bugrelax - Bugs: bug #22055, The processor.run_queue() does not...

 
 
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bug #22055: The processor.run_queue() does not clean up in uni_processor - chain-reaction failures in the test suite.

Submitted by:  Troels E. Linnet <tlinnet>
Submitted on:  Tue 20 May 2014 12:03:56 AM UTC  
 
Category: Test suiteSpecific analysis category: Relaxation dispersion
Priority: 7 - HighSeverity: 3 - Normal
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Open/Closed: Closed
Release: 3.1.7Operating System: All systems

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Fri 30 May 2014 09:39:57 AM UTC, SVN revision 23610:

Merged revisions 23578-23579,23590-23600,23603-23609 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

................
r23578 | bugman | 2014-05-28 22:39:51 +0200 (Wed, 28 May 2014) | 5 lines

Created a file selection wildcard for use in the GUI for selecting peak lists.

This is used in the four user functions which read peak lists.
................
r23579 | bugman | 2014-05-28 22:42:43 +0200 (Wed, 28 May 2014) | 3 lines

Changed all . GUI file selection wildcards to *.
................
r23590 | bugman | 2014-05-29 13:22:39 +0200 (Thu, 29 May 2014) | 3 lines

Initialized merge tracking via "svnmerge" with revisions "1-23214" from
svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_speed
................
r23591 | bugman | 2014-05-29 13:46:48 +0200 (Thu, 29 May 2014) | 199 lines

Merged revisions 23216-23229 via svnmerge from
svn+ssh://bugman@svn.gna.org/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

[...] ........

[...]................

[...] r23592 | bugman | 2014-05-29 13:55:17 +0200 (Thu, 29 May 2014) | 18 lines

[...]

[...] Merged revisions 23239 via svnmerge from

[...] svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_speed

[...]

[...] ........

[...] r23239 | tlinnet | 2014-05-19 14:44:10 +0200 (Mon, 19 May 2014) | 10 lines

[...]

[...] Math-domain catching for model B14.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...] ........

[...]................

[...] r23593 | bugman | 2014-05-29 13:56:16 +0200 (Thu, 29 May 2014) | 18 lines

[...]

[...] Merged revisions 23240 via svnmerge from

[...] svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_speed

[...]

[...] ........

[...] r23240 | tlinnet | 2014-05-19 14:44:12 +0200 (Mon, 19 May 2014) | 10 lines

[...]

[...] Math-domain catching for model CR72.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...] ........

[...]................

[...] r23594 | bugman | 2014-05-29 13:59:18 +0200 (Thu, 29 May 2014) | 321 lines

[...]

[...] Merged revisions 23246-23250,23259,23268-23278,23295-23304 via svnmerge from

[...] svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_speed

[...]

[...] ........

[...] r23246 | tlinnet | 2014-05-20 01:47:30 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model: 'NS CPMG 2-site expanded'.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...] ........

[...] r23247 | tlinnet | 2014-05-20 01:47:32 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model CR72.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] The skipping of test when num_points > 0, is a bad implementation.

[...] If such a case should show, it is best to catch the wrong input for the

[...] calculations. This is best done with a check before running the calculations.

[...] ........

[...] r23248 | tlinnet | 2014-05-20 01:47:34 +0200 (Tue, 20 May 2014) | 11 lines

[...]

[...] Turned of processor.run_queue() when using calc().

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] A weird behaviour was found when running the test-suite.

[...]

[...] Somehow, queued jobs from the last test suite was not flushed and done.

[...] Running the test-suite gave errors on almost all tests.

[...]

[...] Inspecting systemtest which only used calc() for the dispersion API, showed that no jobs was queued

[...] in the calculate() method, and the call to processor.run_queue(), was turned off, solving the problem.

[...] ........

[...] r23249 | tlinnet | 2014-05-20 01:47:37 +0200 (Tue, 20 May 2014) | 4 lines

[...]

[...] An attempt to fix the pipe_control/minimisy.py minimise() call to processor.run_queue().

[...]

[...] It was thought that I was modifying the address of array class(back_calc).

[...] But this does not seem to be the problem.

[...] ........

[...] r23250 | tlinnet | 2014-05-20 02:02:19 +0200 (Tue, 20 May 2014) | 1 line

[...]

[...] Fix for variable num_points not set.

[...] ........

[...] r23259 | tlinnet | 2014-05-20 14:55:11 +0200 (Tue, 20 May 2014) | 34 lines

[...]

[...] Reverted r23250-23248 as the correct fix was done in fixing bug 22055.

[...]

[...] bug #22055 (https://gna.org/bugs/?22055) The processor.run_queue() does not clean up in uni_processor - chain-reaction failures in the test suite.

[...]

[...] The command used was:

[...] svn merge -r23250:r23247 .

[...]

[...] .....

[...] r23250 | tlinnet | 2014-05-20 02:02:19 +0200 (Tue, 20 May 2014) | 1 line

[...]

[...] Fix for variable num_points not set.

[...] ------------------------------------------------------------------------

[...] r23249 | tlinnet | 2014-05-20 01:47:37 +0200 (Tue, 20 May 2014) | 4 lines

[...]

[...] An attempt to fix the pipe_control/minimisy.py minimise() call to processor.run_queue().

[...]

[...] It was thought that I was modifying the address of array class(back_calc).

[...] But this does not seem to be the problem.

[...] ------------------------------------------------------------------------

[...] r23248 | tlinnet | 2014-05-20 01:47:34 +0200 (Tue, 20 May 2014) | 11 lines

[...]

[...] Turned of processor.run_queue() when using calc().

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] A weird behaviour was found when running the test-suite.

[...]

[...] Somehow, queued jobs from the last test suite was not flushed and done.

[...] Running the test-suite gave errors on almost all tests.

[...]

[...] Inspecting systemtest which only used calc() for the dispersion API, showed that no jobs was queued

[...] in the calculate() method, and the call to processor.run_queue(), was turned off, solving the problem.

[...] .....

[...] ........

[...] r23268 | tlinnet | 2014-05-20 22:29:35 +0200 (Tue, 20 May 2014) | 8 lines

[...]

[...] Fix for commit 23246.

[...]

[...] http://svn.gna.org/viewcvs/relax?view=revision&revision=23246

[...]

[...] The testing taking a value to a power was performed wrong.

[...]

[...] This made systemtest Relax_disp.test_hansen_cpmg_data_auto_analysis_numeric

[...] not working.

[...] ........

[...] r23269 | tlinnet | 2014-05-20 22:29:38 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model TSMFK01.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...] ........

[...] r23270 | tlinnet | 2014-05-20 22:29:40 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model TP02.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...] ........

[...] r23271 | tlinnet | 2014-05-20 22:29:41 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model TAP03.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...] ........

[...] r23272 | tlinnet | 2014-05-20 22:29:43 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model DPL94.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...] ........

[...] r23273 | tlinnet | 2014-05-20 22:29:45 +0200 (Tue, 20 May 2014) | 3 lines

[...]

[...] Math-domain catching for model TAP03.

[...]

[...] Another check for division with 0 inserted.

[...] ........

[...] r23274 | tlinnet | 2014-05-20 22:29:47 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model MP05.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...] ........

[...] r23275 | tlinnet | 2014-05-20 22:29:49 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model IT99.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...] ........

[...] r23276 | tlinnet | 2014-05-20 22:29:50 +0200 (Tue, 20 May 2014) | 7 lines

[...]

[...] Removed class object "back_calc" being updated per time point for model LM63.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...] ........

[...] r23277 | tlinnet | 2014-05-20 22:29:52 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model M61.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...] ........

[...] r23278 | tlinnet | 2014-05-20 22:29:54 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model MMQ CR72.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...] ........

[...] r23295 | tlinnet | 2014-05-21 13:02:55 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model CR72 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...] ........

[...] r23296 | tlinnet | 2014-05-21 13:02:56 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model DPL94 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...] ........

[...] r23297 | tlinnet | 2014-05-21 13:02:58 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model IT99 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...] ........

[...] r23298 | tlinnet | 2014-05-21 13:02:59 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model LM63 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...] ........

[...] r23299 | tlinnet | 2014-05-21 13:03:01 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model M61 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...] ........

[...] r23300 | tlinnet | 2014-05-21 13:03:02 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model MP05 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...] ........

[...] r23301 | tlinnet | 2014-05-21 13:03:04 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model TAP03 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...] ........

[...] r23302 | tlinnet | 2014-05-21 13:03:06 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model TP02 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...] ........

[...] r23303 | tlinnet | 2014-05-21 13:03:07 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model TSMFK01 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...] ........

[...] r23304 | tlinnet | 2014-05-21 13:03:09 +0200 (Wed, 21 May 2014) | 5 lines

[...]

[...] Removing unnecessary math-domain catching for model IT99.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models..

[...]

[...] The denominator is always positive.

[...] ........

[...]................

[...] r23595 | bugman | 2014-05-29 14:09:47 +0200 (Thu, 29 May 2014) | 61 lines

[...]

[...] Merged revisions 23333-23334,23338,23342 via svnmerge from

[...] svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_speed

[...]

[...] ........

[...] r23333 | tlinnet | 2014-05-22 15:19:30 +0200 (Thu, 22 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model NS CPMG 2-site expanded with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...] ........

[...] r23334 | tlinnet | 2014-05-22 15:19:32 +0200 (Thu, 22 May 2014) | 18 lines

[...]

[...] Modified unit tests demonstrating edge case 'no Rex' failures of the model 'NS CPMG 2-site expanded'.

[...]

[...] This is to align with the current return of data in the disp_speed branch.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] ........

[...] r23338 | tlinnet | 2014-05-22 16:56:32 +0200 (Thu, 22 May 2014) | 16 lines

[...]

[...] Added 7 unit tests demonstrating edge case 'no Rex' failures of the model 'DPL94'.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] ........

[...] r23342 | tlinnet | 2014-05-22 17:46:50 +0200 (Thu, 22 May 2014) | 5 lines

[...]

[...] Unit test lib/test_ns_cpmg_2site_expanded.py copied to /test_lm63.py.

[...]

[...] They are both of CPMG type.

[...] ........

[...]................

[...] r23596 | bugman | 2014-05-29 14:12:42 +0200 (Thu, 29 May 2014) | 213 lines

[...]

[...] Merged revisions 23348-23351,23356-23359,23364,23413-23420 via svnmerge from

[...] svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_speed

[...]

[...] ........

[...] r23348 | tlinnet | 2014-05-22 18:27:40 +0200 (Thu, 22 May 2014) | 1 line

[...]

[...] Fix for wrong file name in _init_.py.

[...] ........

[...] r23349 | tlinnet | 2014-05-22 18:27:42 +0200 (Thu, 22 May 2014) | 16 lines

[...]

[...] Added 7 unit tests demonstrating edge case 'no Rex' failures of the model 'LM63'.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] ........

[...] r23350 | tlinnet | 2014-05-22 18:27:43 +0200 (Thu, 22 May 2014) | 8 lines

[...]

[...] Critical fix for the math domain catching of model LM63.

[...]

[...] This was discovered with the added 7 unit tests demonstrating edge case 'no Rex' failures.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] ........

[...] r23351 | tlinnet | 2014-05-22 18:30:53 +0200 (Thu, 22 May 2014) | 4 lines

[...]

[...] Unit test _lib/_dispersion/test_ns_cpmg_2site_expanded.py copied to _lib/_dispersion/b14.py.

[...]

[...] They are both of CPMG type, and can be re-used.

[...] ........

[...] r23356 | tlinnet | 2014-05-22 19:15:32 +0200 (Thu, 22 May 2014) | 16 lines

[...]

[...] Added 7 unit tests demonstrating edge case 'no Rex' failures of the model 'B14'.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] ........

[...] r23357 | tlinnet | 2014-05-22 19:15:34 +0200 (Thu, 22 May 2014) | 8 lines

[...]

[...] Critical fix for the math domain catching of model B14.

[...]

[...] This was discovered with the added 7 unit tests demonstrating edge case 'no Rex' failures.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] ........

[...] r23358 | tlinnet | 2014-05-22 19:15:36 +0200 (Thu, 22 May 2014) | 7 lines

[...]

[...] Removed unnecessary math domain checking in model B14.

[...]

[...] They are slowing down the code.

[...]

[...] There is now protection for edge cases, and a last final check, before returning values.

[...]

[...] That should be sufficient.

[...] ........

[...] r23359 | tlinnet | 2014-05-22 19:27:31 +0200 (Thu, 22 May 2014) | 5 lines

[...]

[...] Unit test _lib/_dispersion/test_b14.py copied to _lib/_dispersion/test_cr72.py.

[...]

[...] They are both of CPMG type, and can be re-used.

[...] ........

[...] r23364 | tlinnet | 2014-05-22 22:26:56 +0200 (Thu, 22 May 2014) | 3 lines

[...]

[...] Copied unit test _lib/_dispersion/* to be reused for other models.

[...] ........

[...] r23413 | tlinnet | 2014-05-26 13:38:07 +0200 (Mon, 26 May 2014) | 17 lines

[...]

[...] Added 8 unit tests demonstrating edge case 'no Rex' failures of the model 'CR72'.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] - kex = 1e5,

[...] ........

[...] r23414 | tlinnet | 2014-05-26 13:38:09 +0200 (Mon, 26 May 2014) | 15 lines

[...]

[...] Critical fix for the math domain catching of model CR72.

[...]

[...] This was discovered with the added 8 unit tests demonstrating edge case 'no Rex' failures.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] When kex is large, ex: kex = 1e5, the values of:

[...] etapos = eta_scale * sqrt(Psi + sqrt_psi2_zeta2) / cpmg_frqs

[...]

[...] will exceed possible numerical representation.

[...]

[...] The cathing of these occurences needed to be re-written.

[...] ........

[...] r23415 | tlinnet | 2014-05-26 13:38:11 +0200 (Mon, 26 May 2014) | 17 lines

[...]

[...] Added the 8th unit tests demonstrating edge case 'no Rex' failures of the model 'B14'.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] - kex = 1e5,

[...] ........

[...] r23416 | tlinnet | 2014-05-26 13:38:13 +0200 (Mon, 26 May 2014) | 13 lines

[...]

[...] Critical fix for the math domain catching of model B14.

[...]

[...] This was discovered with the added 8 unit tests demonstrating edge case 'no Rex' failures.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] When kex is large, ex: kex = 1e5, "nan" values where produced,

[...] which was replaced with 1e100.

[...]

[...] The cathing of these occurences needed to be re-written.

[...] ........

[...] r23417 | tlinnet | 2014-05-26 13:50:02 +0200 (Mon, 26 May 2014) | 5 lines

[...]

[...] Critical fix for the math domain catching of model CR72.

[...]

[...] Removed the test for kex >= 1.e5.

[...]

[...] This catching should rather be performed on the math functions instead.

[...] ........

[...] r23418 | tlinnet | 2014-05-26 13:50:05 +0200 (Mon, 26 May 2014) | 7 lines

[...]

[...] Critical fix for the math domain catching of model B14.

[...]

[...] Removed the test for kex >= 1.e5.

[...]

[...] This catching should rather be performed on the math functions instead.

[...]

[...] In this case, it is the cathing of sinh(), not evaluating values above 710.

[...] ........

[...] r23419 | tlinnet | 2014-05-26 14:37:50 +0200 (Mon, 26 May 2014) | 17 lines

[...]

[...] Added the 8th unit tests demonstrating edge case 'no Rex' failures of the model 'LM63'.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] - kex = 1e20,

[...] ........

[...] r23420 | tlinnet | 2014-05-26 14:41:52 +0200 (Mon, 26 May 2014) | 3 lines

[...]

[...] Small fix for 8 unit tests demonstrating edge case 'no Rex' failures of the model 'ns cpmg_2site_expanded'.

[...]

[...] The comparison of R2eff is now divided into a special case for kex having large values.

[...] ........

[...]................

[...] r23597 | bugman | 2014-05-29 14:15:24 +0200 (Thu, 29 May 2014) | 405 lines

[...]

[...] Merged revisions 23425-23426,23431-23452,23455-23463 via svnmerge from

[...] svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_speed

[...]

[...] ........

[...] r23425 | tlinnet | 2014-05-26 16:27:27 +0200 (Mon, 26 May 2014) | 1 line

[...]

[...] Deleted unit test case for lm63 3site.

[...] ........

[...] r23426 | tlinnet | 2014-05-26 16:27:30 +0200 (Mon, 26 May 2014) | 17 lines

[...]

[...] Added 8 unit tests demonstrating edge case 'no Rex' failures of the model 'M61'.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] - kex = 1e20,

[...] ........

[...] r23431 | tlinnet | 2014-05-26 20:13:46 +0200 (Mon, 26 May 2014) | 10 lines

[...]

[...] Added the 8th unit tests demonstrating edge case 'no Rex' failures of the model 'DPL94'.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - kex = 1e20,

[...] ........

[...] r23432 | tlinnet | 2014-05-26 20:13:53 +0200 (Mon, 26 May 2014) | 1 line

[...]

[...] Added "test_m61" to _init_.py in unit test directory.

[...] ........

[...] r23433 | tlinnet | 2014-05-26 20:13:56 +0200 (Mon, 26 May 2014) | 17 lines

[...]

[...] Added 8 unit tests demonstrating edge case 'no Rex' failures of the model 'M61b'.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] - kex = 1e20,

[...] ........

[...] r23434 | tlinnet | 2014-05-26 20:14:01 +0200 (Mon, 26 May 2014) | 10 lines

[...]

[...] Math-domain catching for model M61b.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...] ........

[...] r23435 | tlinnet | 2014-05-26 20:14:03 +0200 (Mon, 26 May 2014) | 1 line

[...]

[...] Modified script to be able to run systemtest Relax_disp.xxx_test_m61b_data_to_m61b.

[...] ........

[...] r23436 | tlinnet | 2014-05-26 20:14:05 +0200 (Mon, 26 May 2014) | 1 line

[...]

[...] Added "test_m61b" to _init_.py file in unit test directory.

[...] ........

[...] r23437 | tlinnet | 2014-05-26 20:14:07 +0200 (Mon, 26 May 2014) | 17 lines

[...]

[...] Added 8 unit tests demonstrating edge case 'no Rex' failures of the model 'IT99'.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] - kex = 1e19,

[...] ........

[...] r23438 | tlinnet | 2014-05-26 23:09:40 +0200 (Mon, 26 May 2014) | 18 lines

[...]

[...] Added 9 unit tests demonstrating edge case 'no Rex' failures of the model 'MMQ CR72'.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] - kex = 1e5,

[...] - dwH = 0.0,

[...] ........

[...] r23439 | tlinnet | 2014-05-26 23:09:43 +0200 (Mon, 26 May 2014) | 8 lines

[...]

[...] Critical fix for the math domain catching of model MMQ CR72.

[...]

[...] This was discovered with the added 9 unit tests demonstrating edge case 'no Rex' failures.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] ........

[...] r23440 | tlinnet | 2014-05-26 23:09:45 +0200 (Mon, 26 May 2014) | 17 lines

[...]

[...] Added 8 unit tests demonstrating edge case 'no Rex' failures of the model 'MP05'.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] - kex = 1e20,

[...] ........

[...] r23441 | tlinnet | 2014-05-26 23:09:47 +0200 (Mon, 26 May 2014) | 10 lines

[...]

[...] Critical fix for the math domain catching of model IT99.

[...]

[...] This was discovered with the added 8 unit tests demonstrating edge case 'no Rex' failures.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The cathing of these occurences needed to be re-written.

[...] ........

[...] r23442 | tlinnet | 2014-05-26 23:09:50 +0200 (Mon, 26 May 2014) | 17 lines

[...]

[...] Added 8 unit tests demonstrating edge case 'no Rex' failures of the model 'TAP03'.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] - kex = 1e20,

[...] ........

[...] r23443 | tlinnet | 2014-05-26 23:09:52 +0200 (Mon, 26 May 2014) | 8 lines

[...]

[...] Critical fix for the math domain catching of model TAP03.

[...]

[...] This was discovered with the added 8 unit tests demonstrating edge case 'no Rex' failures.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] ........

[...] r23444 | tlinnet | 2014-05-26 23:09:54 +0200 (Mon, 26 May 2014) | 17 lines

[...]

[...] Added 8 unit tests demonstrating edge case 'no Rex' failures of the model 'TP02'.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] - kex = 1e20,

[...] ........

[...] r23445 | tlinnet | 2014-05-26 23:09:56 +0200 (Mon, 26 May 2014) | 8 lines

[...]

[...] Critical fix for the math domain catching of model TP02.

[...]

[...] This was discovered with the added 8 unit tests demonstrating edge case 'no Rex' failures.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] ........

[...] r23446 | tlinnet | 2014-05-26 23:09:58 +0200 (Mon, 26 May 2014) | 16 lines

[...]

[...] Added 7 unit tests demonstrating edge case 'no Rex' failures of the model 'TSMFK01'.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] ........

[...] r23447 | tlinnet | 2014-05-26 23:10:00 +0200 (Mon, 26 May 2014) | 10 lines

[...]

[...] Critical fix for the math domain catching of model TSMFK01.

[...]

[...] This was discovered with the added 8 unit tests demonstrating edge case 'no Rex' failures.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The cathing of these occurences needed to be re-written.

[...] ........

[...] r23448 | tlinnet | 2014-05-26 23:10:03 +0200 (Mon, 26 May 2014) | 1 line

[...]

[...] Added missing files to _init_.py in unit_tests/_lib/_dispersion.

[...] ........

[...] r23449 | tlinnet | 2014-05-26 23:23:16 +0200 (Mon, 26 May 2014) | 3 lines

[...]

[...] Copied unit test test_b14.py to test_ns_cpmg_2site_3d.py

[...] ........

[...] r23450 | tlinnet | 2014-05-27 00:08:06 +0200 (Tue, 27 May 2014) | 17 lines

[...]

[...] Added 8 unit tests demonstrating edge case 'no Rex' failures of the model 'NS CPMG 2site 3D'.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] - kex = 1e7,

[...] ........

[...] r23451 | tlinnet | 2014-05-27 00:08:08 +0200 (Tue, 27 May 2014) | 8 lines

[...]

[...] Critical fix for the math domain catching of model NS CPMG 2site 3D.

[...]

[...] This was discovered with the added 8 unit tests demonstrating edge case 'no Rex' failures.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] ........

[...] r23452 | tlinnet | 2014-05-27 00:08:09 +0200 (Tue, 27 May 2014) | 1 line

[...]

[...] Added missing files to _init_.py in unit_tests/_lib/_dispersion.

[...] ........

[...] r23455 | tlinnet | 2014-05-27 12:24:56 +0200 (Tue, 27 May 2014) | 20 lines

[...]

[...] Modified unit tests demonstrating edge cases 'no Rex' failures of the model 'TP02'.

[...]

[...] The cathing of errors for off-resonance R1rho models was implemented wrong.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...] This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] These tests cover all parameter value combinations which result in no exchange:

[...]

[...] - dw = 0.0,

[...] - pA = 1.0,

[...] - kex = 0.0,

[...] - dw = 0.0 and pA = 1.0,

[...] - dw = 0.0 and kex = 0.0,

[...] - pA = 1.0 and kex = 0.0,

[...] - dw = 0.0, pA = 1.0, and kex = 0.0.

[...] - kex = 1e5,

[...] ........

[...] r23456 | tlinnet | 2014-05-27 12:26:20 +0200 (Tue, 27 May 2014) | 5 lines

[...]

[...] Critical fix for the math domain catching of model TP02.

[...]

[...] The cathing of errors for off-resonance R1rho models was implemented wrong.

[...]

[...] This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938.

[...] ........

[...] r23457 | tlinnet | 2014-05-27 12:26:22 +0200 (Tue, 27 May 2014) | 3 lines

[...]

[...] Modified unit tests demonstrating edge cases 'no Rex' failures of the model 'DPL94'.

[...]

[...] This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938.

[...] ........

[...] r23458 | tlinnet | 2014-05-27 12:26:23 +0200 (Tue, 27 May 2014) | 10 lines

[...]

[...] Modified unit tests demonstrating edge cases 'no Rex' failures of the model 'MP05'.

[...]

[...] The cathing of errors for off-resonance R1rho models was implemented wrong.

[...]

[...] This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] ........

[...] r23459 | tlinnet | 2014-05-27 12:26:25 +0200 (Tue, 27 May 2014) | 5 lines

[...]

[...] Critical fix for the math domain catching of model MP05.

[...]

[...] The cathing of errors for off-resonance R1rho models was implemented wrong.

[...]

[...] This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938.

[...] ........

[...] r23460 | tlinnet | 2014-05-27 12:26:26 +0200 (Tue, 27 May 2014) | 9 lines

[...]

[...] Modified unit tests demonstrating edge cases 'no Rex' failures of the model 'TAP03'.

[...]

[...] The cathing of errors for off-resonance R1rho models was implemented wrong.

[...]

[...] This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938.

[...] And post http://article.gmane.org/gmane.science.nmr.relax.devel/5944.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...] ........

[...] r23461 | tlinnet | 2014-05-27 12:26:28 +0200 (Tue, 27 May 2014) | 6 lines

[...]

[...] Critical fix for the math domain catching of model TAP03.

[...]

[...] The cathing of errors for off-resonance R1rho models was implemented wrong.

[...]

[...] This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5938.

[...] And post http://article.gmane.org/gmane.science.nmr.relax.devel/5944.

[...] ........

[...] r23462 | tlinnet | 2014-05-27 12:26:30 +0200 (Tue, 27 May 2014) | 7 lines

[...]

[...] Modified unit tests demonstrating edge cases 'no Rex' failures of the model 'MMQ CR72'.

[...]

[...] This was pointed out in post http://article.gmane.org/gmane.science.nmr.relax.devel/5940.

[...] And in post http://article.gmane.org/gmane.science.nmr.relax.devel/5946.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...] ........

[...] r23463 | tlinnet | 2014-05-27 12:26:32 +0200 (Tue, 27 May 2014) | 4 lines

[...]

[...] Small fix for the math domain catching of model MMQ CR72.

[...]

[...] This was pointed out in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5940.

[...] And in post http://article.gmane.org/gmane.science.nmr.relax.devel/5946.

[...] ........

[...]................

[...] r23598 | bugman | 2014-05-29 14:16:36 +0200 (Thu, 29 May 2014) | 151 lines

[...]

[...] Merged revisions 23465,23473,23483-23487,23502-23504,23526-23531 via svnmerge from

[...] svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_speed

[...]

[...] ........

[...] r23465 | tlinnet | 2014-05-27 12:50:51 +0200 (Tue, 27 May 2014) | 6 lines

[...]

[...] Various spacing fixes in unit test files _lib/_dispersion.

[...]

[...] This is the preparation for merging back disp_speed branch into trunk.

[...] This follows post http://article.gmane.org/gmane.science.nmr.relax.devel/5948.

[...]

[...] Usin the code validator script './devel_scripts/code_validator'.

[...] ........

[...] r23473 | tlinnet | 2014-05-27 17:05:45 +0200 (Tue, 27 May 2014) | 4 lines

[...]

[...] Modified that unit tests having different r20a and r20b values is checking if the correct one is returned.

[...]

[...] This is the preparation for merging back disp_speed branch into trunk.

[...] This follows post http://article.gmane.org/gmane.science.nmr.relax.devel/5948.

[...] ........

[...] r23483 | tlinnet | 2014-05-27 19:11:26 +0200 (Tue, 27 May 2014) | 5 lines

[...]

[...] Modified unit test to have standard population of pA=0.95, and a correctly calculation of dw in ppm to rad/s.

[...]

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...] ........

[...] r23484 | tlinnet | 2014-05-27 19:29:56 +0200 (Tue, 27 May 2014) | 1 line

[...]

[...] Small fix in parameter calculation in unit test _dispersion/test_ns_cpmg_2site_expanded.

[...] ........

[...] r23485 | tlinnet | 2014-05-27 19:29:58 +0200 (Tue, 27 May 2014) | 1 line

[...]

[...] Increased max kex to value 1e18 for unit test of lin/ns_cpmg_2site_expanded.py.

[...] ........

[...] r23486 | tlinnet | 2014-05-27 19:30:00 +0200 (Tue, 27 May 2014) | 1 line

[...]

[...] Increased max kex to value 1e20 for unit test of lib/ns_cpmg_2site_3d.py.

[...] ........

[...] r23487 | tlinnet | 2014-05-27 19:30:02 +0200 (Tue, 27 May 2014) | 6 lines

[...]

[...] Fix for looking for negative values, when all values where converted to positive in matrix in ns_cpmg_2site_3d.py.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...] ........

[...] r23502 | tlinnet | 2014-05-28 11:49:17 +0200 (Wed, 28 May 2014) | 1 line

[...]

[...] Removed nested looping of returning back_calc in lib/ns_cpmg_2site_3d.

[...] ........

[...] r23503 | tlinnet | 2014-05-28 11:49:21 +0200 (Wed, 28 May 2014) | 5 lines

[...]

[...] Removed the 8th unit test for model NS CPMG 2site 3D.

[...]

[...] This was the catching of errors when kex=1e20.

[...]

[...] The model cannot handle this situations, and we need to let it fail.

[...] ........

[...] r23504 | tlinnet | 2014-05-28 11:57:31 +0200 (Wed, 28 May 2014) | 5 lines

[...]

[...] Removed the 8th unit test for model NS CPMG 2site extended.

[...]

[...] This was the catching of errors when kex has high values.

[...]

[...] The model cannot handle this situations, and we need to let it fail.

[...] ........

[...] r23526 | tlinnet | 2014-05-28 16:49:00 +0200 (Wed, 28 May 2014) | 13 lines

[...]

[...] Added the default value lower grid value to be set for the pA parameter.

[...]

[...] This is added in the collected table of specific_analysis/relax_disp/parameter_object.py

[...]

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...] Discussed in post http://thread.gmane.org/gmane.science.nmr.relax.devel/5986.

[...]

[...] In any function, these default values can get accessed by:

[...]

[...] from specific_analyses.relax_disp.parameter_object import Relax_disp_params

[...] PARAMS = Relax_disp_params()

[...] PARAMS.default_value('pA')

[...] PARAMS.grid_lower('pA')

[...] ........

[...] r23527 | tlinnet | 2014-05-28 16:49:02 +0200 (Wed, 28 May 2014) | 4 lines

[...]

[...] Added grid_lower to be handled in specific_analyses/parameter_object.py.

[...]

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...] Discussed in post http://thread.gmane.org/gmane.science.nmr.relax.devel/5986.

[...] ........

[...] r23528 | tlinnet | 2014-05-28 16:49:03 +0200 (Wed, 28 May 2014) | 13 lines

[...]

[...] Added the default value upper grid value to be set for the pA parameter.

[...]

[...] This is added in the collected table of specific_analysis/relax_disp/parameter_object.py.

[...]

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...] Discussed in post http://thread.gmane.org/gmane.science.nmr.relax.devel/5986.

[...]

[...] In any function, these default values can get accessed by:

[...]

[...] from specific_analyses.relax_disp.parameter_object import Relax_disp_params

[...] PARAMS = Relax_disp_params()

[...] PARAMS.default_value('pA')

[...] PARAMS.grid_upper('pA')

[...] ........

[...] r23529 | tlinnet | 2014-05-28 16:49:05 +0200 (Wed, 28 May 2014) | 4 lines

[...]

[...] Added grid_upper to be handled in specific_analyses/parameter_object.py.

[...]

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...] Discussed in post http://thread.gmane.org/gmane.science.nmr.relax.devel/5986.

[...] ........

[...] r23530 | tlinnet | 2014-05-28 16:49:06 +0200 (Wed, 28 May 2014) | 16 lines

[...]

[...] Added all the default values for the lower/upper bounds which is set for the parameters in the grid search.

[...]

[...] This is added in the collected table of specific_analysis/relax_disp/parameter_object.py.

[...] The values were extracted from: specific_analysis/relax_disp/optimisation.py in grid_search_setup().

[...]

[...] This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...] Discussed in post http://thread.gmane.org/gmane.science.nmr.relax.devel/5986.

[...]

[...] In any function, these default values can get accessed by:

[...]

[...] from specific_analyses.relax_disp.parameter_object import Relax_disp_params

[...] PARAMS = Relax_disp_params()

[...] PARAMS.default_

(Browse SVN revision 23610)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 29 May 2014 11:59:18 AM UTC, SVN revision 23594:

Merged revisions 23246-23250,23259,23268-23278,23295-23304 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_speed

........
r23246 | tlinnet | 2014-05-20 01:47:30 +0200 (Tue, 20 May 2014) | 10 lines

Math-domain catching for model: 'NS CPMG 2-site expanded'.

task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.

To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target function in
one go.
........
r23247 | tlinnet | 2014-05-20 01:47:32 +0200 (Tue, 20 May 2014) | 10 lines

Math-domain catching for model CR72.

task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.

The skipping of test when num_points > 0, is a bad implementation.
If such a case should show, it is best to catch the wrong input for the
calculations. This is best done with a check before running the calculations.
........
r23248 | tlinnet | 2014-05-20 01:47:34 +0200 (Tue, 20 May 2014) | 11 lines

Turned of processor.run_queue() when using calc().

task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

A weird behaviour was found when running the test-suite.

Somehow, queued jobs from the last test suite was not flushed and done.
Running the test-suite gave errors on almost all tests.

Inspecting systemtest which only used calc() for the dispersion API, showed that no jobs was queued
in the calculate() method, and the call to processor.run_queue(), was turned off, solving the problem.
........
r23249 | tlinnet | 2014-05-20 01:47:37 +0200 (Tue, 20 May 2014) | 4 lines

An attempt to fix the pipe_control/minimisy.py minimise() call to processor.run_queue().

It was thought that I was modifying the address of array class(back_calc).
But this does not seem to be the problem.
........

[...] r23250 | tlinnet | 2014-05-20 02:02:19 +0200 (Tue, 20 May 2014) | 1 line

[...]

[...] Fix for variable num_points not set.

[...]........

[...] r23259 | tlinnet | 2014-05-20 14:55:11 +0200 (Tue, 20 May 2014) | 34 lines

[...]

[...] Reverted r23250-23248 as the correct fix was done in fixing bug 22055.

[...]

[...] bug #22055 (https://gna.org/bugs/?22055) The processor.run_queue() does not clean up in uni_processor - chain-reaction failures in the test suite.

[...]

[...] The command used was:

[...] svn merge -r23250:r23247 .

[...]

[...] .....

[...] r23250 | tlinnet | 2014-05-20 02:02:19 +0200 (Tue, 20 May 2014) | 1 line

[...]

[...] Fix for variable num_points not set.

[...] ------------------------------------------------------------------------

[...] r23249 | tlinnet | 2014-05-20 01:47:37 +0200 (Tue, 20 May 2014) | 4 lines

[...]

[...] An attempt to fix the pipe_control/minimisy.py minimise() call to processor.run_queue().

[...]

[...] It was thought that I was modifying the address of array class(back_calc).

[...] But this does not seem to be the problem.

[...] ------------------------------------------------------------------------

[...] r23248 | tlinnet | 2014-05-20 01:47:34 +0200 (Tue, 20 May 2014) | 11 lines

[...]

[...] Turned of processor.run_queue() when using calc().

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] A weird behaviour was found when running the test-suite.

[...]

[...] Somehow, queued jobs from the last test suite was not flushed and done.

[...] Running the test-suite gave errors on almost all tests.

[...]

[...] Inspecting systemtest which only used calc() for the dispersion API, showed that no jobs was queued

[...] in the calculate() method, and the call to processor.run_queue(), was turned off, solving the problem.

[...] .....

[...]........

[...] r23268 | tlinnet | 2014-05-20 22:29:35 +0200 (Tue, 20 May 2014) | 8 lines

[...]

[...] Fix for commit 23246.

[...]

[...] http://svn.gna.org/viewcvs/relax?view=revision&revision=23246

[...]

[...] The testing taking a value to a power was performed wrong.

[...]

[...] This made systemtest Relax_disp.test_hansen_cpmg_data_auto_analysis_numeric

[...] not working.

[...]........

[...] r23269 | tlinnet | 2014-05-20 22:29:38 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model TSMFK01.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...]........

[...] r23270 | tlinnet | 2014-05-20 22:29:40 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model TP02.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...]........

[...] r23271 | tlinnet | 2014-05-20 22:29:41 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model TAP03.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...]........

[...] r23272 | tlinnet | 2014-05-20 22:29:43 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model DPL94.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...]........

[...] r23273 | tlinnet | 2014-05-20 22:29:45 +0200 (Tue, 20 May 2014) | 3 lines

[...]

[...] Math-domain catching for model TAP03.

[...]

[...] Another check for division with 0 inserted.

[...]........

[...] r23274 | tlinnet | 2014-05-20 22:29:47 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model MP05.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...]........

[...] r23275 | tlinnet | 2014-05-20 22:29:49 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model IT99.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...]........

[...] r23276 | tlinnet | 2014-05-20 22:29:50 +0200 (Tue, 20 May 2014) | 7 lines

[...]

[...] Removed class object "back_calc" being updated per time point for model LM63.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...]........

[...] r23277 | tlinnet | 2014-05-20 22:29:52 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model M61.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...]........

[...] r23278 | tlinnet | 2014-05-20 22:29:54 +0200 (Tue, 20 May 2014) | 10 lines

[...]

[...] Math-domain catching for model MMQ CR72.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...] These can be found via the --numpy-raise function to the systemtests.

[...]

[...] To make the code look clean, the class object "back_calc" is no longer

[...] being updated per time point, but is updated in the relax_disp target function in

[...] one go.

[...]........

[...] r23295 | tlinnet | 2014-05-21 13:02:55 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model CR72 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...]........

[...] r23296 | tlinnet | 2014-05-21 13:02:56 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model DPL94 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...]........

[...] r23297 | tlinnet | 2014-05-21 13:02:58 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model IT99 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...]........

[...] r23298 | tlinnet | 2014-05-21 13:02:59 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model LM63 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...]........

[...] r23299 | tlinnet | 2014-05-21 13:03:01 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model M61 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...]........

[...] r23300 | tlinnet | 2014-05-21 13:03:02 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model MP05 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...]........

[...] r23301 | tlinnet | 2014-05-21 13:03:04 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model TAP03 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...]........

[...] r23302 | tlinnet | 2014-05-21 13:03:06 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model TP02 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...]........

[...] r23303 | tlinnet | 2014-05-21 13:03:07 +0200 (Wed, 21 May 2014) | 7 lines

[...]

[...] Align math-domain catching for model TSMFK01 with trunk implementation.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

[...]

[...] This is to implement catching of math domain errors, before they occur.

[...]

[...] The catching of errors have to be more careful.

[...]........

[...] r23304 | tlinnet | 2014-05-21 13:03:09 +0200 (Wed, 21 May 2014) | 5 lines

[...]

[...] Removing unnecessary math-domain catching for model IT99.

[...]

[...] task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models..

[...]

[...] The denominator is always positive.

[...]........

[...]

[...]

(Browse SVN revision 23594)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 20 May 2014 03:40:13 PM UTC, SVN revision 23261:

Merged revisions 23254,23260 via svnmerge from
svn+ssh://tlinnet@svn.gna.org/svn/relax/trunk

........
r23254 | bugman | 2014-05-20 13:37:32 +0200 (Tue, 20 May 2014) | 12 lines

Fix for the chain-reaction failures in the test suite.

This fixes bug #22055 (https://gna.org/bugs/?22055), the processor.run_queue() not cleaning up in
uni_processor - chain-reaction failures in the test suite.

The fix was insanely simple, just implementing what was mentioned Gary's FIXME comment in the
run_queue() method of the uni-processor object. The queue execution code has been placed inside a
'try' statement and the queue cleaning up code in a 'finally' statement.

This closes a painfully difficult to find bug that has been in relax since 2006.
........
r23260 | bugman | 2014-05-20 16:19:30 +0200 (Tue, 20 May 2014) | 6 lines

Converted the Mf.test_opendx_s2_te_rex system test into a GUI test.

This is to demonstrate bug #22035 (https://gna.org/bugs/?22035), the dx.map user function being
broken in the GUI.
........

(Browse SVN revision 23261)

Troels E. Linnet <tlinnet>
Project Member
Tue 20 May 2014 12:55:11 PM UTC, SVN revision 23259:

Reverted r23250-23248 as the correct fix was done in fixing bug 22055.

bug #22055 (https://gna.org/bugs/?22055) The processor.run_queue() does not clean up in uni_processor - chain-reaction failures in the test suite.

The command used was:
svn merge -r23250:r23247 .

.....
r23250 | tlinnet | 2014-05-20 02:02:19 +0200 (Tue, 20 May 2014) | 1 line

Fix for variable num_points not set.
------------------------------------------------------------------------
r23249 | tlinnet | 2014-05-20 01:47:37 +0200 (Tue, 20 May 2014) | 4 lines

An attempt to fix the pipe_control/minimisy.py minimise() call to processor.run_queue().

It was thought that I was modifying the address of array class(back_calc).
But this does not seem to be the problem.
------------------------------------------------------------------------
r23248 | tlinnet | 2014-05-20 01:47:34 +0200 (Tue, 20 May 2014) | 11 lines

Turned of processor.run_queue() when using calc().

task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

A weird behaviour was found when running the test-suite.

Somehow, queued jobs from the last test suite was not flushed and done.
Running the test-suite gave errors on almost all tests.

Inspecting systemtest which only used calc() for the dispersion API, showed that no jobs was queued
in the calculate() method, and the call to processor.run_queue(), was turned off, solving the problem.
.....

(Browse SVN revision 23259)

Troels E. Linnet <tlinnet>
Project Member
Tue 20 May 2014 11:38:04 AM UTC, SVN revision 23255:

Merged revisions 23254 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r23254 | bugman | 2014-05-20 13:37:32 +0200 (Tue, 20 May 2014) | 12 lines

Fix for the chain-reaction failures in the test suite.

This fixes bug #22055 (https://gna.org/bugs/?22055), the processor.run_queue() not cleaning up in
uni_processor - chain-reaction failures in the test suite.

The fix was insanely simple, just implementing what was mentioned Gary's FIXME comment in the
run_queue() method of the uni-processor object. The queue execution code has been placed inside a
'try' statement and the queue cleaning up code in a 'finally' statement.

This closes a painfully difficult to find bug that has been in relax since 2006.
........

(Browse SVN revision 23255)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 20 May 2014 11:37:32 AM UTC, SVN revision 23254:

Fix for the chain-reaction failures in the test suite.

This fixes bug #22055 (https://gna.org/bugs/?22055), the processor.run_queue() not cleaning up in
uni_processor - chain-reaction failures in the test suite.

The fix was insanely simple, just implementing what was mentioned Gary's FIXME comment in the
run_queue() method of the uni-processor object. The queue execution code has been placed inside a
'try' statement and the queue cleaning up code in a 'finally' statement.

This closes a painfully difficult to find bug that has been in relax since 2006.

(Browse SVN revision 23254)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 20 May 2014 11:33:15 AM UTC, comment #1:

Decreasing the severity as this only affects the test suite, and only if one test fails first.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 20 May 2014 12:03:56 AM UTC, original submission:

When running:

relax_disp_speed -s Relax_disp --time --numpy-raise -t log.txt

A lot of errors are thrown.

But when I run the test for them self, no errors are thrown.

It seems, that some jobs are left in the queue?

Troels E. Linnet <tlinnet>
Project Member

 

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file #20771:  log.txt added by tlinnet (793kB - text/plain)

 

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  • -unavailable- added by tlinnet (Submitted the item)
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    Follow 10 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Tue 20 May 2014 11:38:21 AM UTCbugmanStatusConfirmed=>Fixed
      Open/ClosedOpen=>Closed
    Tue 20 May 2014 11:33:15 AM UTCbugmanSeverity4 - Important=>3 - Normal
    Tue 20 May 2014 11:32:20 AM UTCbugmanStatusNone=>Confirmed
      Assigned toNone=>bugman
      ReleaseBranches=>3.1.7
      Operating System32-bit GNU/Linux=>All systems
      SummaryThe processor.run_queue() does not clean up in uni_processor?=>The processor.run_queue() does not clean up in uni_processor - chain-reaction failures in the test suite.
    Tue 20 May 2014 11:31:25 AM UTCbugmanCarbon-Copy-=>Added varioustoxins
    Tue 20 May 2014 12:04:36 AM UTCtlinnetAttached File-=>Added log.txt, #20771
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