[phenixbb] Parallel Version of Phenix?
jzhu at idi.harvard.edu
Tue Jun 2 10:17:11 PDT 2009
What about simulated annealing and phasing? I thought some of the
phasing modules are already parallelized in phenix.
On Jun 2, 2009, at 12:36 PM, Ralf W. Grosse-Kunstleve wrote:
>> Are there parts of Phenix that can run on a Linux cluster in
> 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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