Difference between revisions of "Job submission"
From ScientificComputing
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__NOTOC__ | __NOTOC__ | ||
| + | The three ways to access computing resources are | ||
| + | # [[Job_submission#Basic_job_submission|Submit a job through command line]] | ||
| + | # [[Job_submission#Job_script_and_#BSUB_pragmas|Submit a job through a job bash script using #BSUB pragmas]] | ||
| + | # [[Job_submission#Interactive_session_on_a_compute_node|Get an interactive session on a compute node]] | ||
| + | |||
== Basic job submission == | == Basic job submission == | ||
A basic BSUB job submission command consists of three parts: | A basic BSUB job submission command consists of three parts: | ||
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| style="width: 50px; background: #BFE5D9; text-align: center;"| bsub | | style="width: 50px; background: #BFE5D9; text-align: center;"| bsub | ||
| style="width: 100px; background: #B2D9EA;text-align: center; "| LSF options | | style="width: 100px; background: #B2D9EA;text-align: center; "| LSF options | ||
| − | | style="width: 50px; background: #FFBDAF; text-align: center"| job | + | | style="width: 50px; background: #FFBDAF; text-align: center"| Job |
| + | |} | ||
| + | |||
| + | where | ||
| + | {| style="color: black;" | ||
| + | |- | ||
| + | | style="width: 50px; background: #BFE5D9; text-align: center;"| bsub || is the LSF submit command. | ||
| + | |- | ||
| + | | style="width: 100px; background: #B2D9EA;text-align: center; "| LSF options || are for requesting resources and defining job-related options. | ||
| + | |- | ||
| + | | style="width: 50px; background: #FFBDAF; text-align: center"| Job || is a computing job to be submitted. | ||
|} | |} | ||
| − | |||
| − | |||
| − | |||
Here is an example: | Here is an example: | ||
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Generic job. | Generic job. | ||
Job <8146539> is submitted to queue <normal.4h> | Job <8146539> is submitted to queue <normal.4h> | ||
| − | # Job type, e.g., Generic Job or | + | The output includes |
| − | # | + | # Job type, e.g., Generic Job, MPI Job or Abaqus Job |
| − | # The queue, e.g., normal.4h | + | # Unique job ID, e.g., 8146539 |
| + | # The queue, e.g., normal.4h, normal.24h, or normal.120h | ||
| + | |||
| − | == | + | {|style="color: black;" |
| + | |- | ||
| + | | style="width: 150px; color: black;background: #FFBDAF; text-align: center"| '''Job''' | ||
| + | |} | ||
A job can be one of the following: | A job can be one of the following: | ||
{| class="wikitable" | style="background:white;" | {| class="wikitable" | style="background:white;" | ||
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|} | |} | ||
| − | == | + | |
| + | {|style="color: black;" | ||
| + | |- | ||
| + | | style="width: 150px; color: black;background: #B2D9EA; text-align: center"| '''LSF options''' | ||
| + | |} | ||
==== Requesting resources ==== | ==== Requesting resources ==== | ||
{| class="wikitable" | style="background:white;" | {| class="wikitable" | style="background:white;" | ||
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== Interactive session on a compute node == | == 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 | + | 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 | [jarunanp@eu-login-38 ~]$ bsub -n 4 -W 01:00 -Is bash | ||
Generic job. | Generic job. | ||
Revision as of 08:14, 4 February 2021
The three ways to access computing resources are
- Submit a job through command line
- Submit a job through a job bash script using #BSUB pragmas
- Get an interactive session on a compute node
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 job ID, e.g., 8146539
- The queue, e.g., normal.4h, normal.24h, or normal.120h
| 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 ~]$
