Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
09:20:08 (4397): wrapper (7.7.26015): starting
09:20:08 (4397): wrapper: running run_atlas (--nthreads 4)
singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
sys.argv = ['run_atlas', '--nthreads', '4']
THREADS=4
Checking for CVMFS
CVMFS is installed
OS:CentOS Linux release 7.6.1810 (Core) 

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 /home/grid/slots/0/shared/ATLAS.root_0
copy /home/grid/slots/0/shared/input.tar.gz
copy /home/grid/slots/0/shared/RTE.tar.gz
copy /home/grid/slots/0/shared/start_atlas.sh
export ATHENA_PROC_NUMBER=4;start atlas job with PandaID=4443084869
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
running cmd return value is 0
Moving ./HITS.18722398._020196.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-13 09:32:30,045 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-13 09:32:30,046 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-13 09:32:30,046 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-13 09:32:30,046 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4443084869
2019-08-13 09:32:30,046 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722398
2019-08-13 09:32:30,046 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-13 09:32:30,046 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-13 09:32:30,046 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-13 09:32:30,046 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-13 09:32:30,046 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-13 09:32:30,046 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-13 09:32:30,046 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-13 09:32:30,046 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-13 09:32:30,047 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 29082 s
2019-08-13 09:32:30,047 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-13 09:32:30,047 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-13 09:32:30,047 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 11083
2019-08-13 09:32:30,047 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 11083
2019-08-13 09:32:30,047 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-13 09:32:30,047 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-13 09:32:30,047 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-13 09:32:30,047 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-13 09:32:30,047 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4443084869 has completed
2019-08-13 09:32:30,047 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-13 09:32:30,062 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4443084869
2019-08-13 09:32:31,066 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [11083]
2019-08-13 09:32:31,066 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 11083
2019-08-13 09:32:31,067 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-13 09:32:32,072 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-13 09:32:32,072 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=11083
2019-08-13 09:32:32,124 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [11083] (in reverse order)
2019-08-13 09:32:32,166 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-13 09:32:32,166 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-13 09:32:32,166 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-13 09:32:32,166 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-13 09:32:32,677 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-13 09:32:42,719 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-13 09:32:42,720 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-13 09:32:42,770 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35972448256 B)
2019-08-13 09:32:42,771 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-13 09:32:42,771 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-13 09:32:42,781 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-13 09:32:42,815 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-13 09:32:42,821 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 15 threads
2019-08-13 09:32:42,822 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140615422465792)>, <ExcThread(job, started 140615206192896)>, <ExcThread(data, started 140615197800192)>, <ExcThread(queue_monitor, started 140614209369856)>, <ExcThread(copytool_in, started 140614779778816)>, <ExcThread(queue_monitoring, started 140614796564224)>, <ExcThread(failed_post, started 140614200977152)>, <ExcThread(create_data_payload, started 140614804956928)>, <ExcThread(execute_payloads, started 140614192584448)>, <ExcThread(job_monitor, started 140614762993408)>, <ExcThread(payload, started 140615189407488)>, <ExcThread(validate_post, started 140614771386112)>, <ExcThread(validate_pre, started 140614813349632)>, <ExcThread(validate, started 140615181014784)>, <ExcThread(copytool_out, started 140615172622080)>]
2019-08-13 09:32:42,836 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-13 09:32:42,865 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-13 09:32:43,075 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-13 09:32:43,226 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-13 09:32:43,227 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140615422465792)>, <ExcThread(job, started 140615206192896)>, <ExcThread(data, started 140615197800192)>, <ExcThread(queue_monitor, started 140614209369856)>, <ExcThread(queue_monitoring, started 140614796564224)>, <ExcThread(failed_post, started 140614200977152)>, <ExcThread(create_data_payload, started 140614804956928)>, <ExcThread(execute_payloads, started 140614192584448)>, <ExcThread(job_monitor, started 140614762993408)>, <ExcThread(payload, started 140615189407488)>, <ExcThread(validate_post, started 140614771386112)>, <ExcThread(validate, started 140615181014784)>, <ExcThread(copytool_out, started 140615172622080)>]
2019-08-13 09:32:43,227 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-13 09:32:43,227 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-13 09:32:43,291 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-13 09:32:43,354 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-13 09:32:43,528 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-13 09:32:43,529 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140615422465792)>, <ExcThread(job, started 140615206192896)>, <ExcThread(data, started 140615197800192)>, <ExcThread(queue_monitor, started 140614209369856)>, <ExcThread(queue_monitoring, started 140614796564224)>, <ExcThread(failed_post, started 140614200977152)>, <ExcThread(create_data_payload, started 140614804956928)>, <ExcThread(job_monitor, started 140614762993408)>, <ExcThread(validate, started 140615181014784)>, <ExcThread(copytool_out, started 140615172622080)>]
2019-08-13 09:32:43,703 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-13 09:32:43,703 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-13 09:32:43,730 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 9 threads
2019-08-13 09:32:43,731 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140615422465792)>, <ExcThread(job, started 140615206192896)>, <ExcThread(queue_monitor, started 140614209369856)>, <ExcThread(queue_monitoring, started 140614796564224)>, <ExcThread(failed_post, started 140614200977152)>, <ExcThread(create_data_payload, started 140614804956928)>, <ExcThread(job_monitor, started 140614762993408)>, <ExcThread(validate, started 140615181014784)>, <ExcThread(copytool_out, started 140615172622080)>]
2019-08-13 09:32:43,756 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-13 09:32:43,782 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-13 09:32:43,810 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-13 09:32:43,930 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-13 09:32:43,930 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-13 09:32:43,932 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-13 09:32:43,932 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140615422465792)>, <ExcThread(queue_monitor, started 140614209369856)>, <ExcThread(queue_monitoring, started 140614796564224)>, <ExcThread(job_monitor, started 140614762993408)>, <ExcThread(validate, started 140615181014784)>]
2019-08-13 09:32:44,160 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-13 09:32:44,235 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-13 09:32:44,235 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140615422465792)>, <ExcThread(queue_monitor, started 140614209369856)>, <ExcThread(queue_monitoring, started 140614796564224)>, <ExcThread(job_monitor, started 140614762993408)>]
2019-08-13 09:32:44,530 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-13 09:32:44,530 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-13 09:32:44,538 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-13 09:32:44,538 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140615422465792)>, <ExcThread(queue_monitoring, started 140614796564224)>, <ExcThread(job_monitor, started 140614762993408)>]
2019-08-13 09:32:45,837 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-13 09:32:45,854 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-13 09:32:45,854 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140615422465792)>, <ExcThread(job_monitor, started 140614762993408)>]
2019-08-13 09:33:21,802 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 61 s)
2019-08-13 09:33:21,802 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-13 09:33:21,839 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-13 09:33:21,839 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-13 09:33:21,839 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-13 09:33:22 UTC [wrapper] ==== pilot stdout END ====
2019-08-13 09:33:22 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-13 09:33:22 UTC [wrapper] Pilot exit status: 0
2019-08-13 09:33:22 UTC [wrapper] STATUSCODE: 0
2019-08-13 09:33:22 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 13 09:20 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

2019-08-13 09:33:22 UTC [wrapper] Test setup, not cleaning
2019-08-13 09:33:22 UTC [wrapper] ==== wrapper stdout END ====
2019-08-13 09:33:22 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=7990.75s
KernelTime=256.17s
UserTime=28954.73s
CPUUsage=365%
MaxResidentMemory=1945396kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=306996
MinorPageFaults=13921820
Swaps=0
ForcedSwitches=3333753
WaitSwitches=6097388
Inputs=74528840
Outputs=615944
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 216304
drwxrwx--x. 7 grid grid      4096 Aug 13 11:33 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7409065 Aug 13 09:20 agis_ddmendpoints.json
-rw-------. 1 grid grid   4517434 Aug 13 09:20 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 13 09:20 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 13 09:20 APPS
drwxr-xr-x. 2 grid grid         6 Aug 13 09:20 .arc
-rw-------. 1 grid grid       538 Aug 13 09:20 .asetup
-rw-------. 1 grid grid       826 Aug 13 09:21 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 13 09:20 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 13 11:33 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 13 11:25 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 207443211 Aug 13 09:20 EVNT.18605775._000399.pool.root.1
-rw-------. 1 grid grid     98677 Aug 13 11:32 heartbeat.json
-rw-rw-r--. 1 grid grid      5863 Aug 13 09:20 init_data.xml
-rw-rw-r--. 1 grid grid    262356 Aug 13 09:20 input.tar.gz
-rw-------. 1 grid grid       516 Aug 13 11:33 IOhNDmNl7GvnShfckohDCDFpABFKDmABFKDmKIMZDmABFKDmIncS0m.diag
-rw-rw-r--. 1 grid grid       112 Aug 13 09:20 job.xml
-rw-------. 1 grid grid    502949 Aug 13 11:33 log.18722398._020196.job.log.1
-rw-------. 1 grid grid    837489 Aug 13 11:32 log.18722398._020196.job.log.tgz.1
-rw-------. 1 grid grid       391 Aug 13 11:33 output.list
-rw-------. 1 grid grid      2957 Aug 11 20:28 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 11 20:21 pilot2.tar.gz
-rw-------. 1 grid grid     10593 Aug 13 11:33 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 11 20:27 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 13 09:20 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8779 Aug 13 09:20 run_atlas
-rwx------. 1 grid grid     15232 Aug 11 20:28 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 13 11:33 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 13 11:33 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 13 11:33 shared
-rw-rw-r--. 1 grid grid      8688 Aug 13 09:20 start_atlas.sh
-rw-rw-r--. 1 grid grid     18700 Aug 13 11:33 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 13 09:20 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 13 11:33 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
11:33:22 (4397): run_atlas exited; CPU time 28955.121938
11:33:22 (4397): called boinc_finish(0)

</stderr_txt>
]]>

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