Stderr output

<core_client_version>7.12.0</core_client_version>
<![CDATA[
<stderr_txt>
12:02:53 (2845): wrapper (7.7.26015): starting
12:02:53 (2845): wrapper: running run_atlas (--nthreads 2)
singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
sys.argv = ['run_atlas', '--nthreads', '2']
THREADS=2
Checking for CVMFS
CVMFS is installed
OS:cat: /etc/redhat-release: No such file or directory

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 /var/lib/boinc-client/slots/0/shared/start_atlas.sh
copy /var/lib/boinc-client/slots/0/shared/input.tar.gz
copy /var/lib/boinc-client/slots/0/shared/RTE.tar.gz
copy /var/lib/boinc-client/slots/0/shared/ATLAS.root_0
export ATHENA_PROC_NUMBER=2;start atlas job with PandaID=4445903070
cmd = /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec --pwd /var/lib/boinc-client/slots/0 -B /cvmfs,/var /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.18722326._010273.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-16 17:21:34,313 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-16 17:21:34,313 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4445903070
2019-08-16 17:21:34,313 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722326
2019-08-16 17:21:34,313 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-16 17:21:34,313 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-16 17:21:34,313 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-16 17:21:34,313 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-16 17:21:34,313 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-16 17:21:34,314 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-16 17:21:34,314 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-16 17:21:34,314 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-16 17:21:34,314 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 222607 s
2019-08-16 17:21:34,314 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-16 17:21:34,314 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-16 17:21:34,314 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 10079
2019-08-16 17:21:34,314 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 10079
2019-08-16 17:21:34,314 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 2
2019-08-16 17:21:34,315 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-16 17:21:34,315 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-16 17:21:34,315 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-16 17:21:34,315 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4445903070 has completed
2019-08-16 17:21:34,315 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-16 17:21:34,319 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /var/lib/boinc-client/slots/0/PanDA_Pilot-4445903070
2019-08-16 17:21:35,324 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [10079]
2019-08-16 17:21:35,324 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 10079
2019-08-16 17:21:35,324 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-16 17:21:36,326 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-16 17:21:36,326 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=10079
2019-08-16 17:21:36,496 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [10079] (in reverse order)
2019-08-16 17:21:36,542 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-16 17:21:36,543 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-16 17:21:36,543 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-16 17:21:36,543 | 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 17:21:37,052 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-16 17:21:47,557 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-16 17:21:47,557 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /var/lib/boinc-client/slots/0
2019-08-16 17:21:47,591 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (12167675904 B)
2019-08-16 17:21:47,592 | 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 17:21:47,593 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-16 17:21:47,598 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-16 17:21:47,598 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 16 threads
2019-08-16 17:21:47,598 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139700593141504)>, <ExcThread(job, started 139700376889088)>, <ExcThread(validate_pre, started 139699960137472)>, <ExcThread(copytool_out, started 139700351710976)>, <ExcThread(copytool_in, started 139699968530176)>, <ExcThread(failed_post, started 139699381335808)>, <ExcThread(job_monitor, started 139699951744768)>, <ExcThread(data, started 139700368496384)>, <ExcThread(queue_monitoring, started 139700343318272)>, <ExcThread(queue_monitor, started 139699364550400)>, <ExcThread(validate_post, started 139699934959360)>, <ExcThread(create_data_payload, started 139699985315584)>, <ExcThread(execute_payloads, started 139699372943104)>, <ExcThread(monitor, started 139699943352064)>, <ExcThread(payload, started 139700334925568)>, <ExcThread(validate, started 139700360103680)>]
2019-08-16 17:21:47,623 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-16 17:21:47,632 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-16 17:21:47,680 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-16 17:21:47,785 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-16 17:21:47,786 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-16 17:21:47,900 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-16 17:21:47,900 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139700593141504)>, <ExcThread(job, started 139700376889088)>, <ExcThread(validate_pre, started 139699960137472)>, <ExcThread(copytool_out, started 139700351710976)>, <ExcThread(copytool_in, started 139699968530176)>, <ExcThread(failed_post, started 139699381335808)>, <ExcThread(job_monitor, started 139699951744768)>, <ExcThread(queue_monitoring, started 139700343318272)>, <ExcThread(queue_monitor, started 139699364550400)>, <ExcThread(validate_post, started 139699934959360)>, <ExcThread(payload, started 139700334925568)>, <ExcThread(validate, started 139700360103680)>]
2019-08-16 17:21:47,990 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-16 17:21:48,220 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-16 17:21:48,220 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139700593141504)>, <ExcThread(job, started 139700376889088)>, <ExcThread(copytool_out, started 139700351710976)>, <ExcThread(copytool_in, started 139699968530176)>, <ExcThread(failed_post, started 139699381335808)>, <ExcThread(job_monitor, started 139699951744768)>, <ExcThread(queue_monitoring, started 139700343318272)>, <ExcThread(queue_monitor, started 139699364550400)>, <ExcThread(validate_post, started 139699934959360)>, <ExcThread(payload, started 139700334925568)>, <ExcThread(validate, started 139700360103680)>]
2019-08-16 17:21:48,225 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-16 17:21:48,314 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-16 17:21:48,487 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-16 17:21:48,534 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-16 17:21:48,534 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139700593141504)>, <ExcThread(job, started 139700376889088)>, <ExcThread(copytool_out, started 139700351710976)>, <ExcThread(job_monitor, started 139699951744768)>, <ExcThread(queue_monitoring, started 139700343318272)>, <ExcThread(queue_monitor, started 139699364550400)>, <ExcThread(validate_post, started 139699934959360)>, <ExcThread(payload, started 139700334925568)>, <ExcThread(validate, started 139700360103680)>]
2019-08-16 17:21:48,575 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-16 17:21:48,599 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-16 17:21:48,603 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-16 17:21:48,603 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-16 17:21:48,696 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-16 17:21:48,697 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-16 17:21:48,702 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-16 17:21:48,702 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139700593141504)>, <ExcThread(job_monitor, started 139699951744768)>, <ExcThread(queue_monitoring, started 139700343318272)>, <ExcThread(queue_monitor, started 139699364550400)>, <ExcThread(validate, started 139700360103680)>]
2019-08-16 17:21:49,089 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-16 17:21:49,113 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-16 17:21:49,113 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139700593141504)>, <ExcThread(job_monitor, started 139699951744768)>, <ExcThread(queue_monitoring, started 139700343318272)>, <ExcThread(queue_monitor, started 139699364550400)>]
2019-08-16 17:21:49,284 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-16 17:21:49,285 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-16 17:21:49,315 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-16 17:21:49,316 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139700593141504)>, <ExcThread(job_monitor, started 139699951744768)>, <ExcThread(queue_monitoring, started 139700343318272)>]
2019-08-16 17:21:51,226 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-16 17:21:51,240 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-16 17:21:51,241 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139700593141504)>, <ExcThread(job_monitor, started 139699951744768)>]
2019-08-16 17:21:56,795 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-16 17:21:56,795 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-16 17:21:56,799 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-16 17:21:56,799 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-16 17:21:56,799 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-16 17:21:57 UTC [wrapper] ==== pilot stdout END ====
2019-08-16 17:21:57 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-16 17:21:57 UTC [wrapper] Pilot exit status: 0
2019-08-16 17:21:57 UTC [wrapper] STATUSCODE: 0
2019-08-16 17:21:57 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
total 48
-rw-------  1 boinc boinc 11357 jul 25 16:38 LICENSE
drwx------ 14 boinc boinc  4096 aug 15 12:04 pilot
-rwx------  1 boinc boinc 20463 jul 25 16:38 pilot.py
-rw-------  1 boinc boinc     8 aug  7 13:02 PILOTVERSION
-rw-------  1 boinc boinc  2251 jul 25 16:38 README.md
-rw-------  1 boinc boinc   221 jul 25 16:38 TODO.md

2019-08-16 17:21:58 UTC [wrapper] Test setup, not cleaning
2019-08-16 17:21:58 UTC [wrapper] ==== wrapper stdout END ====
2019-08-16 17:21:58 UTC [wrapper] ==== wrapper stderr END ====
2019-08-16 17:21:58 UTC [wrapper] wrapper wrapperexiting ec=0, duration=112724
2019-08-16 17:21:58 UTC [wrapper] apfmon messages muted
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=112724.04s
KernelTime=4567.23s
UserTime=220348.77s
CPUUsage=199%
MaxResidentMemory=2030820kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=2397460
MinorPageFaults=39193885
Swaps=0
ForcedSwitches=5007876
WaitSwitches=60921551
Inputs=543809504
Outputs=1059328
SocketReceived=0
SocketSent=0
Signals=0

nodename=Crystal_Pellet@LinAH125
exitcode=0
******************************WorkDir***********************
total 290720
drwxrwx--x 6 boinc boinc      4096 aug 16 19:22 .
drwxrwx--x 4 boinc boinc      4096 aug 15 13:05 ..
-rw------- 1 boinc boinc   7409162 aug 15 12:05 agis_ddmendpoints.json
-rw------- 1 boinc boinc   4438522 aug 15 12:05 agis_schedconf.cvmfs.json
drwx------ 2 boinc boinc      4096 aug 15 12:03 .alrb
drwxr-xr-x 3 boinc boinc      4096 aug 15 12:03 APPS
-rw------- 1 boinc boinc       549 aug 15 12:03 .asetup
-rw------- 1 boinc boinc       826 aug 15 12:08 .asetup.save
-rw-r--r-- 1 boinc boinc         0 aug 15 12:02 boinc_lockfile
-rw-r--r-- 1 boinc boinc      8192 aug 16 19:22 boinc_mmap_file
-rw-r--r-- 1 boinc boinc       539 aug 16 19:03 boinc_task_state.xml
-rw-r--r-- 1 boinc boinc 279230307 aug 15 12:03 EVNT.18605758._000316.pool.root.1
-rw------- 1 boinc boinc     59517 aug 16 19:21 heartbeat.json
-rw-r--r-- 1 boinc boinc      5851 aug 15 12:02 init_data.xml
-rw-r--r-- 1 boinc boinc    261614 aug 15 12:03 input.tar.gz
-rw-r--r-- 1 boinc boinc       112 aug 15 12:02 job.xml
-rw------- 1 boinc boinc   4984774 aug 16 19:21 log.18722326._010273.job.log.1
-rw------- 1 boinc boinc    866164 aug 16 19:21 log.18722326._010273.job.log.tgz.1
-rw------- 1 boinc boinc       391 aug 16 19:21 output.list
-rw------- 1 boinc boinc      2914 aug 14 19:52 pandaJobData.out
drwx------ 3 boinc boinc      4096 aug  7 13:02 pilot2
-rw-r--r-- 1 boinc boinc    253018 aug 14 19:27 pilot2.tar.gz
-rw------- 1 boinc boinc     10633 aug 16 19:21 pilotlog.txt
-rw------- 1 boinc boinc       515 aug 16 19:21 PpPLDmHdCIvnShfckohDCDFpABFKDmABFKDmmW6aDmABFKDmXUvQMm.diag
-rw-r--r-- 1 boinc boinc      4468 aug 14 19:51 queuedata.json
-rw-r--r-- 1 boinc boinc       815 aug 15 12:03 RTE.tar.gz
-rwxr-xr-x 1 boinc boinc      8779 aug 15 12:02 run_atlas
-rwx------ 1 boinc boinc     12641 aug 14 19:52 runpilot2-wrapper.sh
-rw-r--r-- 1 boinc boinc       692 aug 16 19:21 runtime_log
-rw-r--r-- 1 boinc boinc      7057 aug 16 19:21 runtime_log.err
drwxrwx--x 2 boinc boinc      4096 aug 16 19:22 shared
-rw-r--r-- 1 boinc boinc      8688 aug 15 12:03 start_atlas.sh
-rw-r--r-- 1 boinc boinc     18696 aug 16 19:22 stderr.txt
-rw-r--r-- 1 boinc boinc       107 aug 15 12:02 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r-- 1 boinc boinc        30 aug 16 19:22 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
19:22:04 (2845): run_atlas exited; CPU time 220350.512054
19:22:04 (2845): called boinc_finish(0)

</stderr_txt>
]]>

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