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biocommons / biocommons.seqrepo

non-redundant, compressed, journalled, file-based storage for biological sequences
Apache License 2.0
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112 make fastadir thread safe #118

Closed reece closed 10 months ago

reece commented 1 year ago

@theferrit32 @davmlaw @andreasprlic @ahwagner @jsstevenson

Before merging a fix for #112, I want to make sure that we can reproduce it and understand it.

In my opinion, the problem is not related to threading (as surmised in the original problem report), but is more directly attributable to file descriptor exhaustion and the difficulty in handling that gracefully. See misc/threading-tests/README.md in this PR for some demonstration cases.

My current inclination is to disable caching since that's the safest mode, and then work on reincorporating caching in a subsequent PR.

github-actions[bot] commented 11 months ago

This PR is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.

ahwagner commented 11 months ago

@reece, what is the status of this PR? Are you waiting for action from @theferrit32 here?