Hi Edward. Last time I did a clustering analysis for 78 spins, with no parallisation, with 50 monte carlo simulations, it took 58 Hours.
I compare that to a run with no clustering, which took 8 Hours. Is the clustering calculation so much more expensive? Best Troels Troels Emtekær Linnet 2013/10/7 Edward d'Auvergne <[email protected]> > Hi Troels, > > This is exactly as I would expect as the parallisation is currently at > the level of the spin cluster. Therefore if you have only one > cluster, using MPI will not result in any speed ups. This was > mentioned in the commit message: > > http://thread.gmane.org/gmane.science.nmr.relax.scm/18737 > > I am currently considering how to implement an additional > parallisiation at the Monte Carlo simulation level. My idea is to > have the multi-processor box singleton used in the minimise user > function backend, specifically in the pipe_control.minimise.minimise() > function. Instead of running processor.run_queue() at the end of the > minimise() method of the specific_analyses.relax_disp.api.Relax_disp > class, it is run at the end of the pipe_control.minimise.minimise() > function. This might involve less that 10 lines of code changed to > fully implement Monte Carlo simulation parallisation. But the problem > is that it needs testing to see how the non-parallised analyses handle > this. > > Regards, > > Edward > > On 15 September 2013 19:14, Troels Emtekær Linnet <[email protected]> > wrote: > > Hi Edward. > > > > I try to perform some speed-analysis. > > As mentioned here: > > > > http://wiki.nmr-relax.com/OpenMPI#Results > > > > I am very happy to see, that the analysis time go down from 8 hours, to 2 > > hours, when you change to a computer with 24 CPU's. > > > > Now I am trying to make a cluster analysis. > > But making the monte-carlo analysis for a clustering of 78 residues, > takes > > extremely long time. > > This is for the test, where I only use 1 CPU. > > > > After 1 Hour, it has not even passed simulation 1. > > For the faster computer, is has passed simulation 3. > > But the time for 50 MC simulation, now looks like to take extremely long > > time. > > > > Do you know, if this is expected? > > > > > > > > Troels Emtekær Linnet > > > > _______________________________________________ > > relax (http://www.nmr-relax.com) > > > > This is the relax-devel mailing list > > [email protected] > > > > To unsubscribe from this list, get a password > > reminder, or change your subscription options, > > visit the list information page at > > https://mail.gna.org/listinfo/relax-devel > > >
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