[phenixbb] Parallel Version of Phenix?
Randy J. Read
rjr27 at cam.ac.uk
Tue Jun 2 12:35:47 PDT 2009
In Phaser, the most CPU-intensive parts of the molecular replacement
calculations have been parallelized with OpenMP. Basically, the rule of
thumb is that, if we thought users needed a progress bar to see whether
anything was happening, it was worth making that bit parallel!
This makes some things in Phaser considerably faster if you have a
multi-core machine, but it also increases the memory requirements. So we've
been working to reduce the memory footprint before encouraging too many
people to compile with OpenMP support.
At the moment, we feel that SAD phasing in Phaser is fast enough that in a
pipeline with substructure determination and automatic model-building, it's
nowhere near the limiting step. So there isn't a huge incentive to make
that part parallel.
On Jun 2 2009, Ralf W. Grosse-Kunstleve wrote:
>> What about simulated annealing
>Just the FFT, if you compile from sources with gcc 4.3 or higher.
>> and phasing? I thought some of the
>> phasing modules are already parallelized in phenix.
>That's true. Phaser makes use of OpenMP for some things (I'm uncertain
>about the details). To use these features, you'll also need to compile
>from sources with gcc 4.3 or higher. (The standalone version of phaser
>may actually work with gcc 4.2 or higher.)
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