[phenixbb] Parallel Version of Phenix?

Jianghai Zhu 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.

-- Jianghai

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  
>> parallel.
> Some wizards can take advantage of multiple CPUs:
>  http://phenix-online.org/documentation/running-wizards.htm
> 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.
> Ralf
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