[phenixbb] Parallel Version of Phenix?
Ralf W. Grosse-Kunstleve
rwgk at cci.lbl.gov
Tue Jun 2 09:36:55 PDT 2009
> Are there parts of Phenix that can run on a Linux cluster in parallel.
Some wizards can take advantage of multiple CPUs:
Search for "parallel".
This doesn't speed up individual tasks, but rather tries the same
algorithms with different random seeds in parallel.
> I understand that a good part of Phenix is written in python, but there are
> certainly numerically intensive aspects of structure refinement that could
> be amenable to parallelization.
If you install from sources and you have gcc 4.3 or higher, the core
FFT in refinement will use multiple CPUs. However, there are many
other serial calculations. The speedup due to parallel FFTs is hardly
noticeable. refinement is notoriously difficult to parallelize.
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