There is long thread here http://thread.gmane.org/gmane.comp.python.numeric.general/28135/
Somewhere I saw, that there is maybe a bug here. 2014-06-15 16:53 GMT+02:00 Edward d'Auvergne <[email protected]>: > Hi, > > It does look like there is a bug somewhere in one version of > numpy.dot(). I'll look into this! > > Regards, > > Edward > > > > On 15 June 2014 16:43, Troels Emtekær Linnet <[email protected]> > wrote: > > I am using 1.8 > > > > I am stopping here with more search for this holy grail. > > > > There is clearly some bug somewhere. > > > > > > 2014-06-15 16:25 GMT+02:00 Edward d'Auvergne <[email protected]>: > > > >> Which numpy version are you using? There is a damn good reason why I > >> am pushing this. I know that all of the competition software (at > >> least cpmg_fit and CATIA) uses exactly this storage concept, though in > >> C rather than Python, and for exactly the reason why I am pushing > >> this. We really have to get this working for you! > >> > >> Regards, > >> > >> Edward > >> > >> > >> > >> On 15 June 2014 16:21, Troels Emtekær Linnet <[email protected]> > >> wrote: > >> > Hi Ed. > >> > > >> > I can see that you are pushing for this. > >> > > >> > It wont work! > >> > > >> > > >> > > >> > 2014-06-15 16:12 GMT+02:00 Edward d'Auvergne <[email protected]>: > >> >> > >> >> Hi Troels, > >> >> > >> >> In this change, only in one line have you used the numpy.dot() out > >> >> argument: > >> >> > >> >> + dot(Rexpo, r180x, evolution_matrix) > >> >> > >> >> So it must be working. You can do this for all others, replacing: > >> >> > >> >> - evolution_matrix = dot(evolution_matrix, Rexpo) > >> >> + dot(evolution_matrix, Rexpo, evolution_matrix) > >> >> > >> >> and: > >> >> > >> >> - evolution_matrix = dot(evolution_matrix, > >> >> evolution_matrix) > >> >> + dot(evolution_matrix, evolution_matrix, > >> >> evolution_matrix) > >> >> > >> >> and: > >> >> > >> >> - Mint = evolution_matrix.dot(Mint) > >> >> + dot(evolution_matrix, Mint, Mint) > >> >> > >> >> This should give an observable speed increase of 2 or more. > >> >> > >> >> Regards, > >> >> > >> >> Edward > >> >> > >> >> > >> >> On 15 June 2014 15:15, <[email protected]> wrote: > >> >> > Author: tlinnet > >> >> > Date: Sun Jun 15 15:15:23 2014 > >> >> > New Revision: 23963 > >> >> > > >> >> > URL: http://svn.gna.org/viewcvs/relax?rev=23963&view=rev > >> >> > Log: > >> >> > Made the dot evolution structure faster for NS CPMG 2site 3D. > >> >> > > >> >> > 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=23963&r1=23962&r2=23963&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 15:15:23 2014 > >> >> > @@ -54,7 +54,7 @@ > >> >> > """ > >> >> > > >> >> > # Python module imports. > >> >> > -from numpy import dot, fabs, isfinite, log, min, sum > >> >> > +from numpy import asarray, dot, fabs, isfinite, log, min, sum > >> >> > from numpy.ma import fix_invalid, masked_where > >> >> > > >> >> > > >> >> > @@ -141,6 +141,9 @@ > >> >> > # The matrix R that contains all the contributions to > >> >> > the > >> >> > evolution, i.e. relaxation, exchange and chemical shift evolution. > >> >> > R = rcpmg_3d(R1A=r10a, R1B=r10b, R2A=R2A_si_mi, > >> >> > R2B=R2B_si_mi, pA=pA, pB=pB, dw=dw_si_mi, k_AB=k_AB, k_BA=k_BA) > >> >> > > >> >> > + # The essential evolution matrix. This initialises the > >> >> > structure. > >> >> > + evolution_matrix = asarray(R) * 0.0 > >> >> > + > >> >> > # Loop over the time points, back calculating the > R2eff > >> >> > values. > >> >> > for di in range(num_points_si_mi): > >> >> > # Extract the values from the higher dimensional > >> >> > arrays. > >> >> > @@ -155,12 +158,18 @@ > >> >> > # This matrix is a propagator that will evolve the > >> >> > magnetization with the matrix R for a delay tcp. > >> >> > Rexpo = matrix_exponential(R*tcp_si_mi_di) > >> >> > > >> >> > - # Temp matrix. > >> >> > - t_mat = > >> >> > > >> >> > > Rexpo.dot(r180x).dot(Rexpo).dot(Rexpo).dot(r180x).dot(Rexpo).dot(Rexpo).dot(r180x).dot(Rexpo).dot(Rexpo).dot(r180x).dot(Rexpo) > >> >> > + # The essential evolution matrix. > >> >> > + # This is the first round. > >> >> > + dot(Rexpo, r180x, evolution_matrix) > >> >> > + evolution_matrix = dot(evolution_matrix, Rexpo) > >> >> > + # The second round. > >> >> > + evolution_matrix = dot(evolution_matrix, > >> >> > evolution_matrix) > >> >> > + # The third and fourth round, > >> >> > + evolution_matrix = dot(evolution_matrix, > >> >> > evolution_matrix) > >> >> > > >> >> > # Loop over the CPMG elements, propagating the > >> >> > magnetisation. > >> >> > for j in range(power_si_mi_di/2): > >> >> > - Mint = t_mat.dot(Mint) > >> >> > + Mint = evolution_matrix.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
