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
