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ewels / clusterflow

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
https://ewels.github.io/clusterflow/
GNU General Public License v3.0
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Remove SGE vf memory option #26

Closed ewels closed 9 years ago

ewels commented 9 years ago

Remove the option to use vf for memory assignment. Always use h_vmem instead.

@stu2 - is this going to mess up your work flow at all, or is this ok?

s-andrews commented 9 years ago

In a normal grid engine setup vf doesn't really do anything. It's not enforced by the shepherd and it's not used by the scheduler. If we use h_vmem then at least it's enforced even if it's not used by the scheduler without some additional configuration.

ewels commented 9 years ago

Ok - so it shouldn't do any damage to use h_vmem for everything?

s-andrews commented 9 years ago

That was my take on it, hence removing the option rather than just modifying our default.

ewels commented 9 years ago

Great. I'll remove everything to do with vf or h_vmem and just hardwire these into the grid engine job submission commands then.

ewels commented 9 years ago

Handled in https://github.com/ewels/clusterflow/pull/27