root root       543 Sep  5 13:19 .asetup
-rw------- 1 root root       829 Sep  5 13:22 .asetup.save
drwx------ 2 root root      4096 Sep  5 13:21 .asetup-sysbin_13701
-rw-r--r-- 1 root root         0 Sep  5 13:19 boinc_lockfile
-rw-r--r-- 1 root root      8192 Sep  5 14:27 boinc_mmap_file
-rw-r--r-- 1 root root       536 Sep  5 14:25 boinc_task_state.xml
-rw-r--r-- 1 root root 365251149 Sep  5 13:19 EVNT.14296418._001447.pool.root.1
-rw------- 1 root root       489 Sep  5 14:27 G87LDmM6OPvnShfckohDCDFpABFKDmABFKDmQ6FKDmjBFKDmDQh8Bn.diag
-rw------- 1 root root     13425 Sep  5 14:27 heartbeat.json
-rw-r--r-- 1 root root      8451 Sep  5 13:19 init_data.xml
-rw-r--r-- 1 root root    262889 Sep  5 13:19 input.tar.gz
-rw-r--r-- 1 root root       112 Sep  5 13:19 job.xml
-rw------- 1 root root    178154 Sep  5 14:27 log.000649-3282993-30533._078090.job.log.tgz.1
-rw------- 1 root root    294110 Sep  5 14:27 log.14568781._078090.job.log.1
-rw------- 1 root root       427 Sep  5 14:27 output.list
-rw------- 1 4871 1028      2958 Sep  3 08:36 pandaJobData.out
drwxr-xr-x 3  320  320      4096 Aug 23 07:01 pilot2
-rw-r--r-- 1 root root    255978 Sep  3 07:35 pilot2.tar.gz
-rw------- 1 root root      9188 Sep  5 14:27 pilotlog.txt
-rw------- 1 root root      5077 Sep  5 13:20 queuedata.json
-rw-r--r-- 1 root root       815 Sep  5 13:19 RTE.tar.gz
-rwxr-xr-x 1 root root      8466 Sep  5 13:19 run_atlas
-rwx------ 1 4871 1028     12641 Sep  3 08:36 runpilot2-wrapper.sh
-rw-r--r-- 1 root root       618 Sep  5 14:27 runtime_log
-rw-r--r-- 1 root root      6902 Sep  5 14:27 runtime_log.err
drwxrwx--x 2 root root      4096 Sep  5 14:27 shared
-rw-r--r-- 1 root root      8495 Sep  5 13:19 start_atlas.sh
-rw-r--r-- 1 root root     16947 Sep  5 14:27 stderr.txt
-rw-r--r-- 1 root root       107 Sep  5 13:19 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r-- 1 root root        26 Sep  5 14:27 wrapper_checkpoint.txt

2019-09-05 14:27:54,212: running start_atlas return value is 0
2019-09-05 14:27:54,212: Parent exit 0
2019-09-05 14:27:54,212: child process exit 0
14:27:54 (25149): run_atlas exited; CPU time 1847.568000
14:27:54 (25149): called boinc_finish(0)

</stderr_txt>
]]>

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