Re: r23963 - /branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py -- June 15, 2014

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 <tlinnet@xxxxxxxxxxxxx> 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 <edward@xxxxxxxxxxxxx>:

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 <tlinnet@xxxxxxxxxxxxx>
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 <edward@xxxxxxxxxxxxx>:


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,  <tlinnet@xxxxxxxxxxxxx> 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


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Re: r23963 - /branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py

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