LSF user guide for CFN (chead) users
Table of contents
LSF vs SGE
The CFN cluster used an implementation of the (deprecated) Sun Grid Engine (SGE). The LPC uses IBM’s Load Sharing Facility (LSF) system.
There is a general guide to the LSF for SGE users here: SGE to LSF Conversion.
CFN cluster specifics
| SGE | LSF | Notes |
|---|---|---|
| qstat | bqueues | List available queues |
| qrun | bsub | Submit jobs |
| qstat | bjobinfo | get job info |
Generic job submission script
#!/bin/bash
#BSUB -J my_test_job # LSF job name
#BSUB -o my_test_job.%J.out # Name of the job output file
#BSUB -e my_test_job.%J.error # Name of the job error file
# if you want to receive e-mail notifications on a non-default address
#BSUB -u holder@upenn.edu # *** make sure to set this to your email address
### -- send notification at start --
#BSUB -B
### -- send notification at completion --
#BSUB -N
echo "this is a test"
sleep 15
Run and check with bsub and bjobs
[holder@scisub ~]$ bsub /home/holder/test.sh
Job <9375077> is submitted to queue <bsc_normal>.
[holder@scisub ~]$ bjobs 9375077
JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME
9375077 holder RUN bsc_normal scisub bsc04 *r/test.sh Jun 29 16:03
[holder@scisub ~]$ bjobs 9375077
JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME
9375077 holder RUN bsc_normal scisub bsc04 *r/test.sh Jun 29 16:03
[holder@scisub ~]$ bjobs 9375077
JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME
9375077 holder DONE bsc_normal scisub bsc04 *r/test.sh Jun 29 16:03
when the job is complete, email is sent to holder@upenn.edu.
Had the job been submitted with:
bsub < test.sh
output files would be created and the email would not includ any output.
Supressing completion emails
General cluster organizational differences
The grid computing system