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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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