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automated the internal cache dir location for singularity

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This commit is contained in:
Nicolas Vannieuwkerke 2022-05-20 09:48:19 +02:00
parent b2f7538b33
commit c2b26a734d
2 changed files with 8 additions and 7 deletions
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5
conf/vsc_ugent.config
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@ -32,6 +32,7 @@ profiles {
executor = 'slurm' executor = 'slurm'
queue = 'skitty' queue = 'skitty'
maxRetries = 2 maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER" scratch = "$VSC_SCRATCH_VO_USER"
} }
} }
@ -50,6 +51,7 @@ profiles {
executor = 'slurm' executor = 'slurm'
queue = 'swalot' queue = 'swalot'
maxRetries = 2 maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER" scratch = "$VSC_SCRATCH_VO_USER"
} }
} }
@ -68,6 +70,7 @@ profiles {
executor = 'slurm' executor = 'slurm'
queue = 'victini' queue = 'victini'
maxRetries = 2 maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER" scratch = "$VSC_SCRATCH_VO_USER"
} }
} }
@ -86,6 +89,7 @@ profiles {
executor = 'slurm' executor = 'slurm'
queue = 'kirlia' queue = 'kirlia'
maxRetries = 2 maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER" scratch = "$VSC_SCRATCH_VO_USER"
} }
} }
@ -104,6 +108,7 @@ profiles {
executor = 'slurm' executor = 'slurm'
queue = 'doduo' queue = 'doduo'
maxRetries = 2 maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER" scratch = "$VSC_SCRATCH_VO_USER"
} }
} }

10
docs/vsc_ugent.md
View file

@ -19,16 +19,12 @@ module load Nextflow
nextflow run <pipeline> -profile vsc_ugent,<CLUSTER> <Add your other parameters> nextflow run <pipeline> -profile vsc_ugent,<CLUSTER> <Add your other parameters>
``` ```
I also highly recommend specifying a location of a Singularity cache directory, by specifying the location with the `$SINGULARITY_CACHEDIR` bash environment variable in your `.bash_profile` or `.bashrc` or by adding it to your SLURM/PBS script. If this cache directory is not specified, the cache directory defaults to your `$HOME/.singularity` directory, which does not have a lot of disk space. I also highly recommend specifying a location of a Singularity cache directory, by specifying the location with the `$SINGULARITY_CACHEDIR` bash environment variable in your `.bash_profile` or `.bashrc` or by adding it to your PBS script. If this cache directory is not specified,
```shell
export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity
```
All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway. All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
The config contains a `cleanup` command that removes the `work/` directory automatically once the pipeline has completed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space. The default work directory is set to `$VSC_SCRATCH_VO_USER/work` per this configuration The config contains a `cleanup` command that removes the `work/` directory automatically once the pipeline has completed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space. The default work directory is set to `$VSC_SCRATCH_VO_USER/work` per this configuration
You can also add several TORQUE options to the PBS script. More about this on this [link](http://hpcugent.github.io/vsc_user_docs/pdf/intro-HPC-linux-gent.pdf#appendix.B). You can also add several TORQUE options to the SLURM/PBS script. More about this on this [link](http://hpcugent.github.io/vsc_user_docs/pdf/intro-HPC-linux-gent.pdf#appendix.B).
To submit your job to the cluster by using the following command: To submit your job to the cluster by using the following command:
@ -38,4 +34,4 @@ qsub <script name>.pbs
> **NB:** The profile only works for the clusters `skitty`, `swalot`, `victini`, `kirlia` and `doduo`. > **NB:** The profile only works for the clusters `skitty`, `swalot`, `victini`, `kirlia` and `doduo`.
> **NB:** The default directory where the `work/` and `singularity` (cache directory for images) is located in `$VSC_SCRATCH_VO_USER`. > **NB:** The default directory where the `work/` and `singularity/` (cache directory for images) is located in `$VSC_SCRATCH_VO_USER`.