Hi,
I think this is one of those cases where we will see that a future
numpy version will implement this correctly and fast. I've been
looking into the numpy 1.8.1 source code, and the inplace operation
and the speed of the out argument appear to be unrelated. Anyway,
numpy 2 might implement the out argument correctly for speed, so that
"dot(a, b, c)" is an order of magnitude faster than "c = dot(a, b)",
as it really should be, just like in the BLAS library used by
numpy.dot() where it is much faster.
Regards,
Edward
On 16 June 2014 22:11, <tlinnet@xxxxxxxxxxxxx> wrote:
Author: tlinnet
Date: Mon Jun 16 22:11:56 2014
New Revision: 24007
URL: http://svn.gna.org/viewcvs/relax?rev=24007&view=rev
Log:
Changed the calculation of inner product in model ns cpmg 2site 3d.
The out argument of numpy.dot is buggy, and should not be used.
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=24007&r1=24006&r2=24007&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 Mon Jun 16
22:11:56 2014
@@ -141,9 +141,6 @@
# 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.
@@ -160,10 +157,10 @@
# The essential evolution matrix.
# This is the first round.
- dot(Rexpo, r180x, evolution_matrix)
- dot(evolution_matrix * 1.0, Rexpo, evolution_matrix)
+ evolution_matrix = dot(Rexpo, r180x)
+ evolution_matrix = dot(evolution_matrix, Rexpo)
# The second round.
- dot(evolution_matrix * 1.0, evolution_matrix * 1.0,
evolution_matrix)
+ evolution_matrix = dot(evolution_matrix, evolution_matrix )
# Loop over the CPMG elements, propagating the
magnetisation.
for j in range(power_si_mi_di):
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Re: r24007 - /branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py