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
On 14 January 2014 18:34, Reuti <[email protected]> wrote:
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
