Author: bugman
Date: Tue Jul 22 19:17:43 2014
New Revision: 24661
URL: http://svn.gna.org/viewcvs/relax?rev=24661&view=rev
Log:
Merged revisions 24091-24137,24140-24250,24252-24256,24258-24261 via svnmerge
from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/disp_spin_speed
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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].
[... 1069 lines stripped ...]
r24661 - in /trunk: ./ lib/dispersion/ lib/linear_algebra/ target_functions/ test_suite/shared_data/dispersion/profiling/ te...