Author: bugman
Date: Tue Jul 22 19:21:35 2014
New Revision: 24662
URL: http://svn.gna.org/viewcvs/relax?rev=24662&view=rev
Log:
Merged revisions
24265-24266,24270-24278,24280-24283,24285-24308,24315,24319-24320 via
svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/disp_spin_speed
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
r24276 | tlinnet | 2014-06-24 14:22:23 +0200 (Tue, 24 Jun 2014) | 3 lines
Copied profiling script to ns mmq 3site linear.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
Added:
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.1.2_vs_3.1.1.log
- copied unchanged from r24320,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.1.2_vs_3.1.1.log
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.1.3_vs_3.1.2.log
- copied unchanged from r24320,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.1.3_vs_3.1.2.log
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.1.4_vs_3.1.3.log
- copied unchanged from r24320,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.1.4_vs_3.1.3.log
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.1.5_vs_3.1.4.log
- copied unchanged from r24320,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.1.5_vs_3.1.4.log
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.1.6_vs_3.1.5.log
- copied unchanged from r24320,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.1.6_vs_3.1.5.log
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_2site.py
- copied unchanged from r24320,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_2site.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_3site.py
- copied unchanged from r24320,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_3site.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_3site_linear.py
- copied unchanged from r24320,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_3site_linear.py
Removed:
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.2.2.table.txt
Modified:
trunk/ (props changed)
trunk/lib/dispersion/mmq_cr72.py
trunk/lib/dispersion/ns_cpmg_2site_3d.py
trunk/lib/dispersion/ns_cpmg_2site_star.py
trunk/lib/dispersion/ns_mmq_2site.py
trunk/lib/dispersion/ns_mmq_3site.py
trunk/lib/dispersion/ns_r1rho_2site.py
trunk/lib/dispersion/ns_r1rho_3site.py
trunk/target_functions/relax_disp.py
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all.py
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.1.7_vs_3.1.6.log
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.2.1_vs_3.2.0.log
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.2.2.log
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.2.2_vs_3.2.1.log
trunk/test_suite/shared_data/dispersion/profiling/profiling_mmq_cr72.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site_linear.py
trunk/test_suite/system_tests/relax_disp.py
trunk/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_3d.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/lib/dispersion/mmq_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/mmq_cr72.py?rev=24662&r1=24661&r2=24662&view=diff
Modified: trunk/lib/dispersion/ns_cpmg_2site_3d.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_cpmg_2site_3d.py?rev=24662&r1=24661&r2=24662&view=diff
Modified: trunk/lib/dispersion/ns_cpmg_2site_star.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_cpmg_2site_star.py?rev=24662&r1=24661&r2=24662&view=diff
Modified: trunk/lib/dispersion/ns_mmq_2site.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_mmq_2site.py?rev=24662&r1=24661&r2=24662&view=diff
Modified: trunk/lib/dispersion/ns_mmq_3site.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_mmq_3site.py?rev=24662&r1=24661&r2=24662&view=diff
Modified: trunk/lib/dispersion/ns_r1rho_2site.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_r1rho_2site.py?rev=24662&r1=24661&r2=24662&view=diff
Modified: trunk/lib/dispersion/ns_r1rho_3site.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_r1rho_3site.py?rev=24662&r1=24661&r2=24662&view=diff
Modified: trunk/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp.py?rev=24662&r1=24661&r2=24662&view=diff
Modified:
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all.py
[... 32 lines stripped ...]
r24662 - in /trunk: ./ lib/dispersion/ target_functions/ test_suite/shared_data/dispersion/profiling/ test_suite/system_test...