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update biohpc_gen config to reduce load on slurm DB #834

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merged 2 commits into from
Jan 27, 2025
Merged

update biohpc_gen config to reduce load on slurm DB #834

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update biohpc_gen config to reduce load on slurm DB
nschan Jan 27, 2025
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Merge branch 'master' into biohpc_gen
nschan Jan 27, 2025
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9 changes: 9 additions & 0 deletions conf/biohpc_gen.config
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Expand Up @@ -14,6 +14,15 @@ process {
executor = 'slurm'
queue = { task.memory <= 1536.GB ? (task.time > 2.d || task.memory > 384.GB ? 'biohpc_gen_production' : 'biohpc_gen_normal') : 'biohpc_gen_highmem' }
clusterOptions = '--clusters=biohpc_gen'
array = 25
}

executor {
$slurm {
queueStatInterval = '10 min'
pollInterval = '30 sec'
submitRateLimit = '25sec'
}
}

charliecloud {
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4 changes: 3 additions & 1 deletion docs/biohpc_gen.md
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Expand Up @@ -44,4 +44,6 @@ These are then available as modules (please confirm the module name using module
module load nextflow/24.04.2-gcc12 charliecloud/0.35-gcc12
```

> NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes.
> NB: bioHPC compute nodes are submit hosts. This means you can submit the nextflow head job via sbatch.

> NB: Sometimes you may want to have jobs submitted 'locally' in a large nextflow job. Details on this can be found here https://doku.lrz.de/nextflow-on-hpc-systems-test-operation-788693597.html
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