Difference between revisions of "Job submission"

Latest revision as of 13:06, 8 November 2021

The three ways to access computing resources are

1. Submit a job through command line
2. Submit a job through a job bash script using #BSUB pragmas
3. Get an interactive session on a compute node

Basic job submission

A basic BSUB job submission command consists of three parts:

where

Here is an example:

When the job is submitted, LSF shows job's information:

$ bsub -n 1 -W 4:00 -R "rusage[mem=4096]" "python myscript.py"
Generic job.
Job <8146539> is submitted to queue <normal.4h>

The output includes

1. Job type, e.g., Generic Job, MPI Job or Abaqus Job
2. Unique JobID, e.g., 8146539
3. The queue, e.g., normal.4h, normal.24h, or normal.120h

Note: The JobID is important for monitoring or reporting issues. It is also integrated in the name of the LSF output file. Please don't delete the LSF output file unless you are sure that the job was running fine.

A job can be one of the following:

Requesting resources

It is possible to combine memory and scratch requirements:

-R "rusage[mem=2048, scratch=10000]"

Note: Unlike memory, the batch system does not reserve any disk space for this scratch directory by default. If your job is expected to write large amounts of temporary data (say, more than 250 MB) into $TMPDIR — or anywhere in the local /scratch file system — you must request enough scratch space

Other LSF options

LSF submission line advisor can assist your to find LSF options you need.

Job script and #BSUB pragmas

Create a job script called job_script.bsub

#!/bin/bash
#BSUB -n 24                     # 24 cores
#BSUB -W 8:00                   # 8-hour run-time
#BSUB -R "rusage[mem=4000]"     # 4000 MB per core
#BSUB -J analysis1
#BSUB -o analysis1.out
#BSUB -e analysis1.err
#BSUB -N

source /cluster/apps/local/env2lmod.sh  # Switch to the new software stack
module load gcc/6.3.0 openmpi/4.0.2     # Load modules
cd /path/to/execution/folder            # Change directory
mpirun myprogram arg1                   # Execute the program

Submit a job

$ bsub < job_script.bsub

The options specified on the command line take precedence over the options in the job script.

$ bsub -n 36 < job_script.bsub

Interactive session on a compute node

To run a quick test or a benchmark, you can request an interactive session on a compute node by using the BSUB option

-I, -Ip or -Is

For example:

[jarunanp@eu-login-38 ~]$ bsub -n 4 -W 01:00 -Is bash
Generic job.
Job <161197292> is submitted to queue <normal.4h>.
<<Waiting for dispatch ...>>
<<Starting on eu-ms-001-15>>
[jarunanp@eu-ms-001-15 ~]$

Further reading

• User guide: Using the batch system
• Job arrays
• Job chaining
• X11 forwarding batch interactive jobs
• Multiple shareholder groups
• LSF mini reference

Helper

• LSF Submission Line Advisor