Difference between revisions of "Job submission"
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Revision as of 11:51, 22 January 2021
Basic job submission
A basic BSUB job submission command consists of three parts:
| bsub | LSF options | job |
- The BSUB executable command
- LSF options requesting resources and defining job-related options
- A 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>
- Job type, e.g., Generic Job or MPI Job
- Job ID, e.g., 8146539
- The queue, e.g., normal.4h
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 |
| Scratch space | -R "rusage[scratch=10000]" |
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 ~]$
