Closed muffato closed 6 months ago
We've been regularly hit issues in production: no more space in /var/tmp and then farm nodes closed.
/var/tmp
The problems come from the sort commands leaving files in their /tmp.
sort
/tmp
First, the biocontainer isn't mounting /tmp properly and instead uses /var/tmp, which only has 40 GB. Our workaround is to explicitly mount /tmp.
The second issue comes from LSF killing the sort commands because of MEMLIMIT.
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Description of the bug
We've been regularly hit issues in production: no more space in
/var/tmpand then farm nodes closed.The problems come from the
sortcommands leaving files in their/tmp.First, the biocontainer isn't mounting
/tmpproperly and instead uses/var/tmp, which only has 40 GB. Our workaround is to explicitly mount/tmp.The second issue comes from LSF killing the
sortcommands because of MEMLIMIT.Command used and terminal output
No response
Relevant files
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System information
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