[phenixbb] Parallel Version of Phenix?
Randy J. Read
rjr27 at cam.ac.uk
Wed Jun 3 01:24:02 PDT 2009
Most problems run on machines with, say, 2Gb. Big problems take more
memory, but very few would fail to run on a machine with 8Gb. It's very
case dependent and depends on the amount of branching in the search.
However, this is continually improving as we find places where we can
restrict the growth of memory as the search branches in more directions.
We're just trying to avoid unpleasant surprises for people who turn on
multiple threads for large problems.
On Jun 2 2009, Jianghai Zhu wrote:
>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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>>> phenixbb at phenix-online.org
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