Patch biowulf config #696
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Patch biowulf config #696
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added 2 commits
May 24, 2024 09:24
Add restriction to prevent over-threading. Modify the cache names for nxf_singularity to separate it from singularity cache. Add restriction to prevent user's mis-usage of clusterOption in params.
The executor contents are moved inside of profile, so that it could run individually without cross-talking.
jfy133
approved these changes
May 31, 2024
jfy133
reviewed
May 31, 2024
conf/biowulf.config
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| env { | ||
| SINGULARITY_CACHEDIR="/data/$USER/singularity" | ||
| SINGULARITY_CACHEDIR="/data/$USER/.singularity" |
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Just noticed this, shouldn't this be the same as the path above?
so that is is more clear to be able to reuse in profile
edmundmiller
previously requested changes
Jun 21, 2024
conf/biowulf.config
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| } | ||
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| env { | ||
| SINGULARITY_CACHEDIR="/data/$USER/singularity" | ||
| SINGULARITY_CACHEDIR="/data/$USER/.singularity" |
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Suggested change
| SINGULARITY_CACHEDIR="/data/$USER/.singularity" | |
| SINGULARITY_CACHEDIR="/data/$USER/nxf_singularity_cache" |
move clusterOptions and scratch out of executor, and move them into process.
delete spaces
When solving the conflicts from the recent update on config file from nf-core side, the cachedir is reset to older version. Have to modify it to match our cluster setting.
Deleted the out of date one
Remove the out of dated resourcelimits from params to process. Changed the igenome_base from /fdb/igenomes to /fdb/igenomes_nf.
the recent update of cluster hardware.
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There is bug in this setting, the time without .h will cause user's slurm job submitted with unlimited time, and the job will never got started since it excessed the wall time of slurm partition. Related commit: 32a6072#diff-96a1aad67f506874b7386e703c477b248b02e69624dbdaaa4ba7478d7b7d0f88
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qiyubio
dismissed
edmundmiller’s stale review
SINGULARITY_CACHEDIR in env has been removed, because it does not work as expected.
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name: Update the cluster config
about: patches
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