[phenixbb] Parallelization for optimization of wxu/wxc?

Francois Berenger berenger at riken.jp
Sun Aug 28 18:33:59 PDT 2011

On 08/26/2011 09:14 PM, Nathaniel Echols wrote:
> On Fri, Aug 26, 2011 at 2:09 PM, Francis E Reyes
> <Francis.Reyes at colorado.edu>  wrote:
>> Isn't it parallelized in the nightlies?
> Yes, Ralf and I added this a couple of months ago.  There are a few
> more improvements that we'd like to make, such as setting 'nproc'
> automatically

Maybe this Python code can be helpful:

def get_nb_procs():
     res = None
         # POSIX
         res = os.sysconf('SC_NPROCESSORS_ONLN')
             # {Free|Net|Open}BSD and MacOS X
             res = int(commands.getoutput("sysctl -n hw.ncpu"))
             res = 0
     return res

It is supposed to work well on Linux plus all the explicitly listed 

Best regards,

 > (and adjusting to compensate for system load), and
> fixing a couple of inefficiencies (e.g. after running a grid search to
> identify optimal weight, it then refines *again* with that weight,
> instead of saving the coordinates from the grid search result), but it
> is already a significant improvement.
>> - phenix.refine:
>>   - grid searches parallelized: use 'nproc' parameter to set number of CPUs
>>     to use
>>     - this affects bulk solvent mask optimization, and XYZ and ADP weight
>>       optimization (in addition to TLS identification)
>>     - can reduce runtime by 75% or more depending on settings (see manual for
>>       details)
> FYI, in practice the largest number of CPUs that the weight
> optimization routines will use appears to be 18 cores.  (The automatic
> TLS identification will use as many as possible, but this won't have
> much additional effect.)
> -Nat
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