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MikeAxtell / ShortStack

ShortStack: Comprehensive annotation and quantification of small RNA genes
MIT License
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maple slow on some clusters ... data look-up speed matters #14

Closed MikeAxtell closed 9 years ago

MikeAxtell commented 9 years ago

Correspondence with user found that the same run can take more than a week on a cluster, just takes a few hours on a laptop. Likely because the speed at which certain cluster configurations can read and write to the users working space can be slow. Users should be advised in future FAQ that, for most jobs, running on a cluster is not necessary and can in some cases really slow things down.

MikeAxtell commented 9 years ago

Performance of 3.0 still needs testing on HPC clusters to see if this has been solved.

MikeAxtell commented 9 years ago

Per our testing at least on Penn State's HPC compute clusters, we don't see this issue with 3.0, 3.1, or 3.2 (at present 3.2 is latest release), so I am closing this issue.