Stderr output

<core_client_version>7.7.0</core_client_version>
<![CDATA[
<stderr_txt>
08:15:31 (16536): wrapper (7.7.26015): starting
08:15:31 (16536): 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 grep: pandaJobData.out: No such file or directory
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._018941.pool.root.1 to shared/HITS.pool.root.1
*****************The last 100 lines of the pilot log******************
2019-08-12 08:27:17,136 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722398
2019-08-12 08:27:17,136 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-12 08:27:17,136 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-12 08:27:17,136 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-12 08:27:17,137 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-12 08:27:17,137 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-12 08:27:17,137 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-12 08:27:17,137 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-12 08:27:17,137 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-12 08:27:17,137 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 29493 s
2019-08-12 08:27:17,137 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-12 08:27:17,137 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-12 08:27:17,137 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 23200
2019-08-12 08:27:17,137 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 23200
2019-08-12 08:27:17,137 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 4
2019-08-12 08:27:17,137 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-12 08:27:17,137 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-12 08:27:17,137 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-12 08:27:17,137 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4443051947 has completed
2019-08-12 08:27:17,138 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-12 08:27:17,145 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /home/grid/slots/0/PanDA_Pilot-4443051947
2019-08-12 08:27:18,151 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [23200]
2019-08-12 08:27:18,151 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 23200
2019-08-12 08:27:18,151 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-12 08:27:19,156 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-12 08:27:19,156 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=23200
2019-08-12 08:27:19,210 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [23200] (in reverse order)
2019-08-12 08:27:19,253 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-12 08:27:19,254 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-12 08:27:19,254 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-12 08:27:19,254 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-12 08:27:19,764 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-12 08:27:29,362 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-12 08:27:29,809 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-12 08:27:29,809 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /home/grid/slots/0
2019-08-12 08:27:29,848 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (35618029568 B)
2019-08-12 08:27:29,848 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-12 08:27:29,849 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-12 08:27:29,865 | WARNING  | job_monitor         | pilot.util.common                | should_abort              | job:job_monitor:received graceful stop - abort after this iteration
2019-08-12 08:27:29,881 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-12 08:27:29,892 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-12 08:27:30,054 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-12 08:27:30,055 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-12 08:27:30,061 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-12 08:27:30,083 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 13 threads
2019-08-12 08:27:30,083 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140365372036864)>, <ExcThread(job, started 140365155763968)>, <ExcThread(job_monitor, started 140364623111936)>, <ExcThread(validate_post, started 140364597933824)>, <ExcThread(create_data_payload, started 140365130585856)>, <ExcThread(queue_monitor, started 140364606326528)>, <ExcThread(data, started 140365138978560)>, <ExcThread(copytool_out, started 140364631504640)>, <ExcThread(validate, started 140365147371264)>, <ExcThread(copytool_in, started 140364488894208)>, <ExcThread(queue_monitoring, started 140364589541120)>, <ExcThread(validate_pre, started 140364614719232)>, <ExcThread(execute_payloads, started 140364497286912)>]
2019-08-12 08:27:30,084 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-12 08:27:30,087 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-12 08:27:30,385 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 11 threads
2019-08-12 08:27:30,385 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140365372036864)>, <ExcThread(job, started 140365155763968)>, <ExcThread(job_monitor, started 140364623111936)>, <ExcThread(validate_post, started 140364597933824)>, <ExcThread(create_data_payload, started 140365130585856)>, <ExcThread(queue_monitor, started 140364606326528)>, <ExcThread(data, started 140365138978560)>, <ExcThread(copytool_out, started 140364631504640)>, <ExcThread(queue_monitoring, started 140364589541120)>, <ExcThread(validate_pre, started 140364614719232)>, <ExcThread(execute_payloads, started 140364497286912)>]
2019-08-12 08:27:30,580 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-12 08:27:30,687 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 10 threads
2019-08-12 08:27:30,687 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140365372036864)>, <ExcThread(job, started 140365155763968)>, <ExcThread(job_monitor, started 140364623111936)>, <ExcThread(validate_post, started 140364597933824)>, <ExcThread(create_data_payload, started 140365130585856)>, <ExcThread(queue_monitor, started 140364606326528)>, <ExcThread(data, started 140365138978560)>, <ExcThread(copytool_out, started 140364631504640)>, <ExcThread(queue_monitoring, started 140364589541120)>, <ExcThread(execute_payloads, started 140364497286912)>]
2019-08-12 08:27:30,718 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-12 08:27:30,836 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-12 08:27:30,836 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-12 08:27:30,881 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-12 08:27:30,888 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 7 threads
2019-08-12 08:27:30,889 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140365372036864)>, <ExcThread(job, started 140365155763968)>, <ExcThread(job_monitor, started 140364623111936)>, <ExcThread(create_data_payload, started 140365130585856)>, <ExcThread(queue_monitor, started 140364606326528)>, <ExcThread(queue_monitoring, started 140364589541120)>, <ExcThread(execute_payloads, started 140364497286912)>]
2019-08-12 08:27:31,003 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-12 08:27:31,090 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-12 08:27:31,090 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140365372036864)>, <ExcThread(job, started 140365155763968)>, <ExcThread(job_monitor, started 140364623111936)>, <ExcThread(queue_monitor, started 140364606326528)>, <ExcThread(queue_monitoring, started 140364589541120)>, <ExcThread(execute_payloads, started 140364497286912)>]
2019-08-12 08:27:31,175 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-12 08:27:31,175 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-12 08:27:31,191 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-12 08:27:31,191 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140365372036864)>, <ExcThread(job_monitor, started 140364623111936)>, <ExcThread(queue_monitor, started 140364606326528)>, <ExcThread(queue_monitoring, started 140364589541120)>, <ExcThread(execute_payloads, started 140364497286912)>]
2019-08-12 08:27:31,247 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-12 08:27:31,292 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-12 08:27:31,292 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140365372036864)>, <ExcThread(job_monitor, started 140364623111936)>, <ExcThread(queue_monitor, started 140364606326528)>, <ExcThread(queue_monitoring, started 140364589541120)>]
2019-08-12 08:27:31,604 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-12 08:27:31,604 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-12 08:27:31,614 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-12 08:27:31,695 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-12 08:27:31,695 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140365372036864)>, <ExcThread(job_monitor, started 140364623111936)>, <ExcThread(queue_monitoring, started 140364589541120)>]
2019-08-12 08:27:34,615 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-12 08:27:34,717 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-12 08:27:34,717 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140365372036864)>, <ExcThread(job_monitor, started 140364623111936)>]
2019-08-12 08:28:29,962 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 122 s)
2019-08-12 08:28:29,963 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-12 08:28:30,020 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-12 08:28:30,020 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-12 08:28:30,020 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-12 08:28:30 UTC [wrapper] ==== pilot stdout END ====
2019-08-12 08:28:30 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-12 08:28:30 UTC [wrapper] Pilot exit status: 0
2019-08-12 08:28:30 UTC [wrapper] STATUSCODE: 0
2019-08-12 08:28:30 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 12 08:15 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

2019-08-12 08:28:30 UTC [wrapper] Test setup, not cleaning
2019-08-12 08:28:30 UTC [wrapper] ==== wrapper stdout END ====
2019-08-12 08:28:30 UTC [wrapper] ==== wrapper stderr END ====
***************diag file************
runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=7976.67s
KernelTime=248.03s
UserTime=29367.53s
CPUUsage=371%
MaxResidentMemory=1944632kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=306847
MinorPageFaults=13946322
Swaps=0
ForcedSwitches=3465467
WaitSwitches=6049824
Inputs=74614384
Outputs=631144
SocketReceived=0
SocketSent=0
Signals=0

nodename=David_Cameron@dcameron04.cern.ch
exitcode=0
******************************WorkDir***********************
total 216056
drwxrwx--x. 7 grid grid      4096 Aug 12 10:28 .
drwxr-x--x. 3 grid grid        15 Aug  8 09:08 ..
-rw-------. 1 grid grid   7408939 Aug 12 08:15 agis_ddmendpoints.json
-rw-------. 1 grid grid   4506574 Aug 12 08:15 agis_schedconf.cvmfs.json
drwx------. 2 grid grid         6 Aug 12 08:15 .alrb
drwxr-xr-x. 3 grid grid        17 Aug 12 08:15 APPS
drwxr-xr-x. 2 grid grid         6 Aug 12 08:15 .arc
-rw-------. 1 grid grid       538 Aug 12 08:15 .asetup
-rw-------. 1 grid grid       826 Aug 12 08:16 .asetup.save
-rw-rw-r--. 1 grid grid         0 Aug 12 08:15 boinc_lockfile
-rw-rw-r--. 1 grid grid      8192 Aug 12 10:28 boinc_mmap_file
-rw-rw-r--. 1 grid grid       536 Aug 12 10:22 boinc_task_state.xml
-rw-rw-r--. 1 grid grid 207231732 Aug 12 08:15 EVNT.18605775._000373.pool.root.1
-rw-------. 1 grid grid     88048 Aug 12 10:27 heartbeat.json
-rw-rw-r--. 1 grid grid      5862 Aug 12 08:15 init_data.xml
-rw-rw-r--. 1 grid grid    262355 Aug 12 08:15 input.tar.gz
-rw-rw-r--. 1 grid grid       112 Aug 12 08:15 job.xml
-rw-------. 1 grid grid    490937 Aug 12 10:28 log.18722398._018941.job.log.1
-rw-------. 1 grid grid    831076 Aug 12 10:27 log.18722398._018941.job.log.tgz.1
-rw-------. 1 grid grid       516 Aug 12 10:28 O5iNDm0RzGvnShfckohDCDFpABFKDmABFKDmfz8YDmABFKDmUJ3FFm.diag
-rw-------. 1 grid grid       391 Aug 12 10:28 output.list
-rw-------. 1 grid grid      2957 Aug 11 11:36 pandaJobData.out
drwx------. 3 grid grid       174 Aug  7 13:02 pilot2
-rw-r--r--. 1 grid grid    253018 Aug 11 11:24 pilot2.tar.gz
-rw-------. 1 grid grid     11293 Aug 12 10:28 pilotlog.txt
-rw-r--r--. 1 grid grid      4468 Aug 11 11:35 queuedata.json
-rw-rw-r--. 1 grid grid       815 Aug 12 08:15 RTE.tar.gz
-rwxr-xr-x. 1 grid grid      8648 Aug 12 08:15 run_atlas
-rwx------. 1 grid grid     15232 Aug 11 11:36 runpilot2-wrapper.sh
-rw-rw-r--. 1 grid grid       692 Aug 12 10:28 runtime_log
-rw-rw-r--. 1 grid grid      6807 Aug 12 10:28 runtime_log.err
drwxrwx--x. 2 grid grid       131 Aug 12 10:28 shared
-rw-rw-r--. 1 grid grid      8688 Aug 12 08:15 start_atlas.sh
-rw-rw-r--. 1 grid grid     18849 Aug 12 10:28 stderr.txt
-rw-rw-r--. 1 grid grid       107 Aug 12 08:15 wrapper_26015_x86_64-pc-linux-gnu
-rw-rw-r--. 1 grid grid        27 Aug 12 10:28 wrapper_checkpoint.txt

running start_atlas return value is 0
Parent exit 0
child process exit 0
10:28:30 (16536): run_atlas exited; CPU time 29367.926603
10:28:30 (16536): called boinc_finish(0)

</stderr_txt>
]]>

©2024 CERN