Example LSF script submissions

LSF (Load Sharing Facility) at Sanger Institute. LSF is the workload management platform, job scheduler, for distributed high performance computing owned by IBM used by the Sanger Institute. The software coordinates the execution of multiple jobs on the FARM. Its primary function is to efficiently allocate available resources to incoming jobs based on various scheduling policies.

How to submit?

All scripts are bash scripts with #BSUB notation. To submit them as jobs use the following command:

bsub < myjob.lsf

Converting to bsub inline command

Just copy the options for #BSUB tags from the file to an inline command.

For example:

#!/bin/bash
#BSUB -q normal                                     # name of the queue gpu-lotfollahi
#BSUB -M 8G                                         # 8G RAM memory
#BSUB -R "select[mem>8G] rusage[mem=8G]"            # same as above
#BSUB -o logs/%J.out                                # output file
#BSUB -e logs/%J.err                                # error file
#BSUB -n 4                                          # number of cores in total

[code here]

Turns to

bsub -q normal \
    -M 8G -R "select[mem>8G] rusage[mem=8G]" \
    -o logs/%J.out \
    -e logs/%J.err \
    -n 4 \
    /path/to/your/script.sh

Where [code here] is placed inside /path/to/your/script.sh