At one point at least there were openmp support within brownian dynamics (for the particle perturbations) as well as restraint evaluations.
On Wed, Jul 16, 2014 at 12:33 PM, Barak Raveh barak.raveh@gmail.com wrote:
> So in principle this support can be added with IMP OpenMP pragma macros, > though since most of the computation time typically involves the scoring > function, it is probably wiser to parallelize that part of the code. I know > Daniel did some work in that direction in the past but not sure where it's > gotten, see also > https://integrativemodeling.org/nightly/doc/html/base_2thread__macros_8h.htm... > > It should in theory be pretty simple to add OpenMP statements at some key > computations, based on profiling. > > > On Wed, Jul 16, 2014 at 12:28 PM, Ben Webb ben@salilab.org wrote: > >> On 07/16/2014 02:11 AM, Davide Baù wrote: >> >>> I have set up a Brownian dynamics optimizer as follow: >>> >>> m = IMP.kernel.Model() >>>> >>>> # Brownian Dynamics >>>> bd=IMP.atom.BrownianDynamics(m) >>>> bd.set_maximum_time_step(1000) >>>> >>>> for i in range(1, nrounds): >>>> e = bd.optimize(10) >>>> >>> >>> Is it possible in IMP to parallelize the code to make it faster? >>> >> >> If you really require the output of one optimization to be the input of >> the next, then no, short of parallelizing the restraint evaluation itself. >> Currently the only way to do that is via OpenMP. >> >> If you can instead run nrounds optimizations starting from different >> (e.g. random) starting conditions, parallelization is trivial. You can use >> IMP.parallel or simply run multiple copies of your script, e.g. with >> different random seeds. >> >> Ben >> -- >> ben@salilab.org http://salilab.org/~ben/ >> "It is a capital mistake to theorize before one has data." >> - Sir Arthur Conan Doyle >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> > > > > -- > Barak > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > >