[phenixbb] Parallel Version of Phenix?

[Jianghai Zhu]

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?

-- Jianghai






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  
> 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.
>
> Randy
>
> 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.)
>>
>> Ralf
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>
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