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Mouse-Imaging-Centre / pydpiper

Python code for flexible pipeline control
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pydpiper 2.0.10 provides inappropriate memory specification to qbatch for SGE #350

Open gdevenyi opened 6 years ago

gdevenyi commented 6 years ago

Users of qbatch are required to format their memory specification according to how the queuing system accepts it, qbatch does no testing.

"GB" is not an accepted input format for SGE.

bcdarwin commented 6 years ago

Interesting ... that means qbatch actually isn't an abstraction over the queueing system. I guess I'll add some way to format memory specs to Pydpiper, then.

Sorry for the inconvenience ... the whole reason for the qbatch switch was that we moved from SGE to slurm (so don't have an SGE system for testing anymore).

gdevenyi commented 6 years ago

I can add it I guess. Pypy needs a new release anyways

gdevenyi commented 6 years ago

Time for Travis testing?

gdevenyi commented 6 years ago

Fun fact: PBS documentation doesn't mention capitalized memory submission options as being valid :)

gdevenyi commented 5 years ago

Helping someone get pydpiper working on their cluster and bitten by this again.

I have the interface idea listed at https://github.com/pipitone/qbatch/issues/145, contributions are welcome :)