Author: bugman
Date: Thu May 29 13:46:48 2014
New Revision: 23591
URL: http://svn.gna.org/viewcvs/relax?rev=23591&view=rev
Log:
Merged revisions 23216-23229 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/disp_speed
........
r23216 | tlinnet | 2014-05-18 23:36:14 +0200 (Sun, 18 May 2014) | 13 lines
Huge speed-up for model CR72.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Systemtest Relax_disp.test_cpmg_synthetic_cr72_full_noise_cluster
changes from 7 seconds to 4.5 seconds.
This is won by not checking single values in the R2eff array for math domain
errors, but calculating all steps, and in one single round check for finite
values.
If just one non-finite value is found, the whole array is returned with a
large
penalty of 1e100.
This makes all calculations be the fastest numpy array way.
........
r23217 | tlinnet | 2014-05-18 23:36:17 +0200 (Sun, 18 May 2014) | 12 lines
Fix for systemtest test_cpmg_synthetic_dx_map_points.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is after commit 23216:
The systemtest uses: GRID_INC = None, which have found to be catastrophic:
https://gna.org/bugs/?22032.
Commit 23216 fixed this, and now the found minimization point is much much
better.
Start:
0.8 3.92 0.39964
End:
0.76982 3.9169 0.41353
........
r23218 | tlinnet | 2014-05-19 00:51:15 +0200 (Mon, 19 May 2014) | 9 lines
Critical fixes for systemtest:
Relax_disp.test_hansen_cpmg_data_missing_auto_analysis.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This was found necessary after commit 23216.
It is suspected that when relax have touched boundary values which made
math domain errors, the error cathing have created local minima or
interfered with the simplex search algorithm.
........
r23219 | tlinnet | 2014-05-19 00:51:18 +0200 (Mon, 19 May 2014) | 10 lines
Speed-up of model TSMFK01.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
This is won by not checking single values in the R2eff array for math domain
errors, but calculating all steps, and in one single round check for finite
values.
If just one non-finite value is found, the whole array is returned with a
large
penalty of 1e100.
This makes all calculations be the fastest numpy array way.
........
r23220 | tlinnet | 2014-05-19 00:51:20 +0200 (Mon, 19 May 2014) | 18 lines
Huge speed-up of model B14.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Time test for systemtests:
test_baldwin_synthetic
2.626s -> 1.990s
test_baldwin_synthetic_full
18.326s -> 13.742s
This is won by not checking single values in the R2eff array for math domain
errors, but calculating all steps, and in one single round check for finite
values.
If just one non-finite value is found, the whole array is returned with a
large
penalty of 1e100.
This makes all calculations be the fastest numpy array way.
........
r23221 | tlinnet | 2014-05-19 01:19:02 +0200 (Mon, 19 May 2014) | 20 lines
Speed-up of model TP02.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
The change for running systemtest is:
test_curve_type_r1rho_fixed_time
0.057s -> 0.049s
test_tp02_data_to_ns_r1rho_2site
10.539s -> 10.456s
test_tp02_data_to_tp02
8.608s -> 5.727s
This is won by not checking single values in the R1rho array for math domain
errors, but calculating all steps, and in one single round check for finite
values.
If just one non-finite value is found, the whole array is returned with a
large
penalty of 1e100.
This makes all calculations be the fastest numpy array way.
........
r23222 | tlinnet | 2014-05-19 03:20:43 +0200 (Mon, 19 May 2014) | 14 lines
Huge speed-up for model TAP03.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
The change for running systemtest is:
test_tp02_data_to_tap03
13.869s -> 7.263s
This is won by not checking single values in the R1rho array for math domain
errors, but calculating all steps, and in one single round check for finite
values.
If just one non-finite value is found, the whole array is returned with a
large
penalty of 1e100.
This makes all calculations be the fastest numpy array way.
........
r23223 | tlinnet | 2014-05-19 03:20:46 +0200 (Mon, 19 May 2014) | 8 lines
Speed-up of model MP05.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
The change in systemtest is:
test_tp02_data_to_mp05
10.750s -> 6.644s
........
r23224 | tlinnet | 2014-05-19 03:20:47 +0200 (Mon, 19 May 2014) | 7 lines
Speed-up of model MMQ CR72.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Change in systemtest:
test_sprangers_data_to_mmq_cr72
9.892s -> 4.121s
........
r23225 | tlinnet | 2014-05-19 03:20:49 +0200 (Mon, 19 May 2014) | 7 lines
Speed-up for model M61.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Change in speed is:
test_m61_data_to_m61
6.692s -> 3.480s
........
r23226 | tlinnet | 2014-05-19 03:20:51 +0200 (Mon, 19 May 2014) | 13 lines
Speed-up of model LM63.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Change in systemtest was:
test_hansen_cpmg_data_auto_analysis
13.731s -> 9.971s
test_hansen_cpmg_data_auto_analysis_r2eff
13.370s -> 9.510s
test_hansen_cpmg_data_to_lm63
3.254s -> 2.080s
........
r23227 | tlinnet | 2014-05-19 03:20:53 +0200 (Mon, 19 May 2014) | 10 lines
Speed-up of model IT99.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Change in speed is:
test_hansen_cpmg_data_auto_analysis
9.74s -> 8.330s
test_hansen_cpmg_data_to_it99
4.928s -> 3.138s
........
r23228 | tlinnet | 2014-05-19 03:20:54 +0200 (Mon, 19 May 2014) | 3 lines
Added missing imports of "numpy.array".
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
........
r23229 | tlinnet | 2014-05-19 03:20:56 +0200 (Mon, 19 May 2014) | 8 lines
Speed-up of model DPL94.
task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Change in speed is:
test_dpl94_data_to_dpl94
19.412s -> 4.427s
........
Modified:
trunk/ (props changed)
trunk/lib/dispersion/b14.py
trunk/lib/dispersion/cr72.py
trunk/lib/dispersion/dpl94.py
trunk/lib/dispersion/it99.py
trunk/lib/dispersion/lm63.py
trunk/lib/dispersion/m61.py
trunk/lib/dispersion/mmq_cr72.py
trunk/lib/dispersion/mp05.py
trunk/lib/dispersion/tap03.py
trunk/lib/dispersion/tp02.py
trunk/lib/dispersion/tsmfk01.py
trunk/test_suite/system_tests/relax_disp.py
trunk/test_suite/system_tests/scripts/relax_disp/hansen_data_missing.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/lib/dispersion/b14.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/b14.py?rev=23591&r1=23590&r2=23591&view=diff
Modified: trunk/lib/dispersion/cr72.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/cr72.py?rev=23591&r1=23590&r2=23591&view=diff
Modified: trunk/lib/dispersion/dpl94.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/dpl94.py?rev=23591&r1=23590&r2=23591&view=diff
Modified: trunk/lib/dispersion/it99.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/it99.py?rev=23591&r1=23590&r2=23591&view=diff
Modified: trunk/lib/dispersion/lm63.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/lm63.py?rev=23591&r1=23590&r2=23591&view=diff
Modified: trunk/lib/dispersion/m61.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/m61.py?rev=23591&r1=23590&r2=23591&view=diff
Modified: trunk/lib/dispersion/mmq_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/mmq_cr72.py?rev=23591&r1=23590&r2=23591&view=diff
Modified: trunk/lib/dispersion/mp05.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/mp05.py?rev=23591&r1=23590&r2=23591&view=diff
Modified: trunk/lib/dispersion/tap03.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/tap03.py?rev=23591&r1=23590&r2=23591&view=diff
Modified: trunk/lib/dispersion/tp02.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/tp02.py?rev=23591&r1=23590&r2=23591&view=diff
Modified: trunk/lib/dispersion/tsmfk01.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/tsmfk01.py?rev=23591&r1=23590&r2=23591&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=23591&r1=23590&r2=23591&view=diff
Modified:
trunk/test_suite/system_tests/scripts/relax_disp/hansen_data_missing.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/relax_disp/hansen_data_missing.py?rev=23591&r1=23590&r2=23591&view=diff
r23591 - in /trunk: ./ lib/dispersion/ test_suite/system_tests/ test_suite/system_tests/scripts/relax_disp/