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grid [2018/01/16 11:42]
popel [Rules] |
grid [2018/02/01 14:23]
popel [Advanced usage] |
| See ''man complex'' (run it on lrc or sol machines) for a list of possible resources you may require (in addition to ''mem_free'' etc. discussed above). | See ''man complex'' (run it on lrc or sol machines) for a list of possible resources you may require (in addition to ''mem_free'' etc. discussed above). |
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| ''qsub **-p** -100'' | ''qsub **-p** -99'' |
| Define a priority of your job as a number between -1024 and 0. Only SGE admins may use a number higher than 0. The default is 0, i.e. the highest possible priority. SGE uses the priority to decide when to start which pending job in the queue (it computes a real number called ''prior'', which is reported in ''qstat'', which grows as the job is waiting in the queue). Note that once a job is started, you cannot "unschedule" it, so from that moment on, it is irrelevant what was its priority. | Define a priority of your job as a number between -1024 and 0. Only SGE admins may use a number higher than 0. In January 2018, we changed the default to -100 (it used to be 0). SGE uses the priority to decide when to start which pending job in the queue (it computes a real number called ''prior'', which is reported in ''qstat'', which grows as the job is waiting in the queue). Note that once a job is started, you cannot "unschedule" it, so from that moment on, it is irrelevant what was its priority. You can ask for a higher priority (-99...0) if your job is urgent and/or will finish soon and you want to skip your colleagues' jobs in the queue. You should ask for lower priority (-1024..-101) if you submit many jobs at once or if the jobs are not urgent. |
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| ''qsub **-o** LOG.stdout **-e** LOG.stderr'' | ''qsub **-o** LOG.stdout **-e** LOG.stderr'' |
| * ''-tc j'' run at most j jobs simultaneously | * ''-tc j'' run at most j jobs simultaneously |
| * ''-hold_jid_ad comma_separated_job_list'' array jobs that must finish before this job starts; task //i// of the current job depends only on task //i// of the specified jobs | * ''-hold_jid_ad comma_separated_job_list'' array jobs that must finish before this job starts; task //i// of the current job depends only on task //i// of the specified jobs |
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| | === Delete many jobs at once === |
| | For deleting all your jobs use ''qdel \*''. For deleting array jobs (see above), you can use comma-separated ranges of task ids, e.g. ''qdel -t 1,10,50-100''. |
| | For deleting a range of (normal) job ids, you can use bash expansion (as an alternative to ''seq''), e.g. ''qdel {17979..18028}''. |
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| === Ssh to random sol === | === Ssh to random sol === |
| Ondřej Bojar suggests to add the following alias to your .bashrc (cf. [[#sshcwd]]): | Ondřej Bojar suggests to add the following alias to your .bashrc (cf. [[#sshcwd]]): |
| <code>alias cluster='comp=$(($RANDOM /4095 +1)); ssh -o "StrictHostKeyChecking no" sol$comp'</code> | <code>alias cluster='comp=$(($RANDOM /4095 +1)); ssh -o "StrictHostKeyChecking no" sol$comp'</code> |
| | |
| ===== Job monitoring ===== | ===== Job monitoring ===== |
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