Stderr output

<core_client_version>7.14.2</core_client_version>
<![CDATA[
<stderr_txt>
10:53:14 (33560): wrapper (7.7.26015): starting
10:53:14 (33560): wrapper: running run_atlas (--nthreads 2)
2019-09-04 10:53:14,501: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-09-04 10:53:14,501: sys.argv = ['run_atlas', '--nthreads', '2']
2019-09-04 10:53:14,502: THREADS=2

2019-09-04 10:53:14,503: Checking for CVMFS
2019-09-04 10:53:15,949: CVMFS is installed
2019-09-04 10:53:15,958: OS:cat: /etc/redhat-release: Datei oder Verzeichnis nicht gefunden
2019-09-04 10:53:15,958: This is not SLC6, need to run with Singularity....
2019-09-04 10:53:15,958: Checking Singularity...
2019-09-04 10:53:15,962: Singularity seems to be installed but not working: sh: singularity: Kommando nicht gefunden.
2019-09-04 10:53:15,962: Will use version from CVMFS
2019-09-04 10:53:15,962: Testing the function of Singularity...
2019-09-04 10:53:15,962: 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
2019-09-04 10:53:16,329: Singularity Works...
2019-09-04 10:53:16,330: copy /var/lib/boinc/slots/25/shared/ATLAS.root_0
2019-09-04 10:53:16,700: copy /var/lib/boinc/slots/25/shared/input.tar.gz
2019-09-04 10:53:16,701: copy /var/lib/boinc/slots/25/shared/RTE.tar.gz
2019-09-04 10:53:16,701: copy /var/lib/boinc/slots/25/shared/start_atlas.sh
2019-09-04 10:53:16,701: export ATHENA_PROC_NUMBER=2;
2019-09-04 10:53:16,751: start atlas job with PandaID=4002876565
2019-09-04 10:53:16,751: cmd = /cvmfs/atlas.cern.ch/repo/containers/sw/singularity/x86_64-el7/current/bin/singularity exec --pwd /var/lib/boinc/slots/25 -B /cvmfs,/var /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 sh start_atlas.sh > runtime_log 2> runtime_log.err
2019-09-04 11:28:00,555: running cmd return value is 0
2019-09-04 11:28:00,556: Moving ./HITS.000649-3282754-20018._078090.pool.root.1 to shared/HITS.pool.root.1
2019-09-04 11:28:00,556: *****************The last 100 lines of the pilot log******************
2019-09-04 11:28:00,562: 2019-09-04 09:26:59,392 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 44087
2019-09-04 09:26:59,392 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 44087
2019-09-04 09:26:59,392 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 2
2019-09-04 09:26:59,393 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-09-04 09:26:59,393 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-09-04 09:26:59,393 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-09-04 09:26:59,393 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4002876565 has completed
2019-09-04 09:26:59,393 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-09-04 09:26:59,399 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /var/lib/boinc/slots/25/PanDA_Pilot-4002876565
2019-09-04 09:27:00,408 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [44087]
2019-09-04 09:27:00,408 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 44087
2019-09-04 09:27:00,409 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-09-04 09:27:01,414 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-09-04 09:27:01,414 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=44087
2019-09-04 09:27:01,485 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [44087] (in reverse order)
2019-09-04 09:27:01,543 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-09-04 09:27:01,543 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-09-04 09:27:01,543 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-09-04 09:27:01,543 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-09-04 09:27:01,550 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | ****************************************
2019-09-04 09:27:01,550 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | ***  PanDA Pilot version 2.1.24 (1)  ***
2019-09-04 09:27:01,550 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | ****************************************
2019-09-04 09:27:01,550 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | 
2019-09-04 09:27:01,552 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | pilot is running in a VM
2019-09-04 09:27:01,552 | INFO     | retrieve            | pilot.util.auxiliary             | display_architecture_info | architecture information:
2019-09-04 09:27:01,740 | 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
2019-09-04 09:27:01,744 | INFO     | retrieve            | pilot.util.auxiliary             | pilot_version_banner      | ****************************************
2019-09-04 09:27:12,300 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /var/lib/boinc/slots/25
2019-09-04 09:27:12,337 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (16762535936 B)
2019-09-04 09:27:12,338 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-09-04 09:27:12,338 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-09-04 09:27:12,381 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-09-04 09:27:12,412 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-09-04 09:27:12,412 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-09-04 09:27:12,413 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-09-04 09:27:12,413 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-09-04 09:27:12,438 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-09-04 09:27:12,474 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 12 threads
2019-09-04 09:27:12,474 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139665242937088)>, <ExcThread(job, started 139665022387968)>, <ExcThread(copytool_out, started 139664980424448)>, <ExcThread(execute_payloads, started 139663880746752)>, <ExcThread(queue_monitor, started 139664593766144)>, <ExcThread(copytool_in, started 139664585373440)>, <ExcThread(job_monitor, started 139664618944256)>, <ExcThread(validate_pre, started 139664610551552)>, <ExcThread(validate_post, started 139664576980736)>, <ExcThread(validate, started 139665013995264)>, <ExcThread(failed_post, started 139664568588032)>, <ExcThread(queue_monitoring, started 139664963639040)>]
2019-09-04 09:27:12,679 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-09-04 09:27:12,846 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-09-04 09:27:12,880 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-09-04 09:27:12,881 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139665242937088)>, <ExcThread(job, started 139665022387968)>, <ExcThread(copytool_out, started 139664980424448)>, <ExcThread(queue_monitor, started 139664593766144)>, <ExcThread(copytool_in, started 139664585373440)>, <ExcThread(job_monitor, started 139664618944256)>, <ExcThread(validate_pre, started 139664610551552)>, <ExcThread(validate_post, started 139664576980736)>, <ExcThread(failed_post, started 139664568588032)>, <ExcThread(queue_monitoring, started 139664963639040)>]
2019-09-04 09:27:12,900 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-09-04 09:27:12,992 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-09-04 09:27:13,085 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-09-04 09:27:13,085 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139665242937088)>, <ExcThread(job, started 139665022387968)>, <ExcThread(copytool_out, started 139664980424448)>, <ExcThread(queue_monitor, started 139664593766144)>, <ExcThread(copytool_in, started 139664585373440)>, <ExcThread(job_monitor, started 139664618944256)>, <ExcThread(validate_post, started 139664576980736)>, <ExcThread(failed_post, started 139664568588032)>, <ExcThread(queue_monitoring, started 139664963639040)>]
2019-09-04 09:27:13,284 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-09-04 09:27:13,286 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 8 threads
2019-09-04 09:27:13,287 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139665242937088)>, <ExcThread(job, started 139665022387968)>, <ExcThread(copytool_out, started 139664980424448)>, <ExcThread(queue_monitor, started 139664593766144)>, <ExcThread(job_monitor, started 139664618944256)>, <ExcThread(validate_post, started 139664576980736)>, <ExcThread(failed_post, started 139664568588032)>, <ExcThread(queue_monitoring, started 139664963639040)>]
2019-09-04 09:27:13,430 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-09-04 09:27:13,430 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-09-04 09:27:13,489 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-09-04 09:27:13,490 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139665242937088)>, <ExcThread(job, started 139665022387968)>, <ExcThread(copytool_out, started 139664980424448)>, <ExcThread(job_monitor, started 139664618944256)>, <ExcThread(validate_post, started 139664576980736)>, <ExcThread(failed_post, started 139664568588032)>, <ExcThread(queue_monitoring, started 139664963639040)>]
2019-09-04 09:27:13,544 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-09-04 09:27:13,545 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-09-04 09:27:13,590 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-09-04 09:27:13,591 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139665242937088)>, <ExcThread(copytool_out, started 139664980424448)>, <ExcThread(job_monitor, started 139664618944256)>, <ExcThread(validate_post, started 139664576980736)>, <ExcThread(failed_post, started 139664568588032)>, <ExcThread(queue_monitoring, started 139664963639040)>]
2019-09-04 09:27:13,813 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-09-04 09:27:13,894 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-09-04 09:27:13,894 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139665242937088)>, <ExcThread(copytool_out, started 139664980424448)>, <ExcThread(job_monitor, started 139664618944256)>, <ExcThread(failed_post, started 139664568588032)>, <ExcThread(queue_monitoring, started 139664963639040)>]
2019-09-04 09:27:13,901 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-09-04 09:27:13,946 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-09-04 09:27:13,995 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-09-04 09:27:13,996 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139665242937088)>, <ExcThread(job_monitor, started 139664618944256)>, <ExcThread(queue_monitoring, started 139664963639040)>]
2019-09-04 09:27:15,364 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-09-04 09:27:18,366 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-09-04 09:27:18,367 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-09-04 09:27:18,367 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 139665242937088)>, <ExcThread(job_monitor, started 139664618944256)>]
2019-09-04 09:28:00,124 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 124 s)
2019-09-04 09:28:00,124 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-09-04 09:28:00,127 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-09-04 09:28:00,127 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-09-04 09:28:00,127 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-09-04 09:28:00 UTC [wrapper] ==== pilot stdout END ====
2019-09-04 09:28:00 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-09-04 09:28:00 UTC [wrapper] Pilot exit status: 0
2019-09-04 09:28:00 UTC [wrapper] STATUSCODE: 0
2019-09-04 09:28:00 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
insgesamt 48
-rw------- 1 boinc boinc 11357 25. Jul 16:38 LICENSE
drwx------ 1 boinc boinc   196  4. Sep 10:53 pilot
-rwx------ 1 boinc boinc 20098 22. Aug 11:01 pilot.py
-rw------- 1 boinc boinc     8 23. Aug 15:01 PILOTVERSION
-rw------- 1 boinc boinc  2251 25. Jul 16:38 README.md
-rw------- 1 boinc boinc   760 22. Aug 11:01 setup.py
-rw------- 1 boinc boinc   221 25. Jul 16:38 TODO.md

2019-09-04 09:28:00 UTC [wrapper] Test setup, not cleaning
2019-09-04 09:28:00 UTC [wrapper] ==== wrapper stdout END ====
2019-09-04 09:28:00 UTC [wrapper] ==== wrapper stderr END ====
2019-09-04 09:28:00 UTC [wrapper] wrapper wrapperexiting ec=0, duration=2083
2019-09-04 09:28:00 UTC [wrapper] apfmon messages muted
2019-09-04 11:28:00,567: ***************diag file************
2019-09-04 11:28:00,567: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=2083.22s
KernelTime=127.69s
UserTime=2779.54s
CPUUsage=139%
MaxResidentMemory=1969328kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=131422
MinorPageFaults=6064380
Swaps=0
ForcedSwitches=426811
WaitSwitches=3819227
Inputs=72557768
Outputs=94648
SocketReceived=0
SocketSent=0
Signals=0

nodename=uwe_werths@vagabond-vm
exitcode=0
2019-09-04 11:28:00,576: ******************************WorkDir***********************
2019-09-04 11:28:00,576: insgesamt 369448
drwxrwx--x 1 boinc boinc      1120  4. Sep 11:28 .
drwxrwx--x 1 boinc boinc       324  4. Sep 02:06 ..
-rw------- 1 boinc boinc   7487969  4. Sep 10:53 agis_ddmendpoints.json
-rw------- 1 boinc boinc   4152688  4. Sep 10:53 agis_schedconf.cvmfs.json
drwx------ 1 boinc boinc         0  4. Sep 10:53 .alrb
drwxr-xr-x 1 boinc boinc         6  4. Sep 10:53 APPS
-rw------- 1 boinc boinc       543  4. Sep 10:53 .asetup
-rw------- 1 boinc boinc       829  4. Sep 10:55 .asetup.save
-rw-r--r-- 1 boinc boinc         0  4. Sep 10:53 boinc_lockfile
-rw-r--r-- 1 boinc boinc      8192  4. Sep 11:27 boinc_mmap_file
-rw-r--r-- 1 boinc boinc       535  4. Sep 11:18 boinc_task_state.xml
-rw-r--r-- 1 boinc boinc 365251149  4. Sep 10:53 EVNT.14296418._001447.pool.root.1
-rw------- 1 boinc boinc     14027  4. Sep 11:26 heartbeat.json
-rw------- 1 boinc boinc       502  4. Sep 11:28 hZ7LDmx5OPvnShfckohDCDFpABFKDmABFKDmEHxUDmABFKDmbg1mZn.diag
-rw-r--r-- 1 boinc boinc      6528  4. Sep 10:53 init_data.xml
-rw-r--r-- 1 boinc boinc    262885  4. Sep 10:53 input.tar.gz
-rw-r--r-- 1 boinc boinc       112  4. Sep 10:53 job.xml
-rw------- 1 boinc boinc    505175  4. Sep 11:26 log.000649-3282754-20018._078090.job.log.tgz.1
-rw------- 1 boinc boinc    216650  4. Sep 11:28 log.14568781._078090.job.log.1
-rw------- 1 boinc boinc       427  4. Sep 11:28 output.list
-rw------- 1 boinc boinc      2958  3. Sep 16:36 pandaJobData.out
drwx------ 1 boinc boinc       192 23. Aug 15:01 pilot2
-rw-r--r-- 1 boinc boinc    255978  3. Sep 15:35 pilot2.tar.gz
-rw------- 1 boinc boinc     12028  4. Sep 11:28 pilotlog.txt
-rw------- 1 boinc boinc      5077  4. Sep 10:53 queuedata.json
-rw-r--r-- 1 boinc boinc       815  4. Sep 10:53 RTE.tar.gz
-rwxr-xr-x 1 boinc boinc      8466  4. Sep 10:53 run_atlas
-rwx------ 1 boinc boinc     12641  3. Sep 16:36 runpilot2-wrapper.sh
-rw-r--r-- 1 boinc boinc       618  4. Sep 11:28 runtime_log
-rw-r--r-- 1 boinc boinc      7082  4. Sep 11:28 runtime_log.err
drwxrwx--x 1 boinc boinc       154  4. Sep 11:28 shared
-rw-r--r-- 1 boinc boinc      8534  4. Sep 10:53 start_atlas.sh
-rw-r--r-- 1 boinc boinc     18846  4. Sep 11:28 stderr.txt
-rw-r--r-- 1 boinc boinc       107  4. Sep 10:53 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r-- 1 boinc boinc        26  4. Sep 11:27 wrapper_checkpoint.txt

2019-09-04 11:28:00,576: running start_atlas return value is 0
2019-09-04 11:28:00,577: Parent exit 0
2019-09-04 11:28:00,580: child process exit 0
11:28:00 (33560): run_atlas exited; CPU time 2780.214833
11:28:00 (33560): called boinc_finish(0)

</stderr_txt>
]]>

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