Hi, > Hi Bjoern, > > Is there anything else we (the Galaxy community) can do to help > sort out the ATLAS installation problems?
Thanks for asking. I have indeed a few things I would like some comments. > Another choice might be to use OpenBLAS instead of ATLAS, e.g. > http://stackoverflow.com/questions/11443302/compiling-numpy-with-openblas-integration I have no experience with it. Does it also need to turn off CPU throttling? I would assume so, or how is it optimizing itself? > However, I think we build NumPy without using ATLAS or any > BLAS library. That seems like the most pragmatic solution > in the short term - which I think is what Dan tried here: > http://testtoolshed.g2.bx.psu.edu/view/blankenberg/package_numpy_1_7 I can remove them if that is the consensus. A few points: - fixing the atlas issue can speed up numpy, scipy, R considerably (by 400% in some cases) - as far as I understand that performance gain is due to optimizing itself on specific hardware, for atlas there is no way around to disable CPU throttling (How about OpenBlas?) - it seems to be complicated to deactivate CPU throttling on OS-X - binary installation does not make sense in that case, because ATLAS is self optimizing - Distribution shipped ATLAS packages are not really faster Current state: - Atlas tries two different commands to deactivate CPU throttling. Afaik that only works on some Ubuntu versions, where no root privileges are necessary. - If atlas fails for some reason, numpy/R/scipy installation should not be affected (that's was at least the aim) Questions: - Is it worth the hassle for some speed improvements? pip install numpy, would be so easy? - If we want to support ATLAS, any better idea to how to implement it? Any Tool Shed feature that can help? -> interactive installation? - can we flag a tool dependency as optional? So it can fail? - Can anyone help with testing and fixing it? Any opinions/comments? Bjoern > Thanks, > > Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/