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