Am 14.01.2014 um 18:27 schrieb Ian Johnson: > Reuti, > > There's no file staging installed. The job script is being copied to the > execution host.
Correct (for the job script itself). > The output file *is* being opened in ~smartmate but it is of zero length. I would assume that they is not created at all in this location, only on the nodes. Or do you mean the home directory on the nodes? NB: In Torque there is a file staging for the .o/.e files, but not in SGE. -- Reuti > Thanks, > > Ian > > On Tue, 14 Jan 2014 17:18:06 -0000, Reuti <[email protected]> wrote: > >> Am 14.01.2014 um 18:04 schrieb Ian Johnson: >> >>> Reuti, >>> >>> There is no output from the script at all in the ~smartmate/job.sh.o[0-9]+ >>> files. The home directory of the smartmate user is local disk. However, >>> grid engine is installed on an NFS share. >> >> Do you have any file staging installed? Otherwise the output will not be >> send to the real home directory of the user. Also the input files could be >> missing on the execution host. >> >> -- Reuti >> >> >> >>> Is there other information you require? Is there any way to get the >>> function call that is failing in shepherd, e.g. more verbose tracing? >>> >>> Thanks, >>> >>> Ian >>> >>> On Tue, 14 Jan 2014 15:19:34 -0000, Reuti <[email protected]> >>> wrote: >>> >>>> Hi, >>>> >>>> Am 14.01.2014 um 15:19 schrieb Ian Johnson: >>>> >>>>> I have a simple job, which echoes `date` to stdout, that I'm using to >>>>> test an Open Grid Engine installation. Running qsub as root the job is >>>>> run successfully. However, using another non-superuser, in this case >>>>> smartmate user, the output from qacct -j says that the job has exited >>>>> with exit status 11. The shepherd trace confirms this (see below). >>>> >>>> Do you have any output? 11 means "Resource temporarily unavailable", which >>>> could mean it can't write to the (mounted?) home directory of the user. >>>> How is it mount configured? >>>> >>>> AFAICS the user is known, as otherwise you would face a different error. >>>> >>>> -- Reuti >>>> >>>> >>>>> Would anyone have an idea as to what is going on? Thank you. >>>>> >>>>> <shepherd_trace> >>>>> 01/14/2014 14:08:56 [0:2723]: shepherd called with uid = 0, euid = 0 >>>>> 01/14/2014 14:08:56 [0:2723]: starting up 2011.11 >>>>> 01/14/2014 14:08:56 [0:2723]: setpgid(2723, 2723) returned 0 >>>>> 01/14/2014 14:08:56 [0:2723]: do_core_binding: "binding" parameter not >>>>> found in config file >>>>> 01/14/2014 14:08:56 [0:2723]: no prolog script to start >>>>> 01/14/2014 14:08:56 [0:2723]: parent: forked "job" with pid 2724 >>>>> 01/14/2014 14:08:56 [0:2724]: child: starting son(job, >>>>> /opt/capitati/ge2011.11/smartmate/spool/exec-1/job_scripts/32, 0); >>>>> 01/14/2014 14:08:56 [0:2724]: pid=2724 pgrp=2724 sid=2724 old pgrp=2723 >>>>> getlogin()=root >>>>> 01/14/2014 14:08:56 [0:2723]: parent: job-pid: 2724 >>>>> 01/14/2014 14:08:56 [0:2724]: reading passwd information for user >>>>> 'smartmate' >>>>> 01/14/2014 14:08:56 [0:2724]: setosjobid: uid = 0, euid = 0 >>>>> 01/14/2014 14:08:56 [0:2724]: setting limits >>>>> 01/14/2014 14:08:56 [0:2724]: RLIMIT_CPU setting: (soft >>>>> 18446744073709551615(INFINITY), hard 18446744073709551615(INFINITY)) >>>>> resulting: (soft 18446744073709551615(INFINITY), hard >>>>> 18446744073709551615(INFINITY)) >>>>> 01/14/2014 14:08:56 [0:2724]: RLIMIT_FSIZE setting: (soft >>>>> 18446744073709551615(INFINITY), hard 18446744073709551615(INFINITY)) >>>>> resulting: (soft 18446744073709551615(INFINITY), hard >>>>> 18446744073709551615(INFINITY)) >>>>> 01/14/2014 14:08:56 [0:2724]: RLIMIT_DATA setting: (soft >>>>> 18446744073709551615(INFINITY), hard 18446744073709551615(INFINITY)) >>>>> resulting: (soft 18446744073709551615(INFINITY), hard >>>>> 18446744073709551615(INFINITY)) >>>>> 01/14/2014 14:08:56 [0:2724]: RLIMIT_STACK setting: (soft >>>>> 18446744073709551615(INFINITY), hard 18446744073709551615(INFINITY)) >>>>> resulting: (soft 18446744073709551615(INFINITY), hard >>>>> 18446744073709551615(INFINITY)) >>>>> 01/14/2014 14:08:56 [0:2724]: RLIMIT_CORE setting: (soft >>>>> 18446744073709551615(INFINITY), hard 18446744073709551615(INFINITY)) >>>>> resulting: (soft 18446744073709551615(INFINITY), hard >>>>> 18446744073709551615(INFINITY)) >>>>> 01/14/2014 14:08:56 [0:2724]: RLIMIT_VMEM/RLIMIT_AS setting: (soft >>>>> 18446744073709551615(INFINITY), hard 18446744073709551615(INFINITY)) >>>>> resulting: (soft 18446744073709551615(INFINITY), hard >>>>> 18446744073709551615(INFINITY)) >>>>> 01/14/2014 14:08:56 [0:2724]: RLIMIT_RSS setting: (soft >>>>> 18446744073709551615(INFINITY), hard 18446744073709551615(INFINITY)) >>>>> resulting: (soft 18446744073709551615(INFINITY), hard >>>>> 18446744073709551615(INFINITY)) >>>>> 01/14/2014 14:08:56 [0:2724]: setting environment >>>>> 01/14/2014 14:08:56 [0:2724]: Initializing error file >>>>> 01/14/2014 14:08:56 [0:2724]: switching to intermediate/target user >>>>> 01/14/2014 14:08:56 [0:2723]: wait3 returned 2724 (status: 2816; >>>>> WIFSIGNALED: 0, WIFEXITED: 1, WEXITSTATUS: 11) >>>>> 01/14/2014 14:08:56 [0:2723]: job exited with exit status 11 >>>>> 01/14/2014 14:08:56 [0:2723]: reaped "job" with pid 2724 >>>>> 01/14/2014 14:08:56 [0:2723]: job exited not due to signal >>>>> 01/14/2014 14:08:56 [0:2723]: job exited with status 11 >>>>> 01/14/2014 14:08:56 [0:2723]: now sending signal KILL to pid -2724 >>>>> 01/14/2014 14:08:56 [0:2723]: writing usage file to "usage" >>>>> 01/14/2014 14:08:56 [0:2723]: no tasker to notify >>>>> 01/14/2014 14:08:56 [0:2723]: no epilog script to start >>>>> </shepherd_trace> >>>>> >>>>> <job_script> >>>>> #!/bin/bash >>>>> # >>>>> #$ -j y >>>>> # >>>>> #$ -S /bin/bash >>>>> >>>>> echo "Hello World" >>>>> echo `date` >>>>> </job_script> >>>>> >>>>> Ian Johnson >>>>> Software Engineer >>>>> >>>>> >>>>> Capita Translation and Interpreting >>>>> Riverside Court, Huddersfield Road, Delph, Oldham, OL3 5FZ | Tel (UK): >>>>> +44 845 367 7000 | Tel (US): +1 (800) 579-5010 >>>>> | [email protected] | Skype ID: ian.johnson_als >>>>> www.capitatranslationinterpreting.com >>>>> _______________________________________________ >>>>> users mailing list >>>>> [email protected] >>>>> https://gridengine.org/mailman/listinfo/users >>>> >>> >>> >>> -- >>> Kind regards, >>> >>> Ian Johnson >>> Software Engineer >>> >>> Capita Translation and Interpreting >>> Riverside Court, Huddersfield Road, Delph, Oldham, OL3 5FZ | Tel (UK): +44 >>> 845 367 7000 | Tel (US): +1 (800) 579-5010 >>> | [email protected] | Skype ID: ian.johnson_als >>> www.capitatranslationinterpreting.com >> > > > -- > Kind regards, > > Ian Johnson > Software Engineer > > Capita Translation and Interpreting > Riverside Court, Huddersfield Road, Delph, Oldham, OL3 5FZ | Tel (UK): +44 > 845 367 7000 | Tel (US): +1 (800) 579-5010 > | [email protected] | Skype ID: ian.johnson_als > www.capitatranslationinterpreting.com _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
