Hi Ed. I tried the out argument, but it wont work?
I was more thinking of giving dot two matrices that are both C_CONTIGUOUS. http://wiki.scipy.org/PerformanceTips 2014-06-15 10:33 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi Troels, > > Is this actually faster? I just wrote a script to test this at > https://gna.org/task/index.php?7807#comment199. The log file with the > results is also attached. This is also archived at > http://article.gmane.org/gmane.science.nmr.relax.devel/6240. If you > look at that, I think I can show a way to make the numeric models up > to twice as fast. And that is simply to use the out argument for the > dot product. At least it will minimise the time required for the dot > products, and maybe remove this as the bottleneck. > > Regards, > > Edward > > > > On 15 June 2014 08:53, <[email protected]> wrote: > > Author: tlinnet > > Date: Sun Jun 15 08:53:38 2014 > > New Revision: 23952 > > > > URL: http://svn.gna.org/viewcvs/relax?rev=23952&view=rev > > Log: > > Changed linked matrix/vector inner products into chained dot expressions. > > > > Task #7807 (https://gna.org/task/index.php?7807): Speed-up of > dispersion models for Clustered analysis. > > > > Modified: > > branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py > > > > Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py > > URL: > http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py?rev=23952&r1=23951&r2=23952&view=diff > > > ============================================================================== > > --- branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py > (original) > > +++ branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py Sun Jun > 15 08:53:38 2014 > > @@ -56,6 +56,7 @@ > > # Python module imports. > > from numpy import dot, fabs, isfinite, log, min, ones, ndarray > > from numpy.ma import fix_invalid, masked_less_equal, masked_where > > +import numpy as np > > > > # relax module imports. > > from lib.dispersion.ns_matrices import rcpmg_3d > > @@ -138,9 +139,7 @@ > > > > # Loop over the CPMG elements, propagating the magnetisation. > > for j in range(2*power[i]): > > - Mint = dot(Rexpo, Mint) > > - Mint = dot(r180x, Mint) > > - Mint = dot(Rexpo, Mint) > > + Mint = Rexpo.dot(r180x).dot(Rexpo).dot(Mint) > > > > # The next lines calculate the R2eff using a two-point > approximation, i.e. assuming that the decay is mono-exponential. > > Mx = Mint[1] / pA > > > > > > _______________________________________________ > > relax (http://www.nmr-relax.com) > > > > This is the relax-commits 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-commits > > _______________________________________________ > 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 > _______________________________________________ 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
