[phenixbb] Parallel Version of Phenix?
jzhu at idi.harvard.edu
Tue Jun 2 13:23:10 PDT 2009
How much memories will phaser need in parallel mode? For the new
linux workstations, they are equipped at least 8 GB memories and
memories are cheap. Even my MacBook Pro has 4 GB memories. Would
phaser need more than that?
On Jun 2, 2009, at 3:35 PM, Randy J. Read wrote:
> In Phaser, the most CPU-intensive parts of the molecular replacement
> calculations have been parallelized with OpenMP. Basically, the rule
> thumb is that, if we thought users needed a progress bar to see
> 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
> 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
> 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
>> about the details). To use these features, you'll also need to
>> from sources with gcc 4.3 or higher. (The standalone version of
>> may actually work with gcc 4.2 or higher.)
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