relax SVN archive

Updated the frame order optimisation results for the 2nd CaM pseudo-elliptic cone test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.

Updated the frame order optimisation results for the CaM torsionless isotropic cone test data.

The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo simulations. The new
frame order representation files have been added to the repository, as well as the intermediate
state files.

Deletion of the disp_spin_speed branch as it has been merged back to trunk.

Merged revisions 24362-24364,24510,24612-24615,24619-24637,24641-24648,24650 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_spin_speed

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r24362 | bugman | 2014-06-30 10:41:27 +0200 (Mon, 30 Jun 2014) | 10 lines

Created a master profiling script for comparing the speed between different dispersion models.

This is similar to the disp_profile_all.py script except it only operates on a single relax version.
The output is then simply the timings, with statistics, of the calculation time for 100 function
calls for 100 spins (either 10,000 function calls for single spins or 100 function calls for the
cluster of 100 spins).

The output of the script for the current disp_spin_speed branch code has also been added.
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r24363 | tlinnet | 2014-06-30 11:48:47 +0200 (Mon, 30 Jun 2014) | 5 lines

Critical fix for the recalculation of tau cpmg, when plotting for numerical models.

The interpolated dispersion points with tau_cpgm was calculated with frq, instead of cmpg_frq.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24364 | bugman | 2014-06-30 12:20:31 +0200 (Mon, 30 Jun 2014) | 7 lines

The new dispersion model profiling master script now includes links to the relax wiki.

The models are no longer presented by name but rather by the relax wiki links for each model (see
http://wiki.nmr-relax.com/Category:Relaxation_dispersion for all these links). This is to improve
the Google rank of the relax wiki, as these links may appear in a number of locations.
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r24510 | bugman | 2014-07-10 12:04:53 +0200 (Thu, 10 Jul 2014) | 6 lines

Removal of many unused imports in the disp_spin_speed branch.

These were detected using the devel_scripts/find_unused_imports.py script which uses pylint to find
all unused imports. The false positives also present in the trunk were ignored.
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r24612 | tlinnet | 2014-07-22 15:16:47 +0200 (Tue, 22 Jul 2014) | 13 lines

Reverted r24339 as relax dependency of numpy is now 1.6 where the "out" argument is available.

The command used was:
svn merge -r24339:r24338 .

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r24339 | tlinnet | 2014-06-27 12:58:29 +0200 (Fri, 27 Jun 2014) | 3 lines

Added a list of systemtests to skip, if numpy "out" argument is not available.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24613 | tlinnet | 2014-07-22 15:23:47 +0200 (Tue, 22 Jul 2014) | 13 lines

Reverted r24336 as relax dependency of numpy is now 1.6 where the "einsum" function is available.

The command used was:
svn merge -r24336:r24335 .

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r24336 | tlinnet | 2014-06-27 12:58:22 +0200 (Fri, 27 Jun 2014) | 3 lines

Added to target function that experiment_type_setup() should not be initiated, if numpy.einsum is missing.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
.....
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r24614 | tlinnet | 2014-07-22 15:27:44 +0200 (Tue, 22 Jul 2014) | 18 lines

Reverted r24337 as relax dependency of numpy is now 1.6 where the "out" argument is available.

The command used was:
svn merge -r24337:r24336 .

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r24337 | tlinnet | 2014-06-27 12:58:24 +0200 (Fri, 27 Jun 2014) | 8 lines

Added a numpy "out" argument check to dep_check.py.

This is for checking the out argument of:
numpy.multiply
numpy.add
numpy.subtract

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24615 | tlinnet | 2014-07-22 15:35:16 +0200 (Tue, 22 Jul 2014) | 13 lines

Reverted r24323 as relax dependency of numpy is now 1.6 where "einsum" function is available.

The command used was:
svn merge -r24323:r24322 .

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r24323 | tlinnet | 2014-06-25 19:31:40 +0200 (Wed, 25 Jun 2014) | 3 lines

Implemented a dependency check for numpy einsum, so relax can still start.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24619 | tlinnet | 2014-07-22 16:51:26 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/b14.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24620 | tlinnet | 2014-07-22 16:51:28 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/cr72.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24621 | tlinnet | 2014-07-22 16:51:30 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/dpl94.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24622 | tlinnet | 2014-07-22 16:51:32 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/lm63_3site.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24623 | tlinnet | 2014-07-22 16:51:33 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/lm63.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24624 | tlinnet | 2014-07-22 16:51:35 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/m61b.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24625 | tlinnet | 2014-07-22 16:51:37 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/m61.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24626 | tlinnet | 2014-07-22 16:51:38 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/matrix_exponential.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24627 | tlinnet | 2014-07-22 16:51:40 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/mp05.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24628 | tlinnet | 2014-07-22 16:51:42 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/ns_cpmg_2site_expanded.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24629 | tlinnet | 2014-07-22 16:51:44 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/ns_cpmg_2site_star.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24630 | tlinnet | 2014-07-22 16:51:46 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/ns_mmq_2site.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24631 | tlinnet | 2014-07-22 16:51:48 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/ns_mmq_3site.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24632 | tlinnet | 2014-07-22 16:51:50 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/ns_r1rho_2site.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24633 | tlinnet | 2014-07-22 16:51:51 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/ns_r1rho_3site.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24634 | tlinnet | 2014-07-22 16:51:53 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/tap03.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24635 | tlinnet | 2014-07-22 16:51:55 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/tp02.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24636 | tlinnet | 2014-07-22 16:51:57 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of lib/dispersion/two_point.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24637 | tlinnet | 2014-07-22 16:51:59 +0200 (Tue, 22 Jul 2014) | 3 lines

Code validation of target_functions/relax_disp.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24641 | tlinnet | 2014-07-22 17:53:38 +0200 (Tue, 22 Jul 2014) | 3 lines

Removal of space after for loop in target_functions/relax_disp.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24642 | tlinnet | 2014-07-22 17:53:40 +0200 (Tue, 22 Jul 2014) | 3 lines

Copyright time extension for lib/dispersion/tsmfk01.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24643 | tlinnet | 2014-07-22 17:53:42 +0200 (Tue, 22 Jul 2014) | 3 lines

More removal of space after for loop in target_functions/relax_disp.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24644 | tlinnet | 2014-07-22 17:53:43 +0200 (Tue, 22 Jul 2014) | 3 lines

For model ns mmq 3site, moved the parameter conversion of dw_AB from target function to lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24645 | tlinnet | 2014-07-22 17:53:45 +0200 (Tue, 22 Jul 2014) | 3 lines

Removed chi sum initialisation in func_ns_mmq_2site() as this is not used.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24646 | tlinnet | 2014-07-22 17:53:47 +0200 (Tue, 22 Jul 2014) | 3 lines

Documentation fix for the get_back_calc() function in target_function/relax_disp.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24647 | tlinnet | 2014-07-22 17:56:23 +0200 (Tue, 22 Jul 2014) | 3 lines

Removed unnecessary repetitive calculation of kex**2 in model DPL94.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24648 | tlinnet | 2014-07-22 18:08:22 +0200 (Tue, 22 Jul 2014) | 3 lines

API documentation fixes, where a "\" is the last character on the line. There should be a space " ", ending this characater.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24650 | tlinnet | 2014-07-22 18:21:20 +0200 (Tue, 22 Jul 2014) | 3 lines

Comment space fixing in target_functions/relax_disp.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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Merged revisions 24323-24326,24335-24343,24347-24351,24353,24357,24360 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_spin_speed

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r24323 | tlinnet | 2014-06-25 19:31:40 +0200 (Wed, 25 Jun 2014) | 3 lines

Implemented a dependency check for numpy einsum, so relax can still start.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24324 | tlinnet | 2014-06-25 19:31:45 +0200 (Wed, 25 Jun 2014) | 5 lines

Initiated lengthy profiling script, that shows that doing square numpy matrix_power on strided data, can speed up the calculation by factor 1.5.

The profiling script can quicly be turned into a unit test, and includes small helper functions to calculate how to stride through the data.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24325 | tlinnet | 2014-06-25 20:41:47 +0200 (Wed, 25 Jun 2014) | 7 lines

First try to implement function that will calculate the matrix exponential by striding through data.

Interestingly, it does not work. Theses systemtests will fail.
test_hansen_cpmg_data_to_ns_cpmg_2site_3D
test_hansen_cpmg_data_to_ns_cpmg_2site_3D_full

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24326 | tlinnet | 2014-06-25 20:41:49 +0200 (Wed, 25 Jun 2014) | 3 lines

Added matrix_power to the init file in lib/dispersion.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24335 | tlinnet | 2014-06-27 12:58:20 +0200 (Fri, 27 Jun 2014) | 3 lines

Deleted the printout in dep_check. The printouts are only used for the essential packages before calling sys.exit()

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24336 | tlinnet | 2014-06-27 12:58:22 +0200 (Fri, 27 Jun 2014) | 3 lines

Added to target function that experiment_type_setup() should not be initiated, if numpy.einsum is missing.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24337 | tlinnet | 2014-06-27 12:58:24 +0200 (Fri, 27 Jun 2014) | 8 lines

Added a numpy "out" argument check to dep_check.py.

This is for checking the out argument of:
numpy.multiply
numpy.add
numpy.subtract

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24338 | tlinnet | 2014-06-27 12:58:26 +0200 (Fri, 27 Jun 2014) | 10 lines

Added the missing "self.num_exp" to target function.

Testing on older system, this was failing the systemtest.
It is a wonder how these lines in __init__ could be performed without this?

self.end_index.append(self.num_exp * self.num_spins * self.num_frq)
if model in [MODEL_B14_FULL, MODEL_CR72_FULL, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL]:
self.end_index.append(2 * self.num_exp * self.num_spins * self.num_frq)

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24339 | tlinnet | 2014-06-27 12:58:29 +0200 (Fri, 27 Jun 2014) | 3 lines

Added a list of systemtests to skip, if numpy "out" argument is not available.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24340 | tlinnet | 2014-06-27 13:35:32 +0200 (Fri, 27 Jun 2014) | 6 lines

Fix for unit test passing on old numpy systems.

The error was:
ValueError: setting an array element with a sequence.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24341 | bugman | 2014-06-27 14:24:23 +0200 (Fri, 27 Jun 2014) | 5 lines

Expanded the dispersion target function class documentation.

The NE, NS, NM, NO, and ND notation is now explained.
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r24342 | bugman | 2014-06-27 14:27:27 +0200 (Fri, 27 Jun 2014) | 3 lines

Added Ti and NT to the dispersion target function class documentation.
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r24343 | bugman | 2014-06-27 14:52:08 +0200 (Fri, 27 Jun 2014) | 13 lines

Slight speed up of the 'B14' and 'B14 full' dispersion models by minimising repetitive maths.

Using the disp_profile_all.py script, the speed ups for these two models are:

100 single spins analysis:
B14: 3.944+/-0.032 -> 3.888+/-0.038, 1.014x faster.
B14 full: 4.037+/-0.040 -> 3.940+/-0.025, 1.025x faster.

Cluster of 100 spins analysis:
B14: 0.522+/-0.003 -> 0.507+/-0.008, 1.031x faster.
B14 full: 0.507+/-0.008 -> 0.487+/-0.007, 1.042x faster.
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r24347 | tlinnet | 2014-06-27 17:09:42 +0200 (Fri, 27 Jun 2014) | 3 lines

Initial try to write up a 2x2 matrix by closed form.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24348 | tlinnet | 2014-06-27 17:09:45 +0200 (Fri, 27 Jun 2014) | 3 lines

Made the validation check in profiling of marix_power check all values.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24349 | tlinnet | 2014-06-27 17:12:25 +0200 (Fri, 27 Jun 2014) | 3 lines

Replaced all self.spins with self.NS in target function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24350 | tlinnet | 2014-06-27 17:14:34 +0200 (Fri, 27 Jun 2014) | 3 lines

Replaced all self.num_exp with self.NE in target function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24351 | tlinnet | 2014-06-27 17:16:16 +0200 (Fri, 27 Jun 2014) | 3 lines

Replaced all self.num_frq with self.NM in target function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24353 | bugman | 2014-06-27 17:53:53 +0200 (Fri, 27 Jun 2014) | 18 lines

A very small speed up to the CR72 dispersion models by minimising repetitive maths operations.

The k_BA and k_AB rates are used to simplify the Psi calculation, dropping from 3 to 2
multiplications and removing a squaring operation. The Dpos and Dneg value calculations have been
simplified to drop one multiplication operation. And the calculation of eta_scale / cpmg_frqs now
only occurs once rather than twice.

Using the disp_profile_all.py script, the speed ups for these two models are:

100 single spins analysis:
CR72: 1.608+/-0.025 -> 1.552+/-0.028, 1.036x faster.
CR72 full: 1.795+/-0.043 -> 1.705+/-0.024, 1.053x faster.

Cluster of 100 spins analysis:
CR72: 0.109+/-0.001 -> 0.107+/-0.001, 1.026x faster.
CR72 full: 0.114+/-0.004 -> 0.110+/-0.001, 1.034x faster.
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r24357 | bugman | 2014-06-27 18:32:30 +0200 (Fri, 27 Jun 2014) | 5 lines

Removal of a tonne of unused imports in the lib.dispersion package.

These were identified using the command "pylint * --disable=all --enable=unused-import".
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r24360 | bugman | 2014-06-27 19:01:21 +0200 (Fri, 27 Jun 2014) | 12 lines

A very small speed up to the MMQ CR72 dispersion model by minimising repetitive maths operations.

This matches the recent change for the CR72 model (r24353), though the Psi calculation was already
using the fast form. Using the disp_profile_all.py script, the speed ups are:

100 single spins analysis:
MMQ CR72: 4.276+/-0.066 -> 4.230+/-0.089, 1.011x faster.

Cluster of 100 spins analysis:
MMQ CR72: 0.883+/-0.015 -> 0.862+/-0.010, 1.024x faster.
........

Merged revisions 24265-24266,24270-24278,24280-24283,24285-24308,24315,24319-24320 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_spin_speed

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r24265 | tlinnet | 2014-06-24 10:43:06 +0200 (Tue, 24 Jun 2014) | 3 lines

Modified profiling script for NS R1rho 3site, to be functional.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24266 | tlinnet | 2014-06-24 10:46:17 +0200 (Tue, 24 Jun 2014) | 3 lines

Modified profiling script for ns r1rho 3site linear to be functional.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24270 | tlinnet | 2014-06-24 11:15:43 +0200 (Tue, 24 Jun 2014) | 3 lines

Removed un-used imports in profiling scripts for NS r1rho 3site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24271 | bugman | 2014-06-24 13:46:59 +0200 (Tue, 24 Jun 2014) | 6 lines

Added a relaxation dispersion model profiling log file for relax version 3.1.3 vs. 3.1.2 vs. 3.1.1.

This is the output from the dispersion model profiling master script. It shows that there are no
major speed differences between these relax versions.
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r24272 | bugman | 2014-06-24 13:52:19 +0200 (Tue, 24 Jun 2014) | 5 lines

Added the system information printout to the dispersion model profiling master script output.

This is for the log files comparing one version of relax to the previous version.
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r24273 | tlinnet | 2014-06-24 14:17:59 +0200 (Tue, 24 Jun 2014) | 3 lines

Added profiling script for model mmq cr72,

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24274 | tlinnet | 2014-06-24 14:18:03 +0200 (Tue, 24 Jun 2014) | 5 lines

Fix for the replacement value for invalid values in model MMQ CR72.

The value was set to use r20, but should instead be 1e100.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24275 | tlinnet | 2014-06-24 14:20:31 +0200 (Tue, 24 Jun 2014) | 3 lines

Copied profiling script from mmq cr72, to ns mmq 2site and 3site.
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r24276 | tlinnet | 2014-06-24 14:22:23 +0200 (Tue, 24 Jun 2014) | 3 lines

Copied profiling script to ns mmq 3site linear.
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r24277 | tlinnet | 2014-06-24 14:32:23 +0200 (Tue, 24 Jun 2014) | 3 lines

Implemented profiling script for NS MMQ 2SITE.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24278 | tlinnet | 2014-06-24 14:46:29 +0200 (Tue, 24 Jun 2014) | 3 lines

Implemented profiling script for ns mmq 3site and 3site linear.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24280 | tlinnet | 2014-06-24 14:58:07 +0200 (Tue, 24 Jun 2014) | 3 lines

Speeded up model NS CPMG 2site star, by moving the forming of the propagator matrix out of the for loops, and preform it.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24281 | bugman | 2014-06-24 15:04:47 +0200 (Tue, 24 Jun 2014) | 6 lines

Added a relaxation dispersion model profiling log file for relax version 3.1.4 vs. 3.1.3.

This is the output from the dispersion model profiling master script. It shows that there are no
speed differences.
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r24282 | tlinnet | 2014-06-24 15:27:51 +0200 (Tue, 24 Jun 2014) | 3 lines

Speeded up ns mmq 2site, by moving the forming of evolution matrix out of the for loops, and preform it.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24283 | tlinnet | 2014-06-24 15:36:01 +0200 (Tue, 24 Jun 2014) | 3 lines

Speeded up ns mmq 3site, by moving the forming of evolution matrix out of the for loops, and preform it.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24285 | bugman | 2014-06-24 16:30:19 +0200 (Tue, 24 Jun 2014) | 6 lines

Added a relaxation dispersion model profiling log file for relax version 3.1.5 vs. 3.1.4.

This is the output from the dispersion model profiling master script. It shows that there are no
speed differences.
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r24286 | tlinnet | 2014-06-24 16:35:01 +0200 (Tue, 24 Jun 2014) | 3 lines

Speeded up ns r1rho 2site, by preforming the evolution matrices, and the M0 matrix in the init part of the target function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24287 | tlinnet | 2014-06-24 16:35:05 +0200 (Tue, 24 Jun 2014) | 3 lines

Speeded up ns r1rho 3site, by preforming the evolution matrices, and the M0 matrix in the init part of the target function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24288 | bugman | 2014-06-24 17:06:45 +0200 (Tue, 24 Jun 2014) | 6 lines

Expanded the dispersion model profiling master script to cover all the new profiling scripts.

This includes all 3-site and MMQ models. The list is now complete and covers all models. The only
model not included in 'M61 skew' which has redundant parameters and is not optimisable anyway.
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r24289 | bugman | 2014-06-24 17:47:53 +0200 (Tue, 24 Jun 2014) | 7 lines

Added a relaxation dispersion model profiling log file for relax version 3.1.6 vs. 3.1.5.

This is the output from the dispersion model profiling master script. It shows that there are
almost no speed differences, except for a slight decrease in speed in the 'CR72 full' model for
single spins.
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r24290 | tlinnet | 2014-06-25 02:14:22 +0200 (Wed, 25 Jun 2014) | 3 lines

Split systemtest test_tp02_data_to_ns_r1rho_2site into a setup and test part.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24291 | tlinnet | 2014-06-25 02:14:29 +0200 (Wed, 25 Jun 2014) | 3 lines

Implemented a clustered version of systemtest test_tp02_data_to_ns_r1rho_2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24292 | tlinnet | 2014-06-25 02:14:32 +0200 (Wed, 25 Jun 2014) | 6 lines

Inserted an extremely interesting development in NS R1rho 2site.

If one do a transpose of M0, one can calculate all the matrix evolutions in the start via numpy einsum.
Since M0 is in higher a dimensions, one should not do a numpy transpose, but swap/roll the outer M0 6x1 axis.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24293 | tlinnet | 2014-06-25 02:14:34 +0200 (Wed, 25 Jun 2014) | 5 lines

Shortened the code dramatically for NS R1rho 2site.

It is possible to calculate all in "one" go, after having the trasposer/rolled-back M0 magnetization.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24294 | tlinnet | 2014-06-25 02:14:36 +0200 (Wed, 25 Jun 2014) | 7 lines

Speeded up the code of NS r1rho 2site.

This was essential done to numpy einsum, and doing the dot operations in multiple dimensions.
It was though necessary to realize, that to do the proper dot product operations, the outer two
axis if M0 should be swapped, by rolling the outer axis one back.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24295 | tlinnet | 2014-06-25 02:14:38 +0200 (Wed, 25 Jun 2014) | 7 lines

Speeded up the code of NS r1rho 3site.

This was essential done to numpy einsum, and doing the dot operations in multiple dimensions.
It was though necessary to realize, that to do the proper dot product operations, the outer two
axis if M0 should be swapped, by rolling the outer axis one back.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24296 | tlinnet | 2014-06-25 02:14:40 +0200 (Wed, 25 Jun 2014) | 3 lines

Removed un-used import of rollaxis in ns r1rho 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24297 | tlinnet | 2014-06-25 02:14:42 +0200 (Wed, 25 Jun 2014) | 5 lines

For model NS CPMG 2site 3d, the M0 matrix was preformed for higher dimensionality in init of target function.

The transposes/rolled axis versions was also initiated.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24298 | tlinnet | 2014-06-25 02:14:43 +0200 (Wed, 25 Jun 2014) | 5 lines

Swapped the dot product position, when propagating the magnetisation in model NS CPMG 2site 3D.

This it to try to align to same method as in NS R1rho 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24299 | tlinnet | 2014-06-25 02:14:45 +0200 (Wed, 25 Jun 2014) | 3 lines

Lowered the looping in NS CPMG 2site 3D, by preforming the inital dot product.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24300 | tlinnet | 2014-06-25 02:14:46 +0200 (Wed, 25 Jun 2014) | 3 lines

Speeded up ns cpmg 2site 3d, by preforming the magnetisation.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24301 | tlinnet | 2014-06-25 02:14:48 +0200 (Wed, 25 Jun 2014) | 23 lines

Got rid of the inner evolution of the magnetization.

If the looping over the number of CPMG elements is given by the index l, and the initial magnetization has
been formed, then the number of times for propagation of magnetization is l = power_si_mi_di-1.
If the magnetization matrix "Mint" has the index Mint_(i,k) and the evolution matrix has the index Evol_(k,j), i=1, k=7, j=7
then the dot product is given by: Sum_{k=1}^{k} Mint_(1,k) * Evol_(k,j) = D_(1, j).
The numpy einsum formula for this would be: einsum('ik,kj -> ij', Mint, Evol)

Following evolution will be: Sum_{k=1}^{k} D_(1, j) * Evol_(k,j) = Mint_(1,k) * Evol_(k,j) * Evol_(k,j).
We can then realize, that the evolution matrix can be raised to the power l. Evol_P = Evol**l.
It will then be: einsum('ik,kj -> ij', Mint, Evol_P)

- Get which power to raise the matrix to.
l = power_si_mi_di-1

- Raise the square evolution matrix to the power l.
evolution_matrix_T_pwer_i = matrix_power(evolution_matrix_T_i, l)

Mint_T_i = dot(Mint_T_i, evolution_matrix_T_pwer_i)
or
Mint_T_i = einsum('ik,kj -> ij', Mint_T_i, evolution_matrix_T_pwer_i)

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24302 | tlinnet | 2014-06-25 02:14:50 +0200 (Wed, 25 Jun 2014) | 10 lines

Tried to implement using lib.linear_algebra.matrix_power.square_matrix_power instead of matrix_power from numpy in NS CPMG 2site 3d.

Strangely, then systemtest:
test_hansen_cpmg_data_to_ns_cpmg_2site_3D_full

starts to fail!

This is very weird.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24303 | tlinnet | 2014-06-25 02:14:52 +0200 (Wed, 25 Jun 2014) | 5 lines

Changes to unit test of NS CPMG 2site 3D.

This is after the new initiated M0 matrix in init of target function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24304 | tlinnet | 2014-06-25 03:41:00 +0200 (Wed, 25 Jun 2014) | 3 lines

Double speed in NS CPMG 2site star, after using numpy.linalg.matrix_power instead of the lib version in relax.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24305 | tlinnet | 2014-06-25 03:41:02 +0200 (Wed, 25 Jun 2014) | 3 lines

Triple speed in NS MMQ 2site, after using numpy.linalg.matrix_power instead of the lib version in relax.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24306 | tlinnet | 2014-06-25 03:41:04 +0200 (Wed, 25 Jun 2014) | 13 lines

Small fix for making sure that power is a integer in ns mmq 2site.

Following system tests was failing.
- Relax_disp.test_korzhnev_2005_15n_dq_data
- Relax_disp.test_korzhnev_2005_15n_sq_data
- Relax_disp.test_korzhnev_2005_15n_zq_data
- Relax_disp.test_korzhnev_2005_1h_sq_data
- Relax_disp.test_korzhnev_2005_all_data
- Relax_disp.test_korzhnev_2005_all_data_disp_speed_bug

They should already be integers, but is now solved.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24307 | tlinnet | 2014-06-25 03:41:05 +0200 (Wed, 25 Jun 2014) | 3 lines

Comment and spell fixing in NS CPMG 2site 3d.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24308 | tlinnet | 2014-06-25 03:41:07 +0200 (Wed, 25 Jun 2014) | 3 lines

Triple speed in NS MMQ 3site, after using numpy.linalg.matrix_power instead of the lib version in relax.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24315 | bugman | 2014-06-25 13:23:16 +0200 (Wed, 25 Jun 2014) | 9 lines

Updated the dispersion model profiling comparison of the disp_spin_speed branch vs. relax-3.2.2.

This is for the current revision r24314 and now includes all dispersion models. This shows the
large speed increases in the numeric and MMQ models recently obtained.

Note that something went wrong with the 'NS CPMG 2-site 3D full' model for the clustered analysis,
most times were around 24 seconds except for the first which was strangely 292 seconds.
........
r24319 | bugman | 2014-06-25 17:04:00 +0200 (Wed, 25 Jun 2014) | 7 lines

Updated the relaxation dispersion model profiling log file for relax version 3.2.2 vs. 3.2.1.

This adds the MMQ and 3-site models to the log file. The new information shows that there was a 4.2
times speed up for the 'MMQ CR72' model between these two relax versions, both for single spins and
clustered spins, a much greater improvement than any other of the models.
........
r24320 | bugman | 2014-06-25 17:08:54 +0200 (Wed, 25 Jun 2014) | 7 lines

Removed the now redundant disp_profile_all_3.2.2.table.txt dispersion model profiling table.

As the dispersion model profiling master script now covers all dispersion models, the output from
this script produces this table exactly. Therefore the end of the log files saved from running this
script contains this table.
........

Merged revisions 24091-24137,24140-24250,24252-24256,24258-24261 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_spin_speed

........
r24091 | tlinnet | 2014-06-18 15:44:58 +0200 (Wed, 18 Jun 2014) | 3 lines

Added DPL94 profiling script.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24092 | tlinnet | 2014-06-18 15:58:31 +0200 (Wed, 18 Jun 2014) | 5 lines

Modified profiling script for TSMK01, to use correct parameters k_AB and r20a.

Or else, the lib functions is just calculating with zero?

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24093 | tlinnet | 2014-06-18 16:03:46 +0200 (Wed, 18 Jun 2014) | 5 lines

Changes to profiling script of ns_cpmg_2site_expanded.

The model does not have r20a and r20b, but only r2.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24094 | tlinnet | 2014-06-18 16:07:10 +0200 (Wed, 18 Jun 2014) | 5 lines

Made changes to the profiling script of NS_CPMG_2SITE_3D.

Need to use the full model, when r2a and r2b is specified.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24095 | tlinnet | 2014-06-18 16:17:42 +0200 (Wed, 18 Jun 2014) | 5 lines

Changes to profiling script of ns expanded.

The unpacking can be removed.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24096 | tlinnet | 2014-06-18 16:33:46 +0200 (Wed, 18 Jun 2014) | 5 lines

Fix for the profiling script of NS cpmg 3D.

The model should also be speciffied to full.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24097 | bugman | 2014-06-18 16:39:53 +0200 (Wed, 18 Jun 2014) | 5 lines

The disp_profile_all.py super script now prints out the current relax version information.

This is so that the log files contain information about the repository revision and path.
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r24098 | tlinnet | 2014-06-18 16:44:12 +0200 (Wed, 18 Jun 2014) | 3 lines

Copied profiling script of DPL94 to ns r1rho 2site.
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r24099 | bugman | 2014-06-18 16:44:53 +0200 (Wed, 18 Jun 2014) | 3 lines

Improved the final printout from the disp_profile_all.py dispersion model super profiling script.
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r24100 | tlinnet | 2014-06-18 16:48:50 +0200 (Wed, 18 Jun 2014) | 3 lines

Added profiling script for NS R1rho 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24101 | bugman | 2014-06-18 16:57:40 +0200 (Wed, 18 Jun 2014) | 3 lines

The disp_profile_all.py dispersion model super profiling script is now executable.
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r24102 | bugman | 2014-06-18 17:02:56 +0200 (Wed, 18 Jun 2014) | 8 lines

Decreased all nr_iter values by 10 and added more dispersion models to the super profiling script.

This is for the dispersion model profiling scripts in test_suite/shared_data/dispersion/profiling/,
all controlled by the disp_profile_all.py super profiling script for generating statistics using all
of the other profiling scripts. The number of iterations needed to be decreased as otherwise it
would now take almost 1 day to generate the statistics table.
........
r24103 | tlinnet | 2014-06-18 17:11:24 +0200 (Wed, 18 Jun 2014) | 5 lines

Moved the Ãparter conversion in LM63 3site into the lib function.

This cleans up the target api function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24104 | tlinnet | 2014-06-18 17:12:50 +0200 (Wed, 18 Jun 2014) | 3 lines

Copied profiling script for DPL94 to TAP03.
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r24105 | tlinnet | 2014-06-18 17:13:47 +0200 (Wed, 18 Jun 2014) | 2 lines

Copied profiling script for DPL94 to TP02.
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r24106 | tlinnet | 2014-06-18 17:15:27 +0200 (Wed, 18 Jun 2014) | 2 lines

Copied profiling script for DPL94 to MP05.
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r24107 | tlinnet | 2014-06-18 17:16:24 +0200 (Wed, 18 Jun 2014) | 2 lines

Copied profiling script for DPL94 to M61.
........
r24108 | tlinnet | 2014-06-18 17:21:39 +0200 (Wed, 18 Jun 2014) | 3 lines

Modified profiling script for TAP03 to be used.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24109 | tlinnet | 2014-06-18 17:23:44 +0200 (Wed, 18 Jun 2014) | 3 lines

Modified profiling script for TP02, to be used.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24110 | tlinnet | 2014-06-18 17:27:54 +0200 (Wed, 18 Jun 2014) | 3 lines

Modified profiling script for MP05.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24111 | tlinnet | 2014-06-18 17:31:55 +0200 (Wed, 18 Jun 2014) | 5 lines

Modified profiling script for M61.

This is the last one.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24112 | bugman | 2014-06-18 17:38:42 +0200 (Wed, 18 Jun 2014) | 8 lines

Expansion of the disp_profile_all.py dispersion model super profiling scripts.

The newly added profiling scripts for models 'M61', 'TP02', 'TAP03', and 'MP05' are now included in
the super script to generate statistics for all of these as well. The nr_iter variable has also
been changed to match the other analytic models, so that the standard deviations are lowered and the
statistics are better.
........
r24113 | tlinnet | 2014-06-18 17:39:08 +0200 (Wed, 18 Jun 2014) | 3 lines

Moved the parameter conversion of MMQ CR72 into lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24114 | tlinnet | 2014-06-18 17:52:07 +0200 (Wed, 18 Jun 2014) | 3 lines

Moved the paramter conversions of k_AB, k_BA and pB into lib function of NS MMQ 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24115 | tlinnet | 2014-06-18 17:57:44 +0200 (Wed, 18 Jun 2014) | 3 lines

Moved the parameter conversion from target function to lib function for NS r1rho 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24116 | bugman | 2014-06-18 18:04:44 +0200 (Wed, 18 Jun 2014) | 10 lines

Updated the dispersion model speed statistics for the disp_spin_speed branch vs. relax-3.2.2.

This now includes the 'NS CPMG 2-site 3D', 'DPL94', and 'NS R1rho 2-site' dispersion models. The
timings for the single spin analyses are now comparable to the clustered analysis, as the equivalent
of 100 single spins is being used. The final printout is also in a better format to present for the
relax release messages.

These new results show the insane 160x speed up of the 'DPL94' model!
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r24117 | bugman | 2014-06-18 18:22:56 +0200 (Wed, 18 Jun 2014) | 5 lines

Alignment improvements for the final printout from the dispersion model super profiling script.

The log file has been updated with what the new formatting will look like.
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r24118 | bugman | 2014-06-18 18:34:54 +0200 (Wed, 18 Jun 2014) | 6 lines

Updated the model names in the dispersion model super profiling script.

The 'CR72', 'B14' and 'NS CPMG 2-site 3D' models are the full, slower versions rather than the
faster models with R20 = R20A = R20B. The log file has been updated to match.
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r24119 | tlinnet | 2014-06-18 18:52:37 +0200 (Wed, 18 Jun 2014) | 3 lines

Moved the parameter conversion for ns mmq 3site into lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24120 | bugman | 2014-06-18 18:54:41 +0200 (Wed, 18 Jun 2014) | 6 lines

Updated the dispersion model profiling comparison of the disp_spin_speed branch vs. relax-3.2.2.

The 'M61', 'TP02', 'TAP03', and 'MP05' models are now included. The final printout has been
manually updated to reflect the newest version of the disp_profile_all.py super profiling script.
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r24121 | tlinnet | 2014-06-18 19:01:24 +0200 (Wed, 18 Jun 2014) | 3 lines

Moved the parameter conversion for r1rho 3site into lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24122 | tlinnet | 2014-06-18 19:03:08 +0200 (Wed, 18 Jun 2014) | 3 lines

Copied profiling script for CR72, so there is now a normal and a full version.
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r24123 | tlinnet | 2014-06-18 19:04:01 +0200 (Wed, 18 Jun 2014) | 3 lines

Copied profiling for b14 to normal and full model.
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r24124 | bugman | 2014-06-18 19:08:51 +0200 (Wed, 18 Jun 2014) | 9 lines

Created a text file suitable for use as part of the relax release notes.

This contains the statistically averaged profiling information of the speed of the dispersion models
in the disp_spin_speed branch vs. relax-3.2.2. This file has been created so that it can be used as
part of the release notes for the version of relax that contains the insane speed ups of this
branch. This file will be updated as new models are profiled and if any more speed ups magically
appear.
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r24125 | tlinnet | 2014-06-18 19:10:13 +0200 (Wed, 18 Jun 2014) | 2 lines

Copied profiling script for cpmg 3D.
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r24126 | tlinnet | 2014-06-18 19:11:10 +0200 (Wed, 18 Jun 2014) | 2 lines

Copied profiling script for ns cpmg star.
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r24127 | tlinnet | 2014-06-18 19:12:12 +0200 (Wed, 18 Jun 2014) | 2 lines

copied profiling script for no rex.
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r24128 | tlinnet | 2014-06-18 19:15:19 +0200 (Wed, 18 Jun 2014) | 3 lines

Modified profiling script for B14, to R20A=R20B.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24129 | tlinnet | 2014-06-18 19:20:19 +0200 (Wed, 18 Jun 2014) | 3 lines

Removal of junk, and replacing func.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24130 | tlinnet | 2014-06-18 19:20:21 +0200 (Wed, 18 Jun 2014) | 3 lines

Removal of junk from profiling script.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24131 | tlinnet | 2014-06-18 19:25:29 +0200 (Wed, 18 Jun 2014) | 2 lines

Removal of junk for profiling script CR72 full.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24132 | tlinnet | 2014-06-18 19:25:31 +0200 (Wed, 18 Jun 2014) | 3 lines

Removal of junk from profiling script CR72 and making it work.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24133 | tlinnet | 2014-06-18 19:29:28 +0200 (Wed, 18 Jun 2014) | 3 lines

Removal of junk, and implementing NO REX profiling script.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24134 | tlinnet | 2014-06-18 19:32:18 +0200 (Wed, 18 Jun 2014) | 3 lines

Implemented profiling script for NS CPMG 2site 3D.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24135 | tlinnet | 2014-06-18 19:36:48 +0200 (Wed, 18 Jun 2014) | 3 lines

Implemented profiling script for NS CPMG STAR and STAR FULL.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24136 | tlinnet | 2014-06-18 19:39:44 +0200 (Wed, 18 Jun 2014) | 2 lines

Copied profiling script to be used for LM63.
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r24137 | tlinnet | 2014-06-18 19:41:27 +0200 (Wed, 18 Jun 2014) | 3 lines

Copied profiling script to model IT99.
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r24140 | tlinnet | 2014-06-18 20:17:26 +0200 (Wed, 18 Jun 2014) | 3 lines

Added profiling script for IT99.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24141 | tlinnet | 2014-06-18 20:17:29 +0200 (Wed, 18 Jun 2014) | 3 lines

Implemented profiling script for LM63.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24142 | tlinnet | 2014-06-18 20:22:02 +0200 (Wed, 18 Jun 2014) | 3 lines

Moved the "eta_scale = 2.0**(-3.0/2.0)" out of lib function for mmq cr72, since this is only needs to be computed once.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24143 | tlinnet | 2014-06-18 20:23:51 +0200 (Wed, 18 Jun 2014) | 3 lines

Spell fix in code for ns cpmg 2site expanded.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24144 | tlinnet | 2014-06-18 20:28:05 +0200 (Wed, 18 Jun 2014) | 3 lines

Fix for missing comments.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24145 | tlinnet | 2014-06-18 20:32:40 +0200 (Wed, 18 Jun 2014) | 3 lines

Fix for spaces aroung "=" outside functions.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24146 | tlinnet | 2014-06-18 20:41:35 +0200 (Wed, 18 Jun 2014) | 3 lines

Critical fix for wrong space inserted in ns mmq 3site mq.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24147 | tlinnet | 2014-06-18 20:41:37 +0200 (Wed, 18 Jun 2014) | 5 lines

Fixed the input for unit test of mmq cr72.

The number of input parameters has been lowered.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24148 | tlinnet | 2014-06-18 20:50:32 +0200 (Wed, 18 Jun 2014) | 5 lines

Added additional math domain checking in B14.

This is when v1c is less than 1.0.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24149 | tlinnet | 2014-06-18 20:58:39 +0200 (Wed, 18 Jun 2014) | 3 lines

Comment fixing, for explaining the masking and replacing when dw is zeroÃ.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24150 | tlinnet | 2014-06-18 21:02:57 +0200 (Wed, 18 Jun 2014) | 3 lines

Copied profiling script to be used for profiling the use of higher dimensional data for the numpy eig function.
........
r24151 | tlinnet | 2014-06-19 17:41:41 +0200 (Thu, 19 Jun 2014) | 3 lines

Implemented the collection of the 3D exchange matrix, for rank [NE][NS][NM][NO][ND][7][7].

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24152 | tlinnet | 2014-06-19 17:41:45 +0200 (Thu, 19 Jun 2014) | 5 lines

Implemented test, to see if 3D exchange matrixes are the same.

This can be tested while running systemtest test_hansen_cpmg_data_to_ns_cpmg_2site_3D.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24153 | tlinnet | 2014-06-19 17:41:49 +0200 (Thu, 19 Jun 2014) | 3 lines

Shifted the computation of Rexpo two loops up.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24154 | tlinnet | 2014-06-19 17:41:51 +0200 (Thu, 19 Jun 2014) | 3 lines

Added intermediate step with for loops.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24155 | tlinnet | 2014-06-19 17:41:55 +0200 (Thu, 19 Jun 2014) | 3 lines

Added another intermediate step.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24156 | tlinnet | 2014-06-19 17:41:59 +0200 (Thu, 19 Jun 2014) | 5 lines

Added function to compute the matrix exponential for higher dimensional data of shape [NE][NS][NM][NO][ND][7][7].

This is done by using numpy.einsum, to make the dot product of the last two axis.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24157 | tlinnet | 2014-06-19 17:42:02 +0200 (Thu, 19 Jun 2014) | 7 lines

Inserted intermediate step, to check if the matrix propagator to evolve the magnetization is equal
when done for lower dimensional data of shape [7][7] and higher dimensional data of shape [NE][NS][NM][NO][ND][7][7].

A short example is shown at the wiki:
http://wiki.nmr-relax.com/Numpy_linalg#Ellipsis_broadcasting_in_numpy.einsum

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24158 | tlinnet | 2014-06-19 17:42:05 +0200 (Thu, 19 Jun 2014) | 35 lines

Implemented double speed of model NS CPMG 2site 3D:

This is done by moving the costly calculation of the matrix exponential out of the for loops.
The trick was to find a method to do dot product of higher dimensions.
Thiw was done with numpy.einsum:
Example at:
http://wiki.nmr-relax.com/Numpy_linalg#Ellipsis_broadcasting_in_numpy.einsum

Example:
dot_V_W = einsum('...ij,...jk', V, W_exp_diag)
Where V, and W_exp_diag has shape: [NE][NS][NM][NO][ND][7][7]

The profiling script shows a 2X speed up.

----BEFORE:
SINGLE
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 18.811 18.811 <string>:1(<module>)
1 0.002 0.002 18.811 18.811 pf_3d:407(single)
CLUSTER
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 18.315 18.315 <string>:1(<module>)
1 0.001 0.001 18.315 18.315 pf_3d:431(cluster)

-----AFTER:
SINGLE
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 8.818 8.818 <string>:1(<module>)
1 0.002 0.002 8.818 8.818 pf_3d:407(single)
CLUSTER
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 9.082 9.082 <string>:1(<module>)
1 0.001 0.001 9.082 9.082 pf_3d:431(cluster)

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24159 | tlinnet | 2014-06-19 17:42:14 +0200 (Thu, 19 Jun 2014) | 3 lines

Made notation consistent for variables, using "_i" to clarify extracted data from matrix.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24160 | tlinnet | 2014-06-19 17:42:16 +0200 (Thu, 19 Jun 2014) | 13 lines

Moved the calculation the evolution matrix out of for loops.

The trick is that numpy.einsum allows for dot product of higher dimension:

- The the essential evolution matrix.
- This is a dot product of the outer [7][7] matrix of the Rexpo_mat and r180x_mat matrixes, which
- have the shape [NE][NS][NM][NO][ND][7][7].
- This can be achieved by using numpy einsum, and where ellipsis notation will use the last axis.
evolution_matrix_mat = einsum('...ij,...jk', Rexpo_mat, r180x_mat)
evolution_matrix_mat = einsum('...ij,...jk', evolution_matrix_mat, Rexpo_mat)
evolution_matrix_mat = einsum('...ij,...jk', evolution_matrix_mat, evolution_matrix_mat)

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24161 | tlinnet | 2014-06-19 17:42:20 +0200 (Thu, 19 Jun 2014) | 5 lines

Implemeted systemtest: test_cpmg_synthetic_b14_to_ns3d_cluster

This is to cathc failures of the model, when data is clusted.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24162 | tlinnet | 2014-06-19 17:42:23 +0200 (Thu, 19 Jun 2014) | 3 lines

Removed unused variables in NS CPMG 2site 3D, to clean up the code.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24163 | tlinnet | 2014-06-19 17:42:25 +0200 (Thu, 19 Jun 2014) | 6 lines

Replaced the inner dot product with numpy einsum.

This though slows it down from 8.5 s to 13 s.
This is only as an intermediate step, how to figure to dot product inner parts of the big matrix.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24164 | tlinnet | 2014-06-19 17:42:28 +0200 (Thu, 19 Jun 2014) | 3 lines

Changed back from einsum to dot method, since dot method it faster for square matrixes.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24165 | tlinnet | 2014-06-19 20:17:47 +0200 (Thu, 19 Jun 2014) | 3 lines

Added the ns matrice, rr1rho_3d_rankN, to collect the multi dimensional 3D exchange matrix, of rank [NE][NS][NM][NO][ND][6][6].

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24166 | tlinnet | 2014-06-19 20:17:49 +0200 (Thu, 19 Jun 2014) | 6 lines

Added a check in lib/dispersion/ns_r1hro_2site.py, to see if the newly created multidimensional
ns matrix of rank NE][NS][NM][NO][ND][6][6], is equal to the previous [6][6] matrix.

It is.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24167 | tlinnet | 2014-06-19 20:52:49 +0200 (Thu, 19 Jun 2014) | 5 lines

Added the relax_time to collection of rr1rho_3d_rankN matrix collection.

This is to pre-multiply all elements with the time.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24168 | tlinnet | 2014-06-19 20:52:51 +0200 (Thu, 19 Jun 2014) | 5 lines

Added a check, that the pre- relax_time multiplied multidimensional array, equal the previous.

It does, to the sum of 1.0e-13.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24169 | tlinnet | 2014-06-19 20:52:53 +0200 (Thu, 19 Jun 2014) | 6 lines

Made the function use the new multidimensional R_mat matrix.

Systemtest: test_tp02_data_to_ns_r1rho_2site
still passes.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24170 | tlinnet | 2014-06-19 20:52:55 +0200 (Thu, 19 Jun 2014) | 6 lines

Fix to the matrix_exponential_rankN, to return the exact exponential for any higher dimensional square matrix
of shape [NE][NS][NM][NO][ND][X][X].

The fix was to the eye(X), to make the shape the same as the input shape.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24171 | tlinnet | 2014-06-19 20:52:57 +0200 (Thu, 19 Jun 2014) | 26 lines

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.
........
r24172 | tlinnet | 2014-06-19 21:05:49 +0200 (Thu, 19 Jun 2014) | 3 lines

Made the returned multidimensional rr1rho_3d_rankN, be of float64 type.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24173 | tlinnet | 2014-06-19 21:05:51 +0200 (Thu, 19 Jun 2014) | 3 lines

Cleaned up the code of NS R1rho 2site, and removed the matrix argument to the function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24174 | tlinnet | 2014-06-19 21:05:53 +0200 (Thu, 19 Jun 2014) | 3 lines

Removed the parsing of a matrix to the lib function of NS R1rho 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24175 | tlinnet | 2014-06-20 08:11:47 +0200 (Fri, 20 Jun 2014) | 3 lines

Added the function "rcpmg_star_rankN" for the collection of the multidimensional relaxation matrix for model NS CPMG 2site star.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24176 | tlinnet | 2014-06-20 08:11:49 +0200 (Fri, 20 Jun 2014) | 5 lines

Insert check, that the newly created multidimensional matrix is the same.

They are, but only to the fifth digit.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24177 | tlinnet | 2014-06-20 08:11:51 +0200 (Fri, 20 Jun 2014) | 5 lines

Started using the newly created multidimensional matrix.

test_hansen_cpmg_data_to_ns_cpmg_2site_star

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24178 | tlinnet | 2014-06-20 08:11:53 +0200 (Fri, 20 Jun 2014) | 4 lines

Added the systemtest: test_cpmg_synthetic_b14_to_ns_star_cluster, to check
for the model is still working after change.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24179 | tlinnet | 2014-06-20 08:11:55 +0200 (Fri, 20 Jun 2014) | 59 lines

Started using the newly cR2 variable, extracted from higher dimensional data.

This should be okay, but systemtest test_hansen_cpmg_data_to_ns_cpmg_2site_star, now fails:

Optimised parameter values:
r2 (SQ CPMG - 500.00000000 MHz) 4.998935658499767
r2 (SQ CPMG - 800.00000000 MHz) 6.898256259440341
dw 2.092924953509931
pA 0.986716058519642
kex 2438.044235414625746

Optimised parameters:

Parameter Value (:70) Value (:71)
R2 (500 MHz) 6.95812598916492 4.99893565849977
R2 (800 MHz) 9.39656319607375 6.89825625944034
pA 0.989701272773474 0.986716058519642
dw 5.67316761415756 2.09292495350993
kex 1713.67781672744 2438.04423541463
chi2 52.510693756237 15.1644902423334

F
======================================================================
FAIL: test_hansen_cpmg_data_to_ns_cpmg_2site_star (test_suite.system_tests.relax_disp.Relax_disp)
Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 2-site star' dispersion model.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/tlinnet/software/disp_spin_speed/test_suite/system_tests/relax_disp.py", line 3211, in test_hansen_cpmg_data_to_ns_cpmg_2site_star
self.assertAlmostEqual(spin71.pA, 0.992258541625787, 2)
AssertionError: 0.98671605851964195 != 0.992258541625787 within 2 places

---------------
Compared to systemtest:
It seems that there has been "problems" with residue 71 before.

# Checks for residue :70.
self.assertAlmostEqual(spin70.r2[r20_key1], 6.95543947938561, 1)
self.assertAlmostEqual(spin70.r2[r20_key2], 9.38991914134929, 1)
self.assertAlmostEqual(spin70.pA, 0.989702750971153, 3)
self.assertAlmostEqual(spin70.dw, 5.67527122494516, 1)
self.assertAlmostEqual(spin70.kex/1000, 1715.72032391817/1000, 1)
self.assertAlmostEqual(spin70.chi2, 52.5011991483842, 1)

# Checks for residue :71.
self.assertAlmostEqual(spin71.r2[r20_key1], 4.992594256544, 1)
self.assertAlmostEqual(spin71.pA, 0.992258541625787, 2)
self.assertAlmostEqual(spin71.dw/100, 2.75140650899058/100, 2)
self.assertAlmostEqual(spin71.kex/100000, 2106.60885247431/100000, 2)
self.assertAlmostEqual(spin71.chi2/100, 17.3293856656588/100, 1)

# Test the conversion to k_AB from kex and pA.
self.assertEqual(spin70.k_AB, spin70.kex * (1.0 - spin70.pA))
self.assertEqual(spin71.k_AB, spin71.kex * (1.0 - spin71.pA))

# Test the conversion to k_BA from kex and pA.
self.assertEqual(spin70.k_BA, spin70.kex * spin70.pA)
self.assertEqual(spin71.k_BA, spin71.kex * spin71.pA)

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24180 | tlinnet | 2014-06-20 08:11:57 +0200 (Fri, 20 Jun 2014) | 5 lines

Changes of values to systemtest test_hansen_cpmg_data_to_ns_cpmg_2site_star.

The values are changed, since chi2 is lower than before.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24181 | tlinnet | 2014-06-20 08:19:17 +0200 (Fri, 20 Jun 2014) | 3 lines

Moved the costly finding of matrix exponential out of for loops for eR_tcp.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24182 | tlinnet | 2014-06-20 08:19:20 +0200 (Fri, 20 Jun 2014) | 3 lines

Rearranged the code, to properly show the nested matrix exponentials in dot functions.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24183 | tlinnet | 2014-06-20 08:29:42 +0200 (Fri, 20 Jun 2014) | 3 lines

Moved the costly matrix_exponential of cR2 out of for loops.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24184 | tlinnet | 2014-06-20 08:29:44 +0200 (Fri, 20 Jun 2014) | 3 lines

Rearranged the dot code, for better view.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24185 | tlinnet | 2014-06-20 08:29:46 +0200 (Fri, 20 Jun 2014) | 3 lines

Cleaned up the code in model NS CPMG 2site star.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24186 | tlinnet | 2014-06-20 08:37:29 +0200 (Fri, 20 Jun 2014) | 5 lines

Simplified model CPMG 2site 3D.

The expansion of matrixes to higher dimensionality is not neccessary.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24187 | tlinnet | 2014-06-20 08:48:56 +0200 (Fri, 20 Jun 2014) | 3 lines

Further cleaned up the code in NS CPMG 2site start.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24188 | tlinnet | 2014-06-20 08:53:30 +0200 (Fri, 20 Jun 2014) | 5 lines

Removed input of matrix, Rr, Rex, RCS and R to model NS CPMG 2site star.

These matrixes is now extracted from ns matrix function rcpmg_star_rankN.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24189 | tlinnet | 2014-06-20 09:18:00 +0200 (Fri, 20 Jun 2014) | 6 lines

Implemented the collection of the multidimensional matrix m1 and m2 in model ns mmq 2site.

Inserted also a check, that the newly computed matrix is equal.
They are, to the 6 digit.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24190 | tlinnet | 2014-06-20 09:38:26 +0200 (Fri, 20 Jun 2014) | 3 lines

Started using the newly created multidimensional m1 and m2 matrixes.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24191 | tlinnet | 2014-06-20 09:38:30 +0200 (Fri, 20 Jun 2014) | 3 lines

Moved the costly calculation of matrix_exponential of M1 and M2 out of for loop, in model ns_mmq_2site_mq.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24192 | tlinnet | 2014-06-20 09:38:33 +0200 (Fri, 20 Jun 2014) | 3 lines

Made the function matrix_exponential_rankN also find the exponential if the experiments indices are missing.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24193 | tlinnet | 2014-06-20 09:52:13 +0200 (Fri, 20 Jun 2014) | 5 lines

Fix for an extra axis inserted in eye function, when dimensionality is only [NS][NM][NO][ND].

This also fixes the index in the lib function of ns_mmq_2site_mq.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24194 | tlinnet | 2014-06-20 10:54:01 +0200 (Fri, 20 Jun 2014) | 12 lines

Implemented same functionality in mmq_2site_sq_dq_zq.

Problem, following system test fails!
test_korzhnev_2005_15n_dq_data
test_korzhnev_2005_15n_mq_data
test_korzhnev_2005_15n_sq_data
test_korzhnev_2005_1h_mq_data
test_korzhnev_2005_1h_sq_data
test_korzhnev_2005_all_data
test_korzhnev_2005_all_data_disp_speed_bug

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24195 | tlinnet | 2014-06-20 10:54:04 +0200 (Fri, 20 Jun 2014) | 7 lines

Removed grid search, and lowered number of iterations for systemtest:
test_cpmg_synthetic_b14_to_ns3d_cluster
test_cpmg_synthetic_b14_to_ns_star_cluster

This is to speed them up, since they before took 30 seks.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24196 | tlinnet | 2014-06-20 10:54:06 +0200 (Fri, 20 Jun 2014) | 34 lines

Fix for ns_mmq_2site_mq.

Variable was wrong called.
There seems to be a serious problem more with mq.

test_korzhnev_2005_15n_dq_data
self.assertAlmostEqual(spin.r2[r20_key3], 13.6153887849344, 2)
AssertionError: 13.624172993315323 != 13.6153887849344 within 2 places

test_korzhnev_2005_15n_mq_data
self.assertAlmostEqual(spin.r2[r20_key1], 6.02016436619016, 1)
AssertionError: 0.00032836499986468263 != 6.02016436619016 within 1 places

test_korzhnev_2005_15n_sq_data
self.assertAlmostEqual(spin.kex/1000, 433.176323890829849/1000, 3)
AssertionError: 0.42987451018414946 != 0.43317632389082983 within 3 places

test_korzhnev_2005_1h_mq_data
self.assertAlmostEqual(spin.r2[r20_key2], 0.039223196112941, 2)
AssertionError: 0.033056489136372089 != 0.039223196112941 within 2 places

test_korzhnev_2005_1h_sq_data
self.assertAlmostEqual(spin.chi2, 50.3431330819767, 1)
AssertionError: 50.400683622209989 != 50.3431330819767 within 1 places

test_korzhnev_2005_all_data
self.assertAlmostEqual(spin.r2[r20_key1], 6.67288025927458, 4)
AssertionError: 6.7044178906652689 != 6.67288025927458 within 4 places

test_korzhnev_2005_all_data_disp_speed_bug
self.assertAlmostEqual(spin.chi2/1000, 162.511988511609/1000, 3)
AssertionError: 0.49707952193522587 != 0.162511988511609 within 3 places

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24197 | tlinnet | 2014-06-20 10:54:07 +0200 (Fri, 20 Jun 2014) | 6 lines

Reinserted old code.

This fixes:
test_korzhnev_2005_15n_mq_data

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24198 | tlinnet | 2014-06-20 11:39:04 +0200 (Fri, 20 Jun 2014) | 10 lines

Forcing the dtype to be complex64, instead of complex128.

This solves a range of systemtests.
The one who fails now is:

-test_korzhnev_2005_15n_zq_data
-test_korzhnev_2005_1h_mq_data
-test_korzhnev_2005_1h_sq_data

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24199 | tlinnet | 2014-06-20 12:00:12 +0200 (Fri, 20 Jun 2014) | 7 lines

Forces complex64 in ns_mmq_2site_sq_dq_zq instead complex128.

This fixes systemtests:
- test_korzhnev_2005_15n_zq_data
- test_korzhnev_2005_1h_sq_data

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24200 | tlinnet | 2014-06-20 12:00:15 +0200 (Fri, 20 Jun 2014) | 8 lines

Force complex64 in ns_mmq_2site_mq.

This solves all systemtests.

Forcing to be complex64, does not seems like a long standing solution, since
complex128 is possible.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24201 | tlinnet | 2014-06-20 12:00:18 +0200 (Fri, 20 Jun 2014) | 17 lines

Fix for using the old matrix_exponential of m1.

Onye:
- test_korzhnev_2005_15n_sq_data

Is still failing.
That still uses the matrix_exponential_rankN.

There seems to be a problem with matrix_exponential_rankN, when doing
complex numbers.

Maybe the dtype has to get fixed?
Use it as a input argument?

It must be the einsum

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24202 | tlinnet | 2014-06-20 15:22:16 +0200 (Fri, 20 Jun 2014) | 6 lines

Added the "dtype" argument to function matrix_exponential_rankN.

This is to force the conversion of dtype, if they are of other type.
This can be conversion from complex128 to complex64.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24203 | tlinnet | 2014-06-20 15:22:18 +0200 (Fri, 20 Jun 2014) | 8 lines

Fix the bug: "M2_i = M1_mat", which was causing the problems getting systemtests to pass.

Removed the specifications of which dtype, the initial matrices are created.
They can be converted later, with the specification of dtype to matrix_exponential_rankN().

All systemtests now pass.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24204 | tlinnet | 2014-06-20 15:22:19 +0200 (Fri, 20 Jun 2014) | 5 lines

Moved the Bloch-McConnell matrix for 2-site exchange into lib/dispersion/ns_matrices.py.

This is for consistency with the other code.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24205 | tlinnet | 2014-06-20 15:22:21 +0200 (Fri, 20 Jun 2014) | 3 lines

Moved the matrices for Bloch-McConnell from lib ns_mmq_2site, since they are now defined in ns_matrices.py

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24206 | tlinnet | 2014-06-20 15:48:33 +0200 (Fri, 20 Jun 2014) | 3 lines

Code cleanup and copyright adding to lib/dispersion/ns_matrices.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24207 | tlinnet | 2014-06-20 15:48:35 +0200 (Fri, 20 Jun 2014) | 5 lines

Moved the Bloch-McConnell matrix for 3-site exchange, into the lib/dispersion/ns_matrices.py.

This is to standard the code.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24208 | tlinnet | 2014-06-20 17:42:48 +0200 (Fri, 20 Jun 2014) | 3 lines

Removed m1 and m2 to be sent to lib function of ns mmq 2site, since they are now populated inside the lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24209 | tlinnet | 2014-06-20 17:42:51 +0200 (Fri, 20 Jun 2014) | 3 lines

Implemented the Bloch-McConnell matrix for 3-site exchange, for multidimensional data.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24210 | tlinnet | 2014-06-20 17:42:53 +0200 (Fri, 20 Jun 2014) | 5 lines

Inserted a check, that the new higher dimensional m1 and m2 matrixes are equal to before.

They are, to the 5 digit.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24211 | tlinnet | 2014-06-20 17:42:54 +0200 (Fri, 20 Jun 2014) | 3 lines

Started using the newly created highher dimensional Bloch-McConnell matrix for 3-site exchange.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24212 | tlinnet | 2014-06-20 17:42:56 +0200 (Fri, 20 Jun 2014) | 3 lines

Moved the calculation of the matrix exponential out of for loops for ns mmq 3site mq.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24213 | tlinnet | 2014-06-20 17:42:58 +0200 (Fri, 20 Jun 2014) | 3 lines

Converted ns mmq 3site/sq/dq/zq to calculte the matrix exponential out of the for loops.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24214 | tlinnet | 2014-06-20 17:43:00 +0200 (Fri, 20 Jun 2014) | 3 lines

Removed the complex64 to be used as dtype in matrix exponential. Fix for missing "_i" in variable.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24215 | tlinnet | 2014-06-20 17:54:32 +0200 (Fri, 20 Jun 2014) | 5 lines

Removed m1 and m2 to be sent to target function of ns_mmq_3site_chi2.

They are now populated inside the lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24216 | tlinnet | 2014-06-20 17:54:33 +0200 (Fri, 20 Jun 2014) | 3 lines

Documentation and input fix for ns mmq 2site. The m1 and m2 matrices are populated inside the lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24217 | tlinnet | 2014-06-20 19:13:14 +0200 (Fri, 20 Jun 2014) | 3 lines

Renamed some numerical matrices, to get consistency in naming.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24218 | tlinnet | 2014-06-20 19:13:16 +0200 (Fri, 20 Jun 2014) | 3 lines

Implemented multidimensional r1rho 3d 3site 3D exchange matrix.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24219 | tlinnet | 2014-06-20 19:13:18 +0200 (Fri, 20 Jun 2014) | 5 lines

Inserted check, that newly multi dimensional matrix is equal the old.

It is, to the 13 digit.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24220 | tlinnet | 2014-06-20 19:44:00 +0200 (Fri, 20 Jun 2014) | 3 lines

Started using the newly multidimensional 3D exchange matrix.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24221 | tlinnet | 2014-06-20 19:44:02 +0200 (Fri, 20 Jun 2014) | 3 lines

Moved the calculation of the matrix exponential out of the for loops for ns r1rho 3site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24222 | tlinnet | 2014-06-20 19:44:03 +0200 (Fri, 20 Jun 2014) | 3 lines

Removed the parameter "matrix" to be send to lib function of ns r1rho 3site, since it is now populated inside the lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24223 | tlinnet | 2014-06-20 19:44:05 +0200 (Fri, 20 Jun 2014) | 3 lines

Moved parameter conversion for ns r1rho 3site inside lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24224 | tlinnet | 2014-06-20 20:03:25 +0200 (Fri, 20 Jun 2014) | 3 lines

Cleaned up the Dispersion class target function, for creation of matrices, which is now populated inside the lib functions instead.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24225 | tlinnet | 2014-06-20 20:03:27 +0200 (Fri, 20 Jun 2014) | 3 lines

Removed pA and pB from the matrice population function rcpmg_star_rankN, since they are not used.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24226 | tlinnet | 2014-06-20 20:03:28 +0200 (Fri, 20 Jun 2014) | 3 lines

Removed pA and pB from the matrice population function rr1rho_3d_2site_rankN, since they are not used.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24227 | tlinnet | 2014-06-20 20:03:30 +0200 (Fri, 20 Jun 2014) | 5 lines

Documentation fix for the dimensionality for model ns r1rho 2site.

The data is lined up to be of form [NE][NS][NM][NO][ND].

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24228 | tlinnet | 2014-06-20 20:07:16 +0200 (Fri, 20 Jun 2014) | 3 lines

Removed pA, pB and pC from the matrice population function rr1rho_3d_3site_rankN, since they are not used.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24229 | tlinnet | 2014-06-21 08:42:41 +0200 (Sat, 21 Jun 2014) | 5 lines

Deleted the profiling of eig function profiling script.

This was never implemented.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24230 | tlinnet | 2014-06-21 08:42:45 +0200 (Sat, 21 Jun 2014) | 6 lines

For all profiling scripts, added conversion to numpy array for CPMG frqs and spin_lock, since some models complained in 3.2.2, that
they were of list types.

Also fixed IT99 to only have 1 spin, since clustering is broken in 3.2.2.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24231 | tlinnet | 2014-06-21 08:42:47 +0200 (Sat, 21 Jun 2014) | 6 lines

Modified super profiling script, to allow input to script, where alternative version of relax is positioned.
Collected the variables in a list of lists, for better overview.

Added a print out comment to IT99, to remember the bug.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24232 | tlinnet | 2014-06-21 09:50:09 +0200 (Sat, 21 Jun 2014) | 3 lines

Added comment field to super profiling script.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24233 | tlinnet | 2014-06-21 10:21:27 +0200 (Sat, 21 Jun 2014) | 8 lines

Math domain fix for ns cpmg 2site expanded.

This is when t108 or t112 is zero, in the multidimensional array, a division error occurs.
The elements are first set to 1.0, to allow for computation.
Then elements are later replaced with 1e100.
Lastly, if the elements are not part of the "True" dispersion point structure, they are cleaned out.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24234 | tlinnet | 2014-06-21 10:21:29 +0200 (Sat, 21 Jun 2014) | 6 lines

Precission lowering of systemtest, test_korzhnev_2005_15n_sq_data and test_korzhnev_2005_1h_sq_data.

The systemtests does not fail on Linux 64 bit system, but only on Mac 32 bit system.
This is due to floating error deviations.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24235 | tlinnet | 2014-06-22 22:11:57 +0200 (Sun, 22 Jun 2014) | 3 lines

Added log files for super profiling against tags 3.2.1 and 3.2.2.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24236 | tlinnet | 2014-06-23 11:14:29 +0200 (Mon, 23 Jun 2014) | 5 lines

Copied lib.linear_algebra.matrix_exponential to lib.dispersion.matrix_exponential.

The matrix exponential of higher dimensional data is only used in the dispersion part of relax.
........
r24237 | tlinnet | 2014-06-23 13:04:16 +0200 (Mon, 23 Jun 2014) | 3 lines

Added to __init__, the new lib.dispersion.matrix_exponential module.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24238 | tlinnet | 2014-06-23 13:04:18 +0200 (Mon, 23 Jun 2014) | 3 lines

Added to unit_tests/_lib/_dispersion/__init__.py, the new unit test file: test_matrix_exponential.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24239 | tlinnet | 2014-06-23 13:04:20 +0200 (Mon, 23 Jun 2014) | 7 lines

Added numpy array save files.

They are the numpy array structures, which are send in from systemtest: Relax_disp.test_hansen_cpmg_data_to_ns_cpmg_2site_3D.

These numpy array structures, are used in unit tests.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24240 | tlinnet | 2014-06-23 13:04:22 +0200 (Mon, 23 Jun 2014) | 9 lines

Added unit test unit_tests/_lib/_dispersion/test_matrix_exponential.py to test the matrix exponential from higher dimensional data.

- lib.dispersion.matrix_exponential.matrix_exponential_rankN
will match against
- lib.linear_algebra.matrix_exponential.

Data which is used for comparison, comes from system test: Relax_disp.test_hansen_cpmg_data_to_ns_cpmg_2site_3D.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24241 | tlinnet | 2014-06-23 14:09:24 +0200 (Mon, 23 Jun 2014) | 3 lines

Renamed function to return data in unit test _lib/_dispersion/test_matrix_exponential.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24242 | tlinnet | 2014-06-23 14:09:26 +0200 (Mon, 23 Jun 2014) | 3 lines

Fix to lib/dispersion/matrix_exponential.py, since the svn copy command was used on non-updated version of the file.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24243 | tlinnet | 2014-06-23 14:09:27 +0200 (Mon, 23 Jun 2014) | 5 lines

Added unit test for doing the matrix exponential for complex data.

This test shows, that the dtype=complex64, should be removed from lib/dispersion/ns_mmq_2site.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24244 | tlinnet | 2014-06-23 14:09:29 +0200 (Mon, 23 Jun 2014) | 3 lines

Added data for unit test for the testing of the matrix_exponential_rankN.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24245 | bugman | 2014-06-23 14:14:15 +0200 (Mon, 23 Jun 2014) | 7 lines

Expanded the dispersion profiling master script to handle any two relax versions.

To compare two relax versions, for example 3.2.2 to 3.2.1, either the path1 and path2 variables or
two command line arguments can be supplied. The first path should be for the newest version. This
will allow for comparing the speed differences between multiple relax versions in the future.
........
r24246 | bugman | 2014-06-23 14:15:00 +0200 (Mon, 23 Jun 2014) | 3 lines

Added Troels Linnet to the copyright notice of the dispersion model master profiling script.
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r24247 | tlinnet | 2014-06-23 14:48:04 +0200 (Mon, 23 Jun 2014) | 3 lines

Split matrix_exponential_rankN into matrix_exponential_rank_NE_NS_NM_NO_ND_x_x and matrix_exponential_rank_NS_NM_NO_ND_x_x.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24248 | tlinnet | 2014-06-23 15:45:27 +0200 (Mon, 23 Jun 2014) | 3 lines

Moved numerical solution matrices into the corresponding lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24249 | tlinnet | 2014-06-23 15:58:59 +0200 (Mon, 23 Jun 2014) | 3 lines

Copied profiling scripts, to be used for 3site models and mmq models.
........
r24250 | tlinnet | 2014-06-23 16:23:31 +0200 (Mon, 23 Jun 2014) | 3 lines

Implemented profiling script for LM63, 3 site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24252 | bugman | 2014-06-23 16:42:48 +0200 (Mon, 23 Jun 2014) | 5 lines

Improved the relax version printouts for the dispersion model master profiling script.

This now reports both relax versions.
........
r24253 | bugman | 2014-06-23 16:55:06 +0200 (Mon, 23 Jun 2014) | 5 lines

Fix for a mistake introduced in the previous commit (r24252).

The printout of copied files was incorrect.
........
r24254 | bugman | 2014-06-23 17:37:54 +0200 (Mon, 23 Jun 2014) | 8 lines

Removed a tonne of unused imports from the dispersion model profiling scripts.

This is to allow most of the scripts to run on the relax 3.1.x versions, as well as to clean up the
scripts. The unused imports were found using the command:

pylint test_suite/shared_data/dispersion/profiling/*.py --disable=all --enable=unused-import
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r24255 | bugman | 2014-06-23 19:41:29 +0200 (Mon, 23 Jun 2014) | 8 lines

Added a relaxation dispersion model profiling log file for relax version 3.2.1 vs. 3.2.0.

This is the output from the dispersion model profiling master script. It shows a 2.2 times increase
in speed for the B14 and B14 full models, with all other models remaining at the same speed. This
matches the changes for relax 3.2.1 (https://gna.org/forum/forum.php?forum_id=2462), the main
feature of which is a major bugfix for the B14 models.
........
r24256 | bugman | 2014-06-23 19:55:20 +0200 (Mon, 23 Jun 2014) | 5 lines

The 'relax -v' command is now used for the dispersion model profiling script initial printout.

This is to show the two different relax versions being compared.
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r24258 | bugman | 2014-06-24 09:28:02 +0200 (Tue, 24 Jun 2014) | 13 lines

Modifications to the dispersion model profiling master script.

The info.print_sys_info() function of the current relax version is being called at the start to show
all information about the current system. This is useful to know the speed of the machine, the OS,
the Python version and numpy version. The numpy version is important as future versions might
optimise certain functions that are currently very slow, hence that could be a cause of model speed
differences.

In addition, the path variables path1 and path2 have been renamed to path_new and path_old to make
it clearer which is which. And the individual profiling scripts are no longer copied to the base
directory of the relax versions being compared, and are run in place.
........
r24259 | bugman | 2014-06-24 09:34:34 +0200 (Tue, 24 Jun 2014) | 9 lines

Added a relaxation dispersion model profiling log file for relax version 3.2.2 vs. 3.2.1.

This is the output from the dispersion model profiling master script. It shows that the relax 3.2.2
release did not in fact feature "a large speed up of all analytic relaxation dispersion models" as
described in the release notes at https://gna.org/forum/forum.php?forum_id=2465. For the CPMG
models there is a 1 to 2 times increase in speed. But for the R1rho models, there is a 1 to 2 times
decrease in speed.
........
r24260 | bugman | 2014-06-24 09:36:36 +0200 (Tue, 24 Jun 2014) | 6 lines

Added a relaxation dispersion model profiling log file for relax version 3.2.0 vs. 3.1.7.

This is the output from the dispersion model profiling master script. It shows that there are no
speed differences.
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r24261 | bugman | 2014-06-24 09:36:47 +0200 (Tue, 24 Jun 2014) | 6 lines

Added a relaxation dispersion model profiling log file for relax version 3.1.7 vs. 3.1.6.

This is the output from the dispersion model profiling master script. It shows that there are no
speed differences.
........

Merged revisions 24059-24082,24084-24089 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_spin_speed

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r24059 | tlinnet | 2014-06-17 20:26:37 +0200 (Tue, 17 Jun 2014) | 3 lines

Implemented target function for LM63 3site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24060 | tlinnet | 2014-06-17 20:26:39 +0200 (Tue, 17 Jun 2014) | 3 lines

Implemented the lib function for LM63 3site, for higher dimensional data.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24061 | tlinnet | 2014-06-17 20:26:41 +0200 (Tue, 17 Jun 2014) | 4 lines

Removed the number of disp points in target function for LM63 3site, since it is no Ãlonger used,
but have been replaced with mask replacements.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24062 | tlinnet | 2014-06-18 09:25:45 +0200 (Wed, 18 Jun 2014) | 6 lines

Implemented class function in target class, to return back_calc values as list of lists.

This is the back and forth conversion between the data structures implemented when gathering the data,
and the data send to the library function of higher dimensionality.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24063 | tlinnet | 2014-06-18 09:25:48 +0200 (Wed, 18 Jun 2014) | 3 lines

Used the new class function: get_back_calc(), to get the data in the right structures when interpolating for graphs.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24064 | tlinnet | 2014-06-18 09:25:49 +0200 (Wed, 18 Jun 2014) | 3 lines

Removed superfluous check, after the returned data is now in right structure.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24065 | tlinnet | 2014-06-18 09:41:11 +0200 (Wed, 18 Jun 2014) | 9 lines

Made changes to the dir argument of systemtest Relax_disp.test_r1rho_kjaergaard.

This is to prepare for:
sr #3124 (https://gna.org/support/?3124): Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff
sr #3138 (https://gna.org/support/?3138): Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1]

This is also to test an expected bug, if R1 is not loaded.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24066 | bugman | 2014-06-18 10:12:07 +0200 (Wed, 18 Jun 2014) | 5 lines

The relaxation dispersion target function can now be set up when the optional frqs_H argument is None.

This allows the profiling scripts to run.
........
r24067 | bugman | 2014-06-18 10:12:35 +0200 (Wed, 18 Jun 2014) | 3 lines

Typo fix from the previous commit.
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r24068 | bugman | 2014-06-18 10:14:44 +0200 (Wed, 18 Jun 2014) | 5 lines

More stability fixes for the relaxation dispersion target function initialisation.

The target function can now be initialised when the r1 and chemical_shift arguments are None.
........
r24069 | tlinnet | 2014-06-18 10:29:56 +0200 (Wed, 18 Jun 2014) | 3 lines

Split the systemtest test_r1rho_kjaergaard into a setup function, and a test function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24070 | tlinnet | 2014-06-18 10:30:00 +0200 (Wed, 18 Jun 2014) | 5 lines

Renamed systemtes test_r1rho_kjaergaard to test_r1rho_kjaergaard_auto.

This corresponds to the use of the automatic analysis method.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24071 | tlinnet | 2014-06-18 10:30:02 +0200 (Wed, 18 Jun 2014) | 5 lines

Split systemtest test_r1rho_kjaergaard into test_r1rho_kjaergaard_auto and test_r1rho_kjaergaard_man.

This is to test use of the manual way to analyse.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24072 | bugman | 2014-06-18 10:34:26 +0200 (Wed, 18 Jun 2014) | 8 lines

Modified all of Troels' dispersion profiling scripts to work with older relax versions.

This is in preparation for obtaining some powerful timing statistics. The calls to the r2eff_*()
functions are unnecessary and are the only failure point in the scripts between the current code in
the disp_spin_speed branch and trunk or older versions of relax. So these function calls have been
eliminated.
........
r24073 | tlinnet | 2014-06-18 10:35:42 +0200 (Wed, 18 Jun 2014) | 5 lines

Implemented systemtest test_r1rho_kjaergaard_missing_r1, for safety check if R1 data is not loaded.

The systemtest passes, so target function is safe.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24074 | bugman | 2014-06-18 10:38:16 +0200 (Wed, 18 Jun 2014) | 6 lines

Python 3 support for the dispersion profiling scripts.

The xrange() builtin function does not exist in Python 3, so this is now aliased to range() which is
the same thing.
........
r24075 | tlinnet | 2014-06-18 10:44:04 +0200 (Wed, 18 Jun 2014) | 3 lines

Replaced double or triple hash-tags "##" with single hash-tags "#".

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24076 | tlinnet | 2014-06-18 10:49:10 +0200 (Wed, 18 Jun 2014) | 3 lines

Copyright fixes for all the models, where Troels E. Linnet have made changes to make them functional for higher dimensional data.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24077 | tlinnet | 2014-06-18 10:50:36 +0200 (Wed, 18 Jun 2014) | 5 lines

Copyright fix for model TSMFK01.

Sebastien Morin did not take part of implementing the TSMK01 modelÃ.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24078 | bugman | 2014-06-18 11:31:35 +0200 (Wed, 18 Jun 2014) | 11 lines

Created a super script for profiling the relaxation dispersion models.

This script will execute all of the current profiling scripts in the directory
test_suite/shared_data/dispersion/profiling for both the current version of relax and any other
specified version (current set to the 3.2.2 relax tag). It will run the scripts and relax versions
interleaved N=10 times and extract the func_*() target function call profile timings. This
interleaving makes the numbers much more consistent. Averages and standard deviations are then
calculated, as well as the speed up between the two relax versions. The results are printed out in
a format suitable for the relax release messages.
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r24079 | bugman | 2014-06-18 11:32:33 +0200 (Wed, 18 Jun 2014) | 6 lines

Increased the number of iterations to 1000 in all of the profiling scripts.

This is for better statistics in the disp_profile_all.py script, and makes the number consistent
between the different models.
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r24080 | bugman | 2014-06-18 11:34:03 +0200 (Wed, 18 Jun 2014) | 5 lines

Added a log file for comparing the speed of the disp_speed_branch to relax 3.2.2.

This is from the disp_profile_all.py statistics generating script.
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r24081 | tlinnet | 2014-06-18 11:37:12 +0200 (Wed, 18 Jun 2014) | 3 lines

Made the processor.return_object get the back_calc structure in the expected order.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24082 | bugman | 2014-06-18 11:39:47 +0200 (Wed, 18 Jun 2014) | 5 lines

Fixed the ordering of the relax versions in the dispersion super profiling script disp_profile_all.py.

This has also been fixed in the disp_spin_speed branch to relax 3.2.2 comparison log.
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r24084 | bugman | 2014-06-18 12:06:56 +0200 (Wed, 18 Jun 2014) | 5 lines

Added a log file for comparing the speed of the disp_speed_branch to relax 3.2.1.

This is from the disp_profile_all.py statistics generating script.
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r24085 | bugman | 2014-06-18 14:09:48 +0200 (Wed, 18 Jun 2014) | 7 lines

Added a profiling script for the 'NS CPMG 2-site expanded' dispersion model.

This is the model at http://wiki.nmr-relax.com/NS_CPMG_2-site_expanded. The script was copied from
that of the CR72 model, and it only needed to be changed in a few places. This is the first numeric
model profiling script.
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r24086 | bugman | 2014-06-18 14:48:01 +0200 (Wed, 18 Jun 2014) | 7 lines

Updated the profiling super script and log for the 'NS CPMG 2-site expanded' model.

This is the model at http://wiki.nmr-relax.com/NS_CPMG_2-site_expanded. This shows that the single
spin calculation is 1.8 times faster, and the cluster of 100 11.7 times faster, when compared to
relax 3.2.2.
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r24087 | bugman | 2014-06-18 15:18:50 +0200 (Wed, 18 Jun 2014) | 9 lines

Modified all of the dispersion model profiling scripts.

The single() function for timing the single spin target function speed has been modified to include
a second outer loop over 100 'spins'. This means that the timing numbers are equivalent to the
cluster timings, as both are then over 100 spins. This now allows not only relax version
differences and model differences to be compared, but also the non-clustered and clustered analysis
speeds.
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r24088 | bugman | 2014-06-18 15:20:11 +0200 (Wed, 18 Jun 2014) | 6 lines

Added a script for profiling the 'NS CPMG 2-site 3D' relaxation dispersion model.

This is the model at http://wiki.nmr-relax.com/NS_CPMG_2-site_3D. Again this only involved copying
one of the other scripts and modifying a few variable and function names.
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r24089 | bugman | 2014-06-18 15:22:21 +0200 (Wed, 18 Jun 2014) | 6 lines

Added the 'NS CPMG 2-site 3D' model to the dispersion super profiling script.

To handle the fact that this script has nr_iter set to 100 rather than 1000 (as otherwise it is too
slow), a list of scaling factors has been created to scale all timing numbers to equivalent values.
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Merged revisions 24038-24039,24041-24042,24053-24057 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_spin_speed

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r24038 | tlinnet | 2014-06-17 15:08:26 +0200 (Tue, 17 Jun 2014) | 5 lines

Documentation fix for the initial data structure of cpmg_frqs, spin_lock_nu1, r1.

They were incorrect.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24039 | tlinnet | 2014-06-17 15:49:54 +0200 (Tue, 17 Jun 2014) | 3 lines

Fix for shortening the variables names.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24041 | tlinnet | 2014-06-17 16:51:45 +0200 (Tue, 17 Jun 2014) | 5 lines

First attempt to implement target function for ns_r1rho_2site.

But it does not work yet.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24042 | tlinnet | 2014-06-17 16:51:47 +0200 (Tue, 17 Jun 2014) | 5 lines

First attempt to implement lib function for ns r1rho 2site.

But it does not work yet.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24053 | tlinnet | 2014-06-17 19:04:51 +0200 (Tue, 17 Jun 2014) | 3 lines

Fatal fix for calling inv_relax_time from relax_time variable.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24054 | tlinnet | 2014-06-17 19:08:19 +0200 (Tue, 17 Jun 2014) | 3 lines

Removal of the temporary offset argument.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24055 | tlinnet | 2014-06-17 19:11:07 +0200 (Tue, 17 Jun 2014) | 3 lines

Documentation fix for the dimensionality of the input arrays.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24056 | tlinnet | 2014-06-17 19:27:10 +0200 (Tue, 17 Jun 2014) | 3 lines

Implemented the target function for ns r1rho 3site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24057 | tlinnet | 2014-06-17 19:27:12 +0200 (Tue, 17 Jun 2014) | 3 lines

Implemented the lib function for ns r1rho 3site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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Merged revisions 24018-24019,24022-24023,24026-24027,24032-24036 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/disp_spin_speed

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r24018 | tlinnet | 2014-06-17 11:56:43 +0200 (Tue, 17 Jun 2014) | 5 lines

Fix for systemtest: test_korzhnev_2005_all_data

The masking for replacing values was wrong.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24019 | tlinnet | 2014-06-17 11:56:45 +0200 (Tue, 17 Jun 2014) | 3 lines

Moved the cleaning of data points and replacing of values of out loop for model ns mmq 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24022 | tlinnet | 2014-06-17 12:20:12 +0200 (Tue, 17 Jun 2014) | 6 lines

Fix for structure cleaning and value replacing for model mmq CR72.

System test: test_korzhnev_2005_all_data
revealed how this should be done properly.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24023 | tlinnet | 2014-06-17 12:20:15 +0200 (Tue, 17 Jun 2014) | 5 lines

Fix for systemtest test_korzhnev_2005_all_data_disp_speed_bug.

The precision is lowered, and now matches the original systemtest.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24026 | tlinnet | 2014-06-17 13:07:40 +0200 (Tue, 17 Jun 2014) | 3 lines

Replaced index to numpy array from example [0][si][mi][oi] to [0, si, mi, oi].

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24027 | tlinnet | 2014-06-17 13:07:42 +0200 (Tue, 17 Jun 2014) | 3 lines

More replacing of numpy index.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24032 | tlinnet | 2014-06-17 14:53:47 +0200 (Tue, 17 Jun 2014) | 3 lines

Documentation fix, where a double bracket "[[" has been copied into all lib functions.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24033 | tlinnet | 2014-06-17 14:53:49 +0200 (Tue, 17 Jun 2014) | 3 lines

More fixes for numpy index in lib functions.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24034 | tlinnet | 2014-06-17 14:53:50 +0200 (Tue, 17 Jun 2014) | 3 lines

Restructured target function for ns mmq 3site to the new API structure of higher dimensional data.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24035 | tlinnet | 2014-06-17 14:53:52 +0200 (Tue, 17 Jun 2014) | 3 lines

Reorded the lib function for ns mmq 3site to use higher dimensional data.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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r24036 | tlinnet | 2014-06-17 14:53:54 +0200 (Tue, 17 Jun 2014) | 3 lines

Documentation fix for which dimensionality number of points have.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
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