[phenixbb] phenix.refine nproc

R.D. Oeffner rdo20 at cam.ac.uk
Tue Dec 10 08:02:38 PST 2013

Unless the python installation you use for Phenix is compiled for using 
the OpenMP version of the C-runtime my guess is that running an OpenMP 
version of Phenix will result in strange crashes. That seems to be the 
case on Windows at least.


On 2013-12-10 15:44, Nathaniel Echols wrote:
> On Tue, Dec 10, 2013 at 6:37 AM, de Waal, Parker
> <Parker.DeWaal at vai.org> wrote:
>> I recently compiled phenix 1.8.4-1496 on a CentOS 6.4 server and am
>> having trouble using phenix.refine in parallel using the nproc flag
>> which always runs as a single thread. Please find my input
>> parameters here:
>> https://gist.github.com/anonymous/13b9d4d39ed4d0c9622a [1]
>> I’m wondering if maybe OpenMP isn’t configured properly on our
>> server? Or maybe the correct version is not installed when I
>> compliled phenix. If anyone has any input or experience with a
>> problem such as this I would be extremely grateful.
> The nproc flag has nothing to do with OpenMP - it controls the
> parallelization of the (optional) weight optimization calculations,
> which are simply grid searches and can be easily spread out using
> Python's multiprocessing module.  The separate OpenMP parallelization
> is in the Fast Fourier Transform (FFT) code responsible for
> calculating structure factors and gradients.  The latter is a much
> less efficient use of multiple CPUs, but it will always have an effect
> whether or not your run grid optimization.
> To use OpenMP, first make sure that you have actually compiled OpenMP
> support during installation.  To control the number of processors,
> the environment OMP_NUM_THREADS is used; I'm not sure if this defaults
> to 1 or the number of available CPUs.  I don't think you can safely
> combine this with the Python-level parallelism, but I haven't tested
> that.
> -Nat
> Links:
> ------
> [1] https://gist.github.com/anonymous/13b9d4d39ed4d0c9622a
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