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EuracBiomedicalResearch / batch_centroid

Utility functions to perform batch centroiding of profile mzML files using MSnbase
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Performance tests #3

Open jorainer opened 6 years ago

jorainer commented 6 years ago

Testing the performance of the scripts in converting profile mzML to centroid mzML. This should be done: A) on my local computer B) on the cluster C) on the minicluster

The question is how many processes can we use in parallel before the I/O bottleneck hits.

jorainer commented 6 years ago

Results for my local (mac book, quad-core):

jorainer commented 6 years ago

I did run the tests on mccalc07 with the data (both the profile and centroided) on /scratch with 12 files:

CPU total run time [min] per file [min]
2 250 40
6 100 45
12 55 50

In addition I tested conversion of 24 files in parallel, which took also about 55 minutes and about 50 minutes per file. So, concluding, we can run 24 files in parallel without major I/O problems (as long as not somebody else is using the cluster with heavy I/O!).