Author: bugman
Date: Tue Jul 22 19:13:10 2014
New Revision: 24660
URL: http://svn.gna.org/viewcvs/relax?rev=24660&view=rev
Log:
Merged revisions 24059-24082,24084-24089 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/disp_spin_speed
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
Added:
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all.py
- copied, changed from r24082,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all.py
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.2.1.log
- copied unchanged from r24089,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.2.1.log
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.2.2.log
- copied, changed from r24082,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.2.2.log
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py
- copied unchanged from r24089,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py
- copied unchanged from r24089,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py
Modified:
trunk/ (props changed)
trunk/lib/dispersion/cr72.py
trunk/lib/dispersion/dpl94.py
trunk/lib/dispersion/it99.py
trunk/lib/dispersion/lm63.py
trunk/lib/dispersion/lm63_3site.py
trunk/lib/dispersion/m61.py
trunk/lib/dispersion/m61b.py
trunk/lib/dispersion/mmq_cr72.py
trunk/lib/dispersion/mp05.py
trunk/lib/dispersion/ns_cpmg_2site_3d.py
trunk/lib/dispersion/ns_cpmg_2site_expanded.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/lib/dispersion/tap03.py
trunk/lib/dispersion/tp02.py
trunk/lib/dispersion/tsmfk01.py
trunk/specific_analyses/relax_disp/data.py
trunk/specific_analyses/relax_disp/optimisation.py
trunk/target_functions/relax_disp.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_b14.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_cr72.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_dpl94.py
trunk/test_suite/shared_data/dispersion/profiling/profiling_tsmfk01.py
trunk/test_suite/system_tests/relax_disp.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/lib/dispersion/cr72.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/cr72.py?rev=24660&r1=24659&r2=24660&view=diff
Modified: trunk/lib/dispersion/dpl94.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/dpl94.py?rev=24660&r1=24659&r2=24660&view=diff
Modified: trunk/lib/dispersion/it99.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/it99.py?rev=24660&r1=24659&r2=24660&view=diff
Modified: trunk/lib/dispersion/lm63.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/lm63.py?rev=24660&r1=24659&r2=24660&view=diff
Modified: trunk/lib/dispersion/lm63_3site.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/lm63_3site.py?rev=24660&r1=24659&r2=24660&view=diff
Modified: trunk/lib/dispersion/m61.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/m61.py?rev=24660&r1=24659&r2=24660&view=diff
Modified: trunk/lib/dispersion/m61b.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/m61b.py?rev=24660&r1=24659&r2=24660&view=diff
Modified: trunk/lib/dispersion/mmq_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/mmq_cr72.py?rev=24660&r1=24659&r2=24660&view=diff
Modified: trunk/lib/dispersion/mp05.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/mp05.py?rev=24660&r1=24659&r2=24660&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=24660&r1=24659&r2=24660&view=diff
Modified: trunk/lib/dispersion/ns_cpmg_2site_expanded.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_cpmg_2site_expanded.py?rev=24660&r1=24659&r2=24660&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=24660&r1=24659&r2=24660&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=24660&r1=24659&r2=24660&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=24660&r1=24659&r2=24660&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=24660&r1=24659&r2=24660&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=24660&r1=24659&r2=24660&view=diff
Modified: trunk/lib/dispersion/tap03.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/tap03.py?rev=24660&r1=24659&r2=24660&view=diff
Modified: trunk/lib/dispersion/tp02.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/tp02.py?rev=24660&r1=24659&r2=24660&view=diff
Modified: trunk/lib/dispersion/tsmfk01.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/tsmfk01.py?rev=24660&r1=24659&r2=24660&view=diff
Modified: trunk/specific_analyses/relax_disp/data.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/data.py?rev=24660&r1=24659&r2=24660&view=diff
Modified: trunk/specific_analyses/relax_disp/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/optimisation.py?rev=24660&r1=24659&r2=24660&view=diff
Modified: trunk/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp.py?rev=24660&r1=24659&r2=24660&view=diff
Copied: trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all.py
(from r24082,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all.py?p2=trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all.py&p1=branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all.py&r1=24082&r2=24660&rev=24660&view=diff
Copied:
trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.2.2.log
(from r24082,
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.2.2.log)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.2.2.log?p2=trunk/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.2.2.log&p1=branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_all_3.2.2.log&r1=24082&r2=24660&rev=24660&view=diff
Modified: trunk/test_suite/shared_data/dispersion/profiling/profiling_b14.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/profiling/profiling_b14.py?rev=24660&r1=24659&r2=24660&view=diff
Modified: trunk/test_suite/shared_data/dispersion/profiling/profiling_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/profiling/profiling_cr72.py?rev=24660&r1=24659&r2=24660&view=diff
Modified: trunk/test_suite/shared_data/dispersion/profiling/profiling_dpl94.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/profiling/profiling_dpl94.py?rev=24660&r1=24659&r2=24660&view=diff
Modified:
trunk/test_suite/shared_data/dispersion/profiling/profiling_tsmfk01.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/profiling/profiling_tsmfk01.py?rev=24660&r1=24659&r2=24660&view=diff
Modified: trunk/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=24660&r1=24659&r2=24660&view=diff
r24660 - in /trunk: ./ lib/dispersion/ specific_analyses/relax_disp/ target_functions/ test_suite/shared_data/dispersion/pro...