SGE version 6.08
On 08-Apr-13 23:52, Reuti wrote:
Please keep the list posted.
Am 08.04.2013 um 21:06 schrieb Ehud Barnea:
These 2 lines are there twice probably because of a mistake on my
behalf. I copied them incorrectly (they are just after the first
"page", when redirecting the output of the command to a txt file and
opening it with nano).
The jobs were created by themselves. The output I gave is of 3 jobs
that I did not create. The 3rd one was created right after the first
2 finished (and it was created along with another 30 jobs).
The job IDs were increased one by one, as they usually do when
submitting jobs. Job IDs did not appear twice.
The only commands I ran were
qsub (several times)
qalter (no wrapper, just qalter -q <job id>)
`qresub` is a symbolic link to `qalter`. If you can reproduce this, it
seems to be a wrong interpretation of the intended change of
attributes by `qalter`. Which version of SGE are you using in detail?
But: if the job is resubmitted by accident, then there is no
"version:" showing up at all, as it wasn't modified.
-- Reuti
PS: The "/fastspace/users/barneaeh/Dropbox/SGE/srv/6/evaluat$" is
edited, or does it really end in a "$"?
On Mon, Apr 8, 2013 at 6:22 PM, Reuti <[email protected]
<mailto:[email protected]>> wrote:
Hi,
Am 08.04.2013 um 15:11 schrieb Ehud Barnea:
> Thanks for looking at it. I wasn't sure whether to submit to
the users group or just you.
> Anyway, the I ran the same thing again and the problem occurred
again.
> The job that I moved (with qalter) finished quickly so I
couldn't check it's version, but when it finished it spawned
another 3 new jobs (with new job ids and all of them with version 1).
> After these 3 finished another 30 jobs were spawned (also with
a different job id and all with version 1).
Was the job number increased directly from the original job id
and you ended up in having the same job id twice in the system,
or were new ones created after any later submitted job? Any
`qalter`-wrapper in the way? You edited the output below, or is:
> stderr_path_list: logs
> mail_list: barneaeh@sge01
> stderr_path_list: logs
> mail_list: barneaeh@sge01
really there twice?
-- Reuti
> After doing qalter the only commands I ran were qstat, also at
first I created 5 job arrays and only did qalter on 1 of them, so
I am certain that I did not accidentally created all these jobs.
>
> I supply here the output of qstat -j. The first 2 belong to the
first batch of 3 jobs and the last one is of one of the 30 jobs
the spawned later:
> (it probably doesn't matter, but it sits on a Dropbox folder,
but dropbox isn't active, so it's just a normal folder)
>
> ==============================================================
> job_number: 8698176
> exec_file: job_scripts/8698176
> submission_time: Mon Apr 8 15:55:10 2013
> owner: barneaeh
> uid: 52647
> group: obs
> gid: 1009
> sge_o_home: /storage/users/barneaeh
> sge_o_log_name: barneaeh
> sge_o_path: /fastspace/users/barneaeh/PCL-1.6.0/bin:/fastspace/$
> sge_o_shell: /bin/tcsh
> sge_o_workdir:
/fastspace/users/barneaeh/Dropbox/SGE/srv/6/evaluat$
> sge_o_host: sge01
> account: sge
> cwd: /fastspace/users/barneaeh/Dropbox/SGE/srv/6/evaluat$
> path_aliases: /tmp_mnt/ * * /
> stderr_path_list: logs
> mail_list: barneaeh@sge01
> stderr_path_list: logs
> mail_list: barneaeh@sge01
> notify: FALSE
> job_name: run.sh
> stdout_path_list: logs
> jobshare: 0
> hard_queue_list: intel_all.q
> shell_list: /bin/sh
> env_list:
> script_file: run.sh
> version: 1
> job-array tasks: 1-246:1
> ==============================================================
> job_number: 8698175
> exec_file: job_scripts/8698175
> submission_time: Mon Apr 8 15:55:10 2013
> owner: barneaeh
> uid: 52647
> group: obs
> gid: 1009
> sge_o_home: /storage/users/barneaeh
> sge_o_log_name: barneaeh
> sge_o_path: /fastspace/users/barneaeh/PCL-1.6.0/bin:/fastspace/$
> sge_o_shell: /bin/tcsh
> sge_o_workdir:
/fastspace/users/barneaeh/Dropbox/SGE/srv/6/evaluat$
> sge_o_host: sge01
> account: sge
> cwd: /fastspace/users/barneaeh/Dropbox/SGE/srv/6/evaluat$
> path_aliases: /tmp_mnt/ * * /
> stderr_path_list: logs
> mail_list: barneaeh@sge01
> stderr_path_list: logs
> mail_list: barneaeh@sge01
> notify: FALSE
> job_name: run.sh
> stdout_path_list: logs
> jobshare: 0
> hard_queue_list: intel_all.q
> shell_list: /bin/sh
> env_list:
> script_file: run.sh
> version: 1
> job-array tasks: 1-246:1
> ==============================================================
> job_number: 8698182
> exec_file: job_scripts/8698182
> submission_time: Mon Apr 8 16:00:28 2013
> owner: barneaeh
> uid: 52647
> group: obs
> gid: 1009
> sge_o_home: /storage/users/barneaeh
> sge_o_log_name: barneaeh
> sge_o_path: /fastspace/users/barneaeh/PCL-1.6.0/bin:/fastspace/$
> sge_o_shell: /bin/tcsh
> sge_o_workdir:
/fastspace/users/barneaeh/Dropbox/SGE/srv/6/evaluat$
> sge_o_host: sge01
> account: sge
> cwd: /fastspace/users/barneaeh/Dropbox/SGE/srv/6/evaluat$
> path_aliases: /tmp_mnt/ * * /
> stderr_path_list: logs
> mail_list: barneaeh@sge01
> stderr_path_list: logs
> mail_list: barneaeh@sge01
> notify: FALSE
> job_name: run.sh
> stdout_path_list: logs
> jobshare: 0
> hard_queue_list: intel_all.q
> shell_list: /bin/sh
> env_list:
> script_file: run.sh
> version: 1
> job-array tasks: 1-246:1
>
>
> On Mon, Apr 8, 2013 at 3:43 PM, Reuti
<[email protected] <mailto:[email protected]>>
wrote:
> Am 08.04.2013 um 10:21 schrieb Semi:
>
> > Any ideas about user's question?
> >
> > I am working with job arrays and encountered something weird.
At first a sent several job arrays to obs.q. Then I took one of
the job arrays (that didn't start executing any task) and sent it
to intel_all.q (using qalter).
> > After that the specific tasks started running, however, the
same jobArray was duplicated about 20-30 times. Now qstat shows me:
> > 8698022 0.50500 run.sh barneaeh qw 04/08/2013
10:25:23 1 1-245:1
> > 8698023 0.50500 run.sh barneaeh qw 04/08/2013
10:25:23 1 1-245:1
> > 8698024 0.50500 run.sh barneaeh qw 04/08/2013
10:25:23 1 1-245:1
> > 8698025 0.50500 run.sh barneaeh qw 04/08/2013
10:25:23 1 1-245:1
> > 8698026 0.50500 run.sh barneaeh qw 04/08/2013
10:25:23 1 1-245:1
> > 8698027 0.50500 run.sh barneaeh qw 04/08/2013
10:25:23 1 1-245:1
> > 8698028 0.50500 run.sh barneaeh qw 04/08/2013
10:25:24 1 1-245:1
> > 8698030 0.50500 run.sh barneaeh qw 04/08/2013
10:25:27 1 1-245:1
> > 8698031 0.50500 run.sh barneaeh qw 04/08/2013
10:25:27 1 1-245:1
> > 8698032 0.50500 run.sh barneaeh qw 04/08/2013
10:25:27 1 1-245:1
>
> `qalter` doesn't change the submission time (only increasing
the value of "version:" in `qstat -j <job_id>`). But above they
have different submission times. Was this the time `qalter` was
issued?
>
> All have a value of "version: 1" in `qstat -j <job_id>`?
>
> -- Reuti
>
>
> > This jobArray was the only one with 245, so I am sure it was
duplicated...
> > Now it seems that the job array is run again and again.
> >
> > _______________________________________________
> > users mailing list
> > [email protected] <mailto:[email protected]>
> > https://gridengine.org/mailman/listinfo/users
>
>
_______________________________________________
users mailing list
[email protected]
https://gridengine.org/mailman/listinfo/users
