Quick reference guide Linux

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12. Batch processing

While many batch systems do exist today, only two popular batch systems are described, the commercial LSF and SGE that has been released to the public.

bjobs [-lwadpsr] [-m host] [-u user] [-q queue] [jobID] L
Display status info about LSF batch jobs for users, queues and jobIDs.  
bkill [-l] [-s signal] [-m host] [-q queue] [-J jobname] [jobID] L
Send signal (name or number) to LSF batch jobs on host, in queue or who are identified by jobname or jobID.  
bpeek [-f] [-m host | -q queue | -J jobname | jobID L
Display STDOUT and STDERR of most recently submitted LSF job on host, in queue or which is identified by jobname or jobID.  
bqueues [-lw] [-m host] [-u user] [queue[s] L
Display information about LSF batch queue[s] (in long format with -l).  
bsub [options] [executable [argument[s]]] Lf
Submit a LSF batch request contained in executable. Some useful options:
-I submit an interactive job
-L shell Execute the job in the shell environment
-N notify the submitter by mail at the end of the job
-q queue execute job in queue
-e file send STDERR of job to file
-i file read STDIN of job from file (default from /dev/null)
-o file send STDOUT of job to file instead of sending it by mail
There is also a GUI xbsub to submit a job to LSF. See also the man pages and reference manuals.
 
lsinfo [-lrmt] [resource[s]] L
Display information about the LSF batch system configuration (in long format with -l).  
qdel [-f] job_id_list P
Delete or signal SGE batch system request(s) (with -f also running jobs).  
qhost [-q] [-j] [-F] [-h hosts] [-u user] [-help] P
Show the status of SGE hosts, queues with -q, jobs with -j, resources with -F (optionally only for user).  
qstat [-f] [-q queue] [-u user] P
Display status of SGE batch system requests and queues. Restrict output to queues or users, use full format with -f.  
qsub [options] [scriptfile] [script_arguments] Pf
Submit an SGE batch request contained in scriptfile. Some useful options:
-cwd execute the job from the current working directory
-help print a listing of all options
-j y merge STDERR into STDOUT of the job (default is -j n, no merge)
-m e send mail at the end of the job
-q queue execute job in queue
-v print job information, but do not execute the job
-e file send STDERR of job to file instead of jobname.ejobid
-o file send STDOUT of job to file instead of jobname.ojobid
-hard resource requirements following are regarded hard requirements
-soft resource requirements following are regarded soft requirements
-l resource=value resource requirements definition
See also the man pages and reference manuals.
 
xlsadmin L
GUI to administer the LSF batch system. Users without admin privileges can view the LSF status and configurations.  
xlsbatch L
GUI to monitor jobs and other aspects of the LSF batch system.  

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