Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
02:49:14 (27471): wrapper (7.7.26015): starting
02:49:14 (27471): wrapper: running run_atlas (--nthreads 4)
2019-08-17 02:49:14,086: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-17 02:49:14,086: sys.argv = ['run_atlas', '--nthreads', '4']
2019-08-17 02:49:14,087: THREADS=4

2019-08-17 02:49:14,090: Checking for CVMFS
2019-08-17 02:49:15,955: CVMFS is installed
2019-08-17 02:49:15,958: OS:CentOS Linux release 7.6.1810 (Core) 
2019-08-17 02:49:15,959: This is not SLC6, need to run with Singularity....
2019-08-17 02:49:15,959: Checking Singularity...
2019-08-17 02:49:15,961: Singularity is not installed, using version from CVMFS
2019-08-17 02:49:15,962: Testing the function of Singularity...
2019-08-17 02:49:15,962: 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
2019-08-17 02:49:16,274: Singularity Works...
2019-08-17 02:49:16,274: copy /home/grid/slots/0/shared/ATLAS.root_0
2019-08-17 02:49:16,833: copy /home/grid/slots/0/shared/input.tar.gz
2019-08-17 02:49:16,834: copy /home/grid/slots/0/shared/RTE.tar.gz
2019-08-17 02:49:16,834: copy /home/grid/slots/0/shared/start_atlas.sh
2019-08-17 02:49:16,835: export ATHENA_PROC_NUMBER=4;
2019-08-17 02:49:16,859: start atlas job with PandaID=4443210601
2019-08-17 02:49:16,859: 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
2019-08-17 05:56:33,754: running cmd return value is 0
2019-08-17 05:56:33,757: Moving ./HITS.18722432._020875.pool.root.1 to shared/HITS.pool.root.1
2019-08-17 05:56:33,758: *****************The last 100 lines of the pilot log******************
2019-08-17 05:56:33,767: 2019-08-17 03:55:27,037 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-17 03:55:27,037 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-17 03:55:27,037 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-17 03:55:27,037 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-17 03:55:27,037 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-17 03:55:27,037 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-17 03:55:27,037 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 42021 s
2019-08-17 03:55:27,037 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-17 03:55:27,037 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-17 03:55:27,037 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 1725
2019-08-17 03:55:27,037 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 1725
2019-08-17 03:55:27,037 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-17 03:55:27,038 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-17 03:55:27,038 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-17 03:55:27,038 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-17 03:55:27,038 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4443210601 has completed
2019-08-17 03:55:27,038 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-17 03:55:27,048 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4443210601
2019-08-17 03:55:28,053 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [1725]
2019-08-17 03:55:28,054 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 1725
2019-08-17 03:55:28,054 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-17 03:55:29,059 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-17 03:55:29,059 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=1725
2019-08-17 03:55:29,106 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [1725] (in reverse order)
2019-08-17 03:55:29,145 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-17 03:55:29,145 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-17 03:55:29,145 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-17 03:55:29,145 | 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 03:55:29,653 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-17 03:55:31,670 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-17 03:55:39,655 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-17 03:55:39,655 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-17 03:55:39,694 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35456548864 B)
2019-08-17 03:55:39,695 | 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 03:55:39,695 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-17 03:55:39,705 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-17 03:55:39,764 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 16 threads
2019-08-17 03:55:39,765 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139629063399168)>, <ExcThread(job, started 139628847126272)>, <ExcThread(data, started 139628830340864)>, <ExcThread(queue_monitor, started 139627776177920)>, <ExcThread(validate, started 139628838733568)>, <ExcThread(create_data_payload, started 139628821948160)>, <ExcThread(validate_post, started 139628296263424)>, <ExcThread(execute_payloads, started 139627767785216)>, <ExcThread(failed_post, started 139628279478016)>, <ExcThread(validate_pre, started 139628796770048)>, <ExcThread(monitor, started 139628313048832)>, <ExcThread(copytool_in, started 139628271085312)>, <ExcThread(job_monitor, started 139628262692608)>, <ExcThread(payload, started 139628813555456)>, <ExcThread(copytool_out, started 139628805162752)>, <ExcThread(queue_monitoring, started 139628304656128)>]
2019-08-17 03:55:39,926 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-17 03:55:39,927 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-17 03:55:40,060 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-17 03:55:40,061 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-17 03:55:40,062 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-17 03:55:40,167 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 14 threads
2019-08-17 03:55:40,167 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139629063399168)>, <ExcThread(job, started 139628847126272)>, <ExcThread(queue_monitor, started 139627776177920)>, <ExcThread(validate, started 139628838733568)>, <ExcThread(create_data_payload, started 139628821948160)>, <ExcThread(validate_post, started 139628296263424)>, <ExcThread(execute_payloads, started 139627767785216)>, <ExcThread(failed_post, started 139628279478016)>, <ExcThread(validate_pre, started 139628796770048)>, <ExcThread(monitor, started 139628313048832)>, <ExcThread(copytool_in, started 139628271085312)>, <ExcThread(job_monitor, started 139628262692608)>, <ExcThread(copytool_out, started 139628805162752)>, <ExcThread(queue_monitoring, started 139628304656128)>]
2019-08-17 03:55:40,202 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-17 03:55:40,257 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-17 03:55:40,257 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-17 03:55:40,268 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-08-17 03:55:40,268 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139629063399168)>, <ExcThread(queue_monitor, started 139627776177920)>, <ExcThread(validate, started 139628838733568)>, <ExcThread(create_data_payload, started 139628821948160)>, <ExcThread(validate_post, started 139628296263424)>, <ExcThread(execute_payloads, started 139627767785216)>, <ExcThread(failed_post, started 139628279478016)>, <ExcThread(validate_pre, started 139628796770048)>, <ExcThread(copytool_in, started 139628271085312)>, <ExcThread(job_monitor, started 139628262692608)>, <ExcThread(copytool_out, started 139628805162752)>, <ExcThread(queue_monitoring, started 139628304656128)>]
2019-08-17 03:55:40,592 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-17 03:55:40,603 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-17 03:55:40,671 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-17 03:55:40,672 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139629063399168)>, <ExcThread(queue_monitor, started 139627776177920)>, <ExcThread(create_data_payload, started 139628821948160)>, <ExcThread(validate_post, started 139628296263424)>, <ExcThread(execute_payloads, started 139627767785216)>, <ExcThread(validate_pre, started 139628796770048)>, <ExcThread(copytool_in, started 139628271085312)>, <ExcThread(job_monitor, started 139628262692608)>, <ExcThread(copytool_out, started 139628805162752)>, <ExcThread(queue_monitoring, started 139628304656128)>]
2019-08-17 03:55:40,745 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-17 03:55:40,752 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-17 03:55:40,772 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-08-17 03:55:40,773 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139629063399168)>, <ExcThread(queue_monitor, started 139627776177920)>, <ExcThread(validate_post, started 139628296263424)>, <ExcThread(validate_pre, started 139628796770048)>, <ExcThread(copytool_in, started 139628271085312)>, <ExcThread(job_monitor, started 139628262692608)>, <ExcThread(copytool_out, started 139628805162752)>, <ExcThread(queue_monitoring, started 139628304656128)>]
2019-08-17 03:55:40,901 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-17 03:55:40,974 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-17 03:55:40,975 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139629063399168)>, <ExcThread(queue_monitor, started 139627776177920)>, <ExcThread(validate_pre, started 139628796770048)>, <ExcThread(copytool_in, started 139628271085312)>, <ExcThread(job_monitor, started 139628262692608)>, <ExcThread(copytool_out, started 139628805162752)>, <ExcThread(queue_monitoring, started 139628304656128)>]
2019-08-17 03:55:41,033 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-17 03:55:41,063 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-17 03:55:41,076 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-17 03:55:41,076 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139629063399168)>, <ExcThread(queue_monitor, started 139627776177920)>, <ExcThread(validate_pre, started 139628796770048)>, <ExcThread(job_monitor, started 139628262692608)>, <ExcThread(queue_monitoring, started 139628304656128)>]
2019-08-17 03:55:41,107 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-17 03:55:41,177 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-17 03:55:41,177 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139629063399168)>, <ExcThread(queue_monitor, started 139627776177920)>, <ExcThread(job_monitor, started 139628262692608)>, <ExcThread(queue_monitoring, started 139628304656128)>]
2019-08-17 03:55:41,514 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-17 03:55:41,514 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-17 03:55:41,580 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-17 03:55:41,580 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139629063399168)>, <ExcThread(job_monitor, started 139628262692608)>, <ExcThread(queue_monitoring, started 139628304656128)>]
2019-08-17 03:55:42,706 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-17 03:55:42,789 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-17 03:55:42,789 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139629063399168)>, <ExcThread(job_monitor, started 139628262692608)>]
2019-08-17 03:56:33,241 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 123 s)
2019-08-17 03:56:33,241 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-17 03:56:33,338 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-17 03:56:33,338 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-17 03:56:33,338 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-17 03:56:33 UTC [wrapper] ==== pilot stdout END ====
2019-08-17 03:56:33 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-17 03:56:33 UTC [wrapper] Pilot exit status: 0
2019-08-17 03:56:33 UTC [wrapper] STATUSCODE: 0
2019-08-17 03:56:33 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 02:49 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 03:56:33 UTC [wrapper] Test setup, not cleaning
2019-08-17 03:56:33 UTC [wrapper] ==== wrapper stdout END ====
2019-08-17 03:56:33 UTC [wrapper] ==== wrapper stderr END ====
2019-08-17 03:56:33 UTC [wrapper] wrapper wrapperexiting ec=0, duration=11236
2019-08-17 03:56:33 UTC [wrapper] apfmon messages muted
2019-08-17 05:56:33,771: ***************diag file************
2019-08-17 05:56:33,771: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=11236.55s
KernelTime=313.35s
UserTime=41860.63s
CPUUsage=375%
MaxResidentMemory=1945104kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=368788
MinorPageFaults=15928159
Swaps=0
ForcedSwitches=4869801
WaitSwitches=7638877
Inputs=89406128
Outputs=746712
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
2019-08-17 05:56:33,781: ******************************WorkDir***********************
2019-08-17 05:56:33,781: total 229752
drwxrwx--x. 6 grid grid      4096 Aug 17 05:56 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7411700 Aug 17 02:49 agis_ddmendpoints.json
-rw-------. 1 grid grid   4399526 Aug 17 02:49 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 17 02:49 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 17 02:49 APPS
-rw-------. 1 grid grid       538 Aug 17 02:49 .asetup
-rw-------. 1 grid grid       826 Aug 17 02:50 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 17 02:49 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 17 05:56 boinc_mmap_file
-rw-rw-r--. 1 grid grid       537 Aug 17 05:48 boinc_task_state.xml
-rw-------. 1 grid grid       517 Aug 17 05:56 BOUNDmCSbHvnShfckohDCDFpABFKDmABFKDmT77ZDmABFKDmJND8Ho.diag
-rw-rw-r--. 1 grid grid 221190581 Aug 17 02:49 EVNT.18605781._000431.pool.root.1
-rw-------. 1 grid grid    108555 Aug 17 05:55 heartbeat.json
-rw-rw-r--. 1 grid grid      5866 Aug 17 02:49 init_data.xml
-rw-rw-r--. 1 grid grid    261624 Aug 17 02:49 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 17 02:49 job.xml
-rw-------. 1 grid grid    622066 Aug 17 05:56 log.18722432._020875.job.log.1
-rw-------. 1 grid grid    844483 Aug 17 05:55 log.18722432._020875.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 17 05:56 output.list
-rw-------. 1 grid grid      2958 Aug 13 04:10 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 13 03:26 pilot2.tar.gz
-rw-------. 1 grid grid     12440 Aug 17 05:56 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 13 04:10 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 17 02:49 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8466 Aug 17 02:49 run_atlas
-rwx------. 1 grid grid     12641 Aug 13 04:10 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 17 05:56 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 17 05:56 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 17 05:56 shared
-rw-rw-r--. 1 grid grid      8688 Aug 17 02:49 start_atlas.sh
-rw-rw-r--. 1 grid grid     20292 Aug 17 05:56 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 17 02:49 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        28 Aug 17 05:56 wrapper_checkpoint.txt

2019-08-17 05:56:33,781: running start_atlas return value is 0
2019-08-17 05:56:33,781: Parent exit 0
2019-08-17 05:56:33,783: child process exit 0
05:56:33 (27471): run_atlas exited; CPU time 41861.018487
05:56:33 (27471): called boinc_finish(0)

</stderr_txt>
]]>

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