How to submit Jobs to ERISOne?

When submitting jobs on the ERISOne cluster, all jobs should be submitted through the LSF scheduler. This How-To will explain how to submit your job to the various queues of the scheduler.

Submitting A Job

To submit a job to a queue, use the bsub command. In this command, the LSF script and queue will also be specified.

For example, there is a test LSF script within the lsf folder of the hold folder. It we wanted to submit that script to the short queue we would type the command:

 bsub -q short < test.lsf

The -q indicator allows you to specify which queue you would like to send your job to. To learn more about the various queues, go to the Queue Selection section below.

Never forget to use the character "<" between bsub and your script file name in your command line.

To make sure that your job was successfully submitted, use the bjobs command. This command lists all current job. When using the bjobs command after submitting the test.lsf job above, you should get an output similar to this:

$ bjobs

JOBID   USER    STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME

600305  bmm78   PEND  short      eris1n3                 test       Jun  5 10:10

 

LSF Commands

Command Description 
bjobs List the current jobs, use option "-lp" to see the pending reasons
bhosts List the host and current workloads
lshosts List the host and their static resource information 
bhist Displays historical information about jobs
bpeek Displays the stdout and stderr output for an unfinished job
bqueues List information about the queues
brequeue Kills and requeue a job
bresume Resume a suspended job
bkill Kills a job

Queue Selection

The job schedule offers several job queues to which you can submit jobs. Each queue is optimized for different types of jobs, based on several attributes:

  • Run Time
  • Memory Requirement
  • Number of CPUs Used in Parallel

Available Queues

Queue Default Mem Max Mem Min Runtime Max Runtime CPU
VSHORT 1 GB 4 GB - 15 min 1
SHORT 2 GB 4 GB 10 s 1 h 1
MEDIUM 2 GB 8 GB 1 min 24 hr  < 4
NORMAL 2 GB 8 GB 1 min 3 days < 6
LONG 2 GB 8 GB 1 min 1 week < 4
VLONG 2 GB 8 GB 1 min  4 weeks  < 4 
BIG 8 GB 498 GB 1 min  4 weeks  < 6
BIG-MULTI 8 GB 498 GB 1 min 4 weeks 4 - 12

Templates

Within your home folder, there are several LSF templates that you can base your script on. To reach this folder navigate to the following folder:

cd ~/lsf/templates/bsub/

When you list the contents of the bsub directory, you will see a set of examples for all the different queues.

           

User the cat or more command to see the contents of the files:

cat example_short_3GB.lsf

To use one of the templates, make a copy of the file for your own modifications.   

 

 


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