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Can you share your conclusions in the MDA issue MDAnalysis/mdanalysis#2975 for discussion so that other interested parties can also comment?
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I can confirm it should be an
OpenBlas
issue. Fornumpy
built withmkl
, the default num_of_thread will be 6 (the physical core number), so the oversubscribing won't be happening.The problem now is,
OpenBlas
always uses all hyperthreading in default, which the numerical code doesn't seem to benefit from (?), and also tend to cause the troubles mentioned above. I guess we should limit threads to the number of physical cores for all theMDAnalysis
code...beforeOpenBlas
changes its default.