Author: bugman
Date: Tue Jul 22 19:04:10 2014
New Revision: 24656
URL: http://svn.gna.org/viewcvs/relax?rev=24656&view=rev
Log:
Merged revisions 23864-23877,23880,23888-23934,23937-23942,23946 via svnmerge
from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/disp_spin_speed
........
r23864 | tlinnet | 2014-06-12 12:12:58 +0200 (Thu, 12 Jun 2014) | 14 lines
Changed target function for model CR72.
To CR72 is now also the input of the parameters of R20A, R20B and dw.
dw is tested for zero, to return flat lines.
It is faster to search in the smaller numpy array, than the 5 dimensional
dw array.
This is for speed-up.
R20A and R20B is also subtracted, to see if the full model should be used.
In the same way, it is faster to subtract the smaller array.
These small tricks are expected to give 5-10 pct. speeed-up.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23865 | tlinnet | 2014-06-12 12:12:59 +0200 (Thu, 12 Jun 2014) | 5 lines
Made the lib function of CR72 accept the R20A, R20B and dw of the original
array.
This is for speed-up.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23866 | tlinnet | 2014-06-12 12:13:01 +0200 (Thu, 12 Jun 2014) | 3 lines
Changed unit-tests, to send in the original R20A, R20B and dw_orig to the
testing of the lib function CR72.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23867 | tlinnet | 2014-06-12 12:13:03 +0200 (Thu, 12 Jun 2014) | 3 lines
Changed profiling script to send R20A, R20B and dw, as original parameters
to the lib function.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23868 | tlinnet | 2014-06-12 12:23:18 +0200 (Thu, 12 Jun 2014) | 11 lines
Changed target function for model B14.
To B14 now also send the input of the original parameters dw.
dw is tested for zero, to return flat lines.
It is faster to search in the smaller numpy array, than the 5 dimensional
dw array.
This is for speed-up.
These small tricks are expected to give 5-10 pct. speeed-up.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23869 | tlinnet | 2014-06-12 12:23:20 +0200 (Thu, 12 Jun 2014) | 5 lines
Made the lib function of B14 accept dw of the original array.
This is for speed-up.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23870 | tlinnet | 2014-06-12 12:23:21 +0200 (Thu, 12 Jun 2014) | 3 lines
Changed unit-tests, to send in the original dw_orig to the testing of the
lib function B14.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23871 | tlinnet | 2014-06-12 12:23:23 +0200 (Thu, 12 Jun 2014) | 3 lines
Changed profiling script to send dw as original parameters to the lib
function B14.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23872 | tlinnet | 2014-06-12 12:31:42 +0200 (Thu, 12 Jun 2014) | 5 lines
Copied profiling script for CR72 model to TSMFK01 model.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23873 | tlinnet | 2014-06-12 13:18:56 +0200 (Thu, 12 Jun 2014) | 3 lines
Indention fix in cr72.py and b14.py.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23874 | tlinnet | 2014-06-12 13:18:58 +0200 (Thu, 12 Jun 2014) | 3 lines
Modified profiling script to be used for model TSMFK01.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23875 | tlinnet | 2014-06-12 13:19:00 +0200 (Thu, 12 Jun 2014) | 3 lines
Modified target function for model TSMFK01, to send in dw as original
parameter.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23876 | tlinnet | 2014-06-12 13:19:02 +0200 (Thu, 12 Jun 2014) | 3 lines
Modified lib function for model TSMFK01 to accept dw_orig as input and
replaced functions to find math domain errors into maske replacements.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23877 | tlinnet | 2014-06-12 13:19:04 +0200 (Thu, 12 Jun 2014) | 3 lines
Made unit tests for model TSMFK01 send in R20A and dw as a numpy array.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23880 | tlinnet | 2014-06-12 13:56:12 +0200 (Thu, 12 Jun 2014) | 32 lines
Large increase in speed for model TSMFK01 by changing target functions to
use multidimensional numpy arrays in calculation.
This is done by restructuring data into multidimensional arrays of
dimension [NE][NS][NM][NO][ND], which are
number of spins, number of magnetic field strength, number of offsets,
maximum number of dispersion point.
The speed comes from using numpy ufunc operations.
The new version is 2.4X as fast per spin calculation, and 54X as fast for
clustered analysis.
The different in timings for 3 spectrometer frequencies, calculated for 1
spin or 100 clustered spins with 1000 iterations are:
----
VERSION 3.2.2
----
1 spin:
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 0.262 0.262 <string>:1(<module>)
100 spin:
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 25.391 25.391 <string>:1(<module>)
----
New version
---
1 spin:
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 0.111 0.111 <string>:1(<module>)
100 spin:
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 0.468 0.468 <string>:1(<module>)
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23888 | tlinnet | 2014-06-12 20:07:59 +0200 (Thu, 12 Jun 2014) | 3 lines
Replacing math domain checking in model DPL94, with masked array
replacement.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23889 | tlinnet | 2014-06-12 20:08:01 +0200 (Thu, 12 Jun 2014) | 5 lines
Fix for import missing error in lib function dpl94.
Needed to import numpy any() function.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23890 | tlinnet | 2014-06-12 20:08:03 +0200 (Thu, 12 Jun 2014) | 5 lines
First try to speed up model DPL94.
This has not succeded, since systemtest:
Relax_disp.test_dpl94_data_to_dpl94 stiÃll fails.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23891 | tlinnet | 2014-06-12 20:08:06 +0200 (Thu, 12 Jun 2014) | 3 lines
Trying to move some of the structures into its own part.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23892 | tlinnet | 2014-06-12 20:08:08 +0200 (Thu, 12 Jun 2014) | 7 lines
Fix for forgetting to multiply frqs to power 2.
This was found by inspecting all print out before and after implementation.
New implementation of DPL94 now passes all system and unit tests.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23893 | tlinnet | 2014-06-12 20:08:10 +0200 (Thu, 12 Jun 2014) | 5 lines
Moved the expansion of the R1 structure out of the for loops.
This is to speed-up the __init__ of the class of the target function.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23894 | tlinnet | 2014-06-12 20:35:04 +0200 (Thu, 12 Jun 2014) | 3 lines
Moved the packing of errors and values out of for loop in the __init__
class of target function.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23895 | tlinnet | 2014-06-12 20:35:06 +0200 (Thu, 12 Jun 2014) | 5 lines
Moved the multi dimensional expansion of inv_relax_times out of for loop.
This can be done for all structures, which does not have missing points.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23896 | tlinnet | 2014-06-12 20:35:08 +0200 (Thu, 12 Jun 2014) | 3 lines
For inv_relax_times, expanded one axis, and tiled up to NR spins, before
reshaping and blowing up to full structure.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23897 | tlinnet | 2014-06-12 20:35:10 +0200 (Thu, 12 Jun 2014) | 3 lines
Moved the expansion of frqs out of for loops.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23898 | tlinnet | 2014-06-12 23:11:38 +0200 (Thu, 12 Jun 2014) | 3 lines
Documentation fix for description of input arrays to lib functions.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23899 | tlinnet | 2014-06-13 07:20:57 +0200 (Fri, 13 Jun 2014) | 3 lines
Converted TAP03 model to use multi dimensional numpy arrays.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23900 | tlinnet | 2014-06-13 07:21:00 +0200 (Fri, 13 Jun 2014) | 3 lines
Made dw in unit tests of TAP03 be of numpy array.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23901 | tlinnet | 2014-06-13 07:21:02 +0200 (Fri, 13 Jun 2014) | 5 lines
Replaced the loop structure in target function of TAP03 with numpy arrays.
This makes the model faster.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23902 | tlinnet | 2014-06-13 07:21:04 +0200 (Fri, 13 Jun 2014) | 5 lines
Reordered the initialization structure of the special numpy arrays.
This was done in the init part of the target function of relaxation
dispersion.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23903 | tlinnet | 2014-06-13 07:26:14 +0200 (Fri, 13 Jun 2014) | 3 lines
Added model MODEL_TSMFK01 also get self.tau_cpmg calculated in init part.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23904 | tlinnet | 2014-06-13 08:18:23 +0200 (Fri, 13 Jun 2014) | 5 lines
Methods to replace math domain errors in model TP02, has been replaced with
numpy masks.
Documentation is also fixed.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23905 | tlinnet | 2014-06-13 08:18:25 +0200 (Fri, 13 Jun 2014) | 3 lines
Fix for sending in dw as numpy array in unit tests of model TP02.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23906 | tlinnet | 2014-06-13 08:18:27 +0200 (Fri, 13 Jun 2014) | 5 lines
Replaced target function for model TP02, to use higher dimensional numpy
array structures.
That makes the model much faster.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23907 | tlinnet | 2014-06-13 08:21:48 +0200 (Fri, 13 Jun 2014) | 3 lines
Fix for adding model TP02 to part of init class to initialize preparation
of higher dimension numpy structures.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23908 | tlinnet | 2014-06-13 10:10:04 +0200 (Fri, 13 Jun 2014) | 3 lines
Made the NOREX model af faster numpy array calculation.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23909 | tlinnet | 2014-06-13 10:10:07 +0200 (Fri, 13 Jun 2014) | 5 lines
Removed an unnecessary frq_struct in init of target function.
frqs can just be expanded, and back_calc is cleaned afterwards with
disp_struct.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23910 | tlinnet | 2014-06-13 10:33:43 +0200 (Fri, 13 Jun 2014) | 5 lines
Methods to replace math domain errors in model M61, has been replaced with
numpy masks.
Documentation is also fixed.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23911 | tlinnet | 2014-06-13 10:33:44 +0200 (Fri, 13 Jun 2014) | 3 lines
Fix for sending in r1rho_prime and phi_ex_scaled as numpy array in unit
tests of model M61.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23912 | tlinnet | 2014-06-13 10:33:46 +0200 (Fri, 13 Jun 2014) | 5 lines
Replaced target function for model M61, to use higher dimensional numpy
array structures.
That makes the model much faster.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23913 | tlinnet | 2014-06-13 11:06:15 +0200 (Fri, 13 Jun 2014) | 5 lines
Methods to replace math domain errors in model M61b, has been replaced with
numpy masks.
Documentation is also fixed.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23914 | tlinnet | 2014-06-13 11:06:17 +0200 (Fri, 13 Jun 2014) | 3 lines
Fix for sending in r1rho_prime and dw as numpy array in unit tests of model
M61b.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23915 | tlinnet | 2014-06-13 11:06:18 +0200 (Fri, 13 Jun 2014) | 5 lines
Replaced target function for model M61b, to use higher dimensional numpy
array structures.
That makes the model much faster.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23916 | tlinnet | 2014-06-13 11:17:52 +0200 (Fri, 13 Jun 2014) | 6 lines
Removed number of points to be send to lib function of model TTSMFK01.
These are not used anymore.
Also removed in corresponding unit tests.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23917 | tlinnet | 2014-06-13 11:17:53 +0200 (Fri, 13 Jun 2014) | 8 lines
Removed number of points and pB to be send to lib function of model TP02.
Number of points are not used anymore.
pB is calculated in lib function insted.
Also removed in corresponding unit tests.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23918 | tlinnet | 2014-06-13 11:21:16 +0200 (Fri, 13 Jun 2014) | 5 lines
Removed number of points and pB to send to lib function of model TP02.
pB is calculated in lib function insted.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23919 | tlinnet | 2014-06-13 11:47:38 +0200 (Fri, 13 Jun 2014) | 11 lines
Removed number of points, pB, k_AB, k_BA to be send to lib function of
model B14.
Number of points are not used anymore.
pB is calculated in lib function insted.
k_AB, and k_BA are calculated in lib functions instead.
Fixed in target function.
Fixed in lib function.
Fixed in corresponding unit tests.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23920 | tlinnet | 2014-06-13 11:47:40 +0200 (Fri, 13 Jun 2014) | 5 lines
Fix for sending number of points in target function of TSMK01.
This was removed in lib function.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23921 | tlinnet | 2014-06-13 11:47:42 +0200 (Fri, 13 Jun 2014) | 10 lines
Removed number of points, pB, to be send to lib function of model TAP03.
Number of points are not used anymore.
pB is calculated in lib function insted.
Fixed in target function.
Fixed in lib function.
Fixed in corresponding unit tests
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23922 | tlinnet | 2014-06-13 11:47:45 +0200 (Fri, 13 Jun 2014) | 9 lines
Removed number of points, to be send to lib function of model CR72.
Number of points are not used anymore.
Fixed in target function.
Fixed in lib function.
Fixed in corresponding unit tests
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23923 | tlinnet | 2014-06-13 11:55:44 +0200 (Fri, 13 Jun 2014) | 9 lines
Removed number of points, to be send to lib function of model DPL94.
Number of points are not used anymore.
Fixed in target function.
Fixed in lib function.
Fixed in corresponding unit tests
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23924 | tlinnet | 2014-06-13 11:55:46 +0200 (Fri, 13 Jun 2014) | 9 lines
Removed number of points, to be send to lib function of model M61.
Number of points are not used anymore.
Fixed in target function.
Fixed in lib function.
Fixed in corresponding unit tests
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23925 | tlinnet | 2014-06-13 11:55:48 +0200 (Fri, 13 Jun 2014) | 9 lines
Removed number of points, to be send to lib function of model M61b.
Number of points are not used anymore.
Fixed in target function.
Fixed in lib function.
Fixed in corresponding unit tests
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23926 | tlinnet | 2014-06-13 12:16:49 +0200 (Fri, 13 Jun 2014) | 8 lines
Methods to replace math domain errors in model MP05, has been replaced with
numpy masks.
number of points has been removed, as the masks utility replaces this.
Calculataion of pB, has been moved to lib function for simplicity.
Documentation is also fixed.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23927 | tlinnet | 2014-06-13 12:16:51 +0200 (Fri, 13 Jun 2014) | 3 lines
Fix for sending in dw as numpy array in unit tests of model MP05.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
r23928 | tlinnet | 2014-06-13 12:16:52 +0200 (Fri, 13 Jun 2014) | 5 lines
Replaced target function for model MP05, to use higher dimensional numpy
array structures.
That makes the model much faster.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
........
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r24656 - in /trunk: ./ lib/dispersion/ target_functions/ test_suite/shared_data/dispersion/profiling/ test_suite/system_test...