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Ada:Batch Job Submission

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Job Submission: the bsub command

bsub < jobfile                  # Submits specified job for processing by LSF

Here is an illustration,

$ bsub < sample1.job
Verifying job submission parameters...
Job <224139> is submitted to default queue <devel>.

The first thing LSF does upon submission is to tag your job with a numeric identifier, a job id. Above, that identifier is 224139. You will need it in order to track or manage (kill or modify) your jobs. Next, note that the default current working directory for the job is the directory you submitted the job from. If that's not what you need, you must explicitly indicate that, as we do above when we cd into a specific directory. On job completion, LSF will place in the submission directory the file stdout1.224139. It contains a log of job events and other data directed to standard out. Always inspect this file for useful information.

By default, a job executes under the environment of the submitting process. This you can change by using the -L shell option (see below) and/or by specifying at the start of the job script the shell that will execute it. For example, if you want the job to execute under the C-shell, the first command above the #BSUB directives should be #!/bin/csh.


Job tracking and control commands

bjobs [-u all or user_name] [[-l] job_id]    # displays job information per user(s) or job_id, in summary or detail (-l) form, respectively.
bpeek [-f] job_id                            # displays the current contents of stdout and stderr output of an executing job.
bkill job_id                                 # kills, suspends, or resumes unfinished jobs. See man bkill for details.
bmod [bsub_options]   job_id                 # Modifies job submission options of a job. See man bmod for details.
lsload [node_name]                           # Lists on std out a node's utilization. Use bjobs -l jobid
                                             # to get the names of nodes associated with a jobid. See man lsload for details.

All of the above have decent man pages, if you're interested in more detail.

Examples

$ bjobs -u all
JOBID      STAT  USER             QUEUE      JOB_NAME             NEXEC_HOST SLOTS RUN_TIME        TIME_LEFT
223537     RUN   adinar           long       NOR_Q                1          20    400404 second(s) 8:46 L
223547     RUN   adinar           long       NOR_Q                1          20    399830 second(s) 8:56 L
223182     RUN   tengxj1025       long       pro_at16_lowc        10         280   325922 second(s) 5:27 L
229307     RUN   natalieg         long       LES_MORE             3          900   225972 second(s) 25:13 L
229309     RUN   tengxj1025       long       pro_atat_lowc        7          280   223276 second(s) 33:58 L
229310     RUN   tengxj1025       long       cg16_lowc            5          280   223228 second(s) 33:59 L
. . .             . . .     . . .

$ bjobs -l 229309

Job <229309>, Job Name <pro_atat_lowc>, User <tengxj1025>, Project <default>, M
                          ail <czjnbb@gmail.com>, Status <RUN>, Queue <long>, J
                          ob Priority <250000>, Command <## job name;#BSUB -J p
                          ro_atat_lowc; ## send stderr and stdout to the same f
                          ile ;#BSUB -o info.%J; ## login shell to avoid copyin
                          g env from login session;## also helps the module fun
                          ction work in batch jobs;#BSUB -L /bin/bash; ## 30 mi
                          nutes of walltime ([HH:]MM);#BSUB -W 96:00; ## numpro
                          cs;#BSUB -n 280; . . .
                          . . .

 RUNLIMIT
 5760.0 min of nxt1449
Tue Nov  4 21:34:43 2014: Started on 280 Hosts/Processors <nxt1449> <nxt1449> <
                          nxt1449> <nxt1449> <nxt1449> <nxt1449>  ...
                          . . .

Execution
                          CWD </scratch/user/tengxj1025/EXTD/pro_atat/lowc/md>;
Fri Nov  7 12:05:55 2014: Resource usage collected.
                          The CPU time used is 67536997 seconds.
                          MEM: 44.4 Gbytes;  SWAP: 0 Mbytes;  NTHREAD: 862

                          HOST: nxt1449
                          MEM: 3.2 Gbytes;  SWAP: 0 Mbytes; CPU_TIME: 9004415 s
                          econds . . .
                          . . .
                          . . .


$ bmod -W 46:00 229309            # resets wall-clock time to 46 hrs for job 229309



Node Utilization. It may happen that a job uses its allocated nodes inefficiently. Sometimes this is unavoidable, but many times it is very avoidable. It is unavoidable, for instance, if the amount of memory used per node is a large fraction of the total for that node, and only 1 cpu is used. In that case, cpu utilization will be at best at 5% (1/20) in a regular node. A handy tool, more practical than lsload, for tracking node utilization is the lnu homegrown command.

lnu [-h] [-l] -j jobid          # lists on stdout the utilization across all nodes for an executing job. See examples below.

Examples

$ lnu -l -j 795375
Job          User                 Queue        Status Node  Cpus
795375       jomber23             medium            R    4    80   
        HOST_NAME       status  r15s   r1m  r15m   ut    pg  ls    it   tmp   swp   mem    Assigned Cores
        nxt1417             ok  20.0  21.0  21.0  97%   0.0   0 94976  366M  3.7G 41.6G    20
        nxt1764 (L)         ok  19.7  20.0  20.0  95%   0.0   0 95040  366M  3.7G 41.5G    20
        nxt2111             ok  20.0  20.0  20.0  98%   0.0   0 91712  370M  4.2G 41.5G    20
        nxt2112             ok  20.0  21.1  21.0  97%   0.0   0 91712  370M  4.2G 41.6G    20
=========================================================================================================

$ lnu -l -j 753454
Job          User                 Queue        Status Node  Cpus
753454       ajochoa              long              R    1    20   
        HOST_NAME       status  r15s   r1m  r15m   ut    pg  ls    it   tmp   swp   mem    Assigned Cores
        nxt1222 (L)         ok   4.3   4.5   6.2  20%   0.0   0 54464  422M  4.7G 52.9G    20
=========================================================================================================

The utilization (ut) and memory paging (pg), overall, are probably the most significant. Note that the tmp, swp, and mem refer to available amounts respectively.