Job submission

The three ways to access computing resources are

Basic job submission

A basic BSUB job submission command consists of three parts:

bsub

LSF options

Job

where

bsub	is the LSF submit command.
LSF options	are for requesting resources and defining job-related options.
Job	is a computing job to be submitted.

Here is an example:

bsub

-n 1 -W 4:00 -R "rusage[mem=4096]"

"python myscript.py"

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

Job type, e.g., Generic Job, MPI Job or Abaqus Job
Unique JobID, e.g., 8146539
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.

Job

A job can be one of the following:

Job	Command	Examples of job submission command
a single Linux command	cmd
a program with its path	/path/to/myprogram	bsub ./bin/hello
a command or program with its arguments	cmd arg1 arg2	bsub echo hello
multiple commands	"cmd1 ; cmd2"	bsub "date; pwd; ls -l"
piped command	"cmd1 \| cmd2"
a command with I/O redirection, quote	"cmd<in >out"	bsub "du -sk /scratch > du.out"
a here document, passed via "<<"	<< EOF ... EOF
a shell script, passed via "<"	< script	bsub < hello.sh

LSF options

Requesting resources

Resources	Format	Default values
Maximum run time	-W HH:MM	04:00 (4 hours)
Number of processors	-n nprocs	1 processor
Memory	-R "rusage[mem=2048]"	1024 MB per core
Local scratch space	-R "rusage[scratch=10000]"	0 MB

Other LSF options

-o outfile	append job’s standard output to outfile
-e errfile	append job’s error messages to errfile
-R "rusage[...]"	advanced resource requirement (memory,...)
-J jobname	assign a jobname to the job
-w "depcond"	wait until dependency condition is satisfied
-Is	submit an interactive job with pseudo-terminal
-B /-N	send an email when the job begins/ends
-u user@domain	use this address instead of username@ethz.ch

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

module load gcc/6.3.0 openmpi/3.0.2
cd /path/to/execution/folder
mpirun myprogram arg1

Submit a job

$ bsub < 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 ~]$