https://github.com/cellgeni/bsubs
LSF Submission examples
https://github.com/cellgeni/bsubs
Last synced: 5 months ago
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LSF Submission examples
- Host: GitHub
- URL: https://github.com/cellgeni/bsubs
- Owner: cellgeni
- License: mit
- Created: 2024-08-29T09:31:54.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2024-09-12T00:51:39.000Z (almost 2 years ago)
- Last Synced: 2025-09-10T04:57:31.970Z (9 months ago)
- Language: Shell
- Homepage:
- Size: 5.86 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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`