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ccdmb / predector

Effector prediction pipeline based on protein properties.
Apache License 2.0
11 stars 7 forks source link

BUG: SignalP 6 too slow on Supercomputer. #49

Closed darcyabjones closed 3 years ago

darcyabjones commented 3 years ago

SignalP 6 works well enough on cloud instances and laptops etc, but it seems to take forever on Zeus. I suspect it has something to do with the network file-system.

See if we can do something about that. They also create a lot of files and plots we don't need without any way to turn it off. That will be killing performance, but shouldn't be as much as what I'm seeing. Should email them and ask for an option to disable per-protein plots etc.

darcyabjones commented 3 years ago

It looks like the OMP implementation creates some sort of Lock, which doesn't play nicely with external parallelisation. Reverted to OMP based threading with f9108b6 .