Re: r24171 - /branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py -- June 23, 2014

Hi Ed.

I think we can kill the for loops over the spins.

If I find a way to access the array for all spins, and then only loop over
mi, and di, to make the dot product according to the power of the tau_cpmg,
then
we have saved the costly clustering for loop.

I have been looking into strides:
http://wiki.nmr-relax.com/Numpy_linalg#Stride_tricks

But I haven't figured it out yet.

Best
Troels


2014-06-23 10:03 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:

Interesting!  If the magnetisation propagation can also be shifted out
of the loops, then the loops will disappear and the numeric models
will become far quicker.  With a matrix exponential, maybe this is
possible.  I'll think about this for a while.

Regards,

Edward


On 19 June 2014 20:52,  <tlinnet@xxxxxxxxxxxxx> wrote:

Author: tlinnet
Date: Thu Jun 19 20:52:57 2014
New Revision: 24171

URL: http://svn.gna.org/viewcvs/relax?rev=24171&view=rev
Log:
Moved the costly calculation of the matrix exponential out of for loops.

It was the numpy.eig and numpy.inv which was draining power.

This speeds up model NS R1rho 2site, by a factor 4X:
BEFORE:
Single:
   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
        1    0.000    0.000   32.552   32.552 <string>:1(<module>)
        1    0.002    0.002   32.552   32.552 pf_nsr1rho2site:530(single)
Cluster:
   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
        1    0.000    0.000   33.307   33.307 <string>:1(<module>)
        1    0.008    0.008   33.307   33.307

pf_nsr1rho2site:554(cluster)


AFTER:
Single:
   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
        1    0.000    0.000    8.286    8.286 <string>:1(<module>)
        1    0.002    0.002    8.286    8.286 pf_nsr1rho2site:530(single)
Cluster:
   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
        1    0.000    0.000    8.223    8.223 <string>:1(<module>)
        1    0.007    0.007    8.223    8.223

pf_nsr1rho2site:554(cluster)


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_r1rho_2site.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
URL:

http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py?rev=24171&r1=24170&r2=24171&view=diff

==============================================================================

--- branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py

(original)

+++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py   Thu Jun

19 20:52:57 2014

@@ -56,7 +56,7 @@
 # relax module imports.
 from lib.dispersion.ns_matrices import rr1rho_3d, rr1rho_3d_rankN
 from lib.float import isNaN
-from lib.linear_algebra.matrix_exponential import matrix_exponential
+from lib.linear_algebra.matrix_exponential import matrix_exponential,

matrix_exponential_rankN



 def ns_r1rho_2site(M0=None, matrix=None, r1rho_prime=None, omega=None,

offset=None, r1=0.0, pA=None, dw=None, kex=None, spin_lock_fields=None,
relax_time=None, inv_relax_time=None, back_calc=None, num_points=None):

@@ -106,6 +106,9 @@
     # The matrix that contains all the contributions to the evolution,

i.e. relaxation, exchange and chemical shift evolution.

     R_mat = rr1rho_3d_rankN(R1=r1, r1rho_prime=r1rho_prime, pA=pA,

pB=pB, dw=dw, omega=omega, offset=offset, w1=spin_lock_fields, k_AB=k_AB,
k_BA=k_BA, relax_time=relax_time)


+    # This matrix is a propagator that will evolve the magnetization

with the matrix R.

+    Rexpo_mat = matrix_exponential_rankN(R_mat)
+
     # Loop over spins.
     for si in range(NS):
         # Loop over the spectrometer frequencies.
@@ -135,19 +138,16 @@

                 # Loop over the time points, back calculating the R2eff

values.

                 for j in range(num_points_i):
-                    # The matrix that contains all the contributions to

the evolution, i.e. relaxation, exchange and chemical shift evolution.

-                    R_mat_i = R_mat[0, si, mi, oi, j]
-
                     # The following lines rotate the magnetization

previous to spin-lock into the weff frame.

                     theta = atan2(spin_lock_fields_i[j], dA)
                     M0[0] = sin(theta)    # The A state initial X

magnetisation.

                     M0[2] = cos(theta)    # The A state initial Z

magnetisation.


                     # This matrix is a propagator that will evolve the

magnetization with the matrix R.

-                    Rexpo = matrix_exponential(R_mat_i)
+                    Rexpo_i = Rexpo_mat[0, si, mi, oi, j]

                     # Magnetization evolution.
-                    MA = dot(M0, dot(Rexpo, M0))
+                    MA = dot(M0, dot(Rexpo_i, M0))

                     # The next lines calculate the R1rho using a

two-point approximation, i.e. assuming that the decay is mono-exponential.

                     if MA <= 0.0 or isNaN(MA):


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Re: r24171 - /branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py

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