Merged revisions 24543,24549-24550,24562,24638,24652-24664,24668 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

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r24543 | bugman | 2014-07-16 20:34:10 +0200 (Wed, 16 Jul 2014) | 3 lines

Added the missing timing module to the relax library package _all_ list.
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r24549 | bugman | 2014-07-17 14:56:24 +0200 (Thu, 17 Jul 2014) | 5 lines

Removed the line wrapping in the epydoc parameter section of the optimisation function docstrings.

This is for the pipe_control.minimise module.
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r24550 | bugman | 2014-07-17 14:57:01 +0200 (Thu, 17 Jul 2014) | 3 lines

More docstring line wrapping removal from pipe_control.minimise.
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r24562 | bugman | 2014-07-18 10:58:56 +0200 (Fri, 18 Jul 2014) | 7 lines

Bug fix for the parameter units descriptions.

This only affects a few rare parameters. The specific analysis API parameter object units() method
was incorrectly checking if the units value is a function - it was checking the parameter conversion
factor instead.
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r24638 | bugman | 2014-07-22 17:06:47 +0200 (Tue, 22 Jul 2014) | 6 lines

Modified the align_tensor.init user function so that the parameters are now optional.

This allows alignment tensors to be initialised without specifying the parameter values for that
tensor.
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r24652 | bugman | 2014-07-22 18:37:02 +0200 (Tue, 22 Jul 2014) | 3 lines

Initialized merge tracking via "svnmerge" with revisions "1-23718" from
svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_spin_speed
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r24653 | bugman | 2014-07-22 18:50:50 +0200 (Tue, 22 Jul 2014) | 348 lines

Merged revisions 23722-23742 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_spin_speed

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r23722 | tlinnet | 2014-06-07 21:43:16 +0200 (Sat, 07 Jun 2014) | 6 lines

Modified profiling script to have different number of NCYC points per frequency.

This is to complicate the data, so any errournous reshaping of data is discovered.
It is expected, that experiments can have different number of NCYC points per spectrometer frequency.

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23723 | tlinnet | 2014-06-07 21:43:19 +0200 (Sat, 07 Jun 2014) | 55 lines

[...]

[...] Initial try to alter the target function calc_CR72_chi2.

[...]

[...] This is the first test to restructure the arrays, to allow for higher dimensional computation.

[...] All numpy arrays have to have same shape to allow to multiply together.

[...] The dimensions should be [ei][si][mi][oi][di]. [Experiment][spins][spec. frq][offset][disp points].

[...] This is complicated with number of disp point can change per spectrometer frequency.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

[...]

[...] This implementation brings a high overhead.

[...] The first test shows no winning of time.

[...] The creation of arrays takes all the time.

[...]

[...] Checked on MacBook Pro

[...] 2.4 GHz Intel Core i5

[...] 8 GB 1067 Mhz DDR3 RAM.

[...] Python Distribution -- Python 2.7.3 |EPD 7.3-2 (32-bit)|

[...]

[...] Timing for:

[...] 3 fields, [600. * 1E6, 800. * 1E6, 900. * 1E6]

[...] ('sfrq: ', 600000000.0, 'number of cpmg frq', 15)

[...] ('sfrq: ', 800000000.0, 'number of cpmg frq', 20)

[...] ('sfrq: ', 900000000.0, 'number of cpmg frq', 22)

[...] iterations of function call: 1000

[...]

[...] Timed for simulating 1 or 100 clustered spins.

[...]

[...] For TRUNK

[...]

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 3000 0.267 0.000 0.313 0.000 cr72.py:100(r2eff_CR72)

[...] 1000 0.056 0.000 0.434 0.000 relax_disp.py:456(calc_CR72_chi2)

[...] 3000 0.045 0.000 0.061 0.000 chi2.py:32(chi2)

[...]

[...] 100 spins:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 300000 26.315 0.000 30.771 0.000 cr72.py:100(r2eff_CR72)

[...] 1000 5.498 0.005 42.660 0.043 relax_disp.py:456(calc_CR72_chi2)

[...] 300000 4.438 0.000 6.021 0.000 chi2.py:32(chi2)

[...]

[...] TESTING

[...]

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 19013 0.278 0.000 0.278 0.000 {numpy.core.multiarray.array}

[...] 1000 0.191 0.000 0.777 0.001 relax_disp.py:457(calc_CR72_chi2)

[...] 1000 0.147 0.000 0.197 0.000 cr72.py:101(r2eff_CR72)

[...] 3000 0.044 0.000 0.061 0.000 chi2.py:32(chi2)

[...]

[...] 100 spins:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1504904 25.215 0.000 25.215 0.000 {numpy.core.multiarray.array}

[...] 1000 17.261 0.017 51.180 0.051 relax_disp.py:457(calc_CR72_chi2)

[...] 300000 4.637 0.000 6.310 0.000 chi2.py:32(chi2)

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

[...] r23724 | tlinnet | 2014-06-07 21:43:21 +0200 (Sat, 07 Jun 2014) | 4 lines

[...]

[...] Temporary changed the lib/dispersion/cr72.py function to unsafe state.

[...]

[...] This change turns-off all the safety measures, since they have to be re-implemented

[...] for higher dimensional structures.

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

[...] r23725 | tlinnet | 2014-06-07 22:36:00 +0200 (Sat, 07 Jun 2014) | 71 lines

[...]

[...] Altered profiling script to report cumulative timings and save to temporary files.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

[...]

[...] This indeed shows that the efficiency has gone down:

[...]

[...] -----

[...]

[...] Checked on MacBook Pro

[...] 2.4 GHz Intel Core i5

[...] 8 GB 1067 Mhz DDR3 RAM.

[...] Python Distribution -- Python 2.7.3 |EPD 7.3-2 (32-bit)|

[...]

[...] Timing for:

[...] 3 fields, [600. * 1E6, 800. * 1E6, 900. * 1E6]

[...] ('sfrq: ', 600000000.0, 'number of cpmg frq', 15)

[...] ('sfrq: ', 800000000.0, 'number of cpmg frq', 20)

[...] ('sfrq: ', 900000000.0, 'number of cpmg frq', 22)

[...] iterations of function call: 1000

[...]

[...] Timed for simulating 1 or 100 clustered spins.

[...]

[...] For TRUNK

[...]

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 0.434 0.434 :1()

[...] 1 0.001 0.001 0.434 0.434 pf:354(single)

[...] 1000 0.002 0.000 0.432 0.000 pf:340(calc)

[...] 1000 0.007 0.000 0.429 0.000 relax_disp.py:908(func_CR72_full)

[...] 1000 0.054 0.000 0.416 0.000 relax_disp.py:456(calc_CR72_chi2)

[...] 3000 0.256 0.000 0.300 0.000 cr72.py:100(r2eff_CR

[...]

[...] 100 spins:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 42.035 42.035 :1()

[...] 1 0.002 0.002 42.035 42.035 pf:378(cluster)

[...] 1000 0.004 0.000 41.957 0.042 pf:340(calc)

[...] 1000 0.011 0.000 41.953 0.042 relax_disp.py:908(func_CR72_full)

[...] 1000 5.378 0.005 41.928 0.042 relax_disp.py:456(calc_CR72_chi2)

[...] 300000 25.942 0.000 30.276 0.000 cr72.py:100(r2eff_CR72)

[...] 300000 4.362 0.000 5.903 0.000 chi2.py:32(chi2)

[...]

[...] TESTING

[...]

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 0.792 0.792 :1()

[...] 1 0.001 0.001 0.792 0.792 pf:354(single)

[...] 1000 0.002 0.000 0.789 0.001 pf:340(calc)

[...] 1000 0.011 0.000 0.787 0.001 relax_disp.py:966(func_CR72_full)

[...] 1000 0.187 0.000 0.769 0.001 relax_disp.py:457(calc_CR72_chi2)

[...] 26013 0.290 0.000 0.290 0.000 {numpy.core.multiarray.array}

[...] 1000 0.147 0.000 0.198 0.000 cr72.py:101(r2eff_CR72)

[...] 2001 0.002 0.000 0.086 0.000 numeric.py:167(asarray)

[...] 3000 0.045 0.000 0.062 0.000 chi2.py:32(chi2)

[...]

[...] 100 spins:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 46.821 46.821 :1()

[...] 1 0.002 0.002 46.821 46.821 pf:378(cluster)

[...] 1000 0.004 0.000 46.744 0.047 pf:340(calc)

[...] 1000 0.017 0.000 46.740 0.047 relax_disp.py:966(func_CR72_full)

[...] 1000 15.422 0.015 46.708 0.047 relax_disp.py:457(calc_CR72_chi2)

[...] 1511904 23.475 0.000 23.475 0.000 {numpy.core.multiarray.array}

[...] 300000 4.175 0.000 5.668 0.000 chi2.py:32(chi2)

[...] 2001 0.004 0.000 4.804 0.002 numeric.py:167(asarray)

[...] 1000 0.010 0.000 2.438 0.002 fromnumeric.py:1774(amax)

[...] 1000 0.006 0.000 2.428 0.002 fromnumeric.py:32(_wrapit)

[...] 300000 0.353 0.000 1.493 0.000 fromnumeric.py:1379(sum)

[...] 1000 1.281 0.001 1.444 0.001 cr72.py:101(r2eff_CR72)

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

[...] r23726 | tlinnet | 2014-06-07 23:18:15 +0200 (Sat, 07 Jun 2014) | 3 lines

[...]

[...] Added print out of chi2 to profile script.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23727 | tlinnet | 2014-06-07 23:18:18 +0200 (Sat, 07 Jun 2014) | 3 lines

[...]

[...] Moved the creation of special numpy structures outside target function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23728 | tlinnet | 2014-06-08 13:14:34 +0200 (Sun, 08 Jun 2014) | 5 lines

[...]

[...] Modified profiling script to calculate correct values when setting up R2eff values.

[...]

[...] This is to test, that the return of chi2 gets zero.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23729 | tlinnet | 2014-06-08 13:14:36 +0200 (Sun, 08 Jun 2014) | 31 lines

[...]

[...] Removing looping over exp and offset indicies in calc_chi2. They are always 0 anyway.

[...]

[...] This brings a little speed.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

[...]

[...] ----

[...] Profiling.

[...]

[...] 1000 iterations

[...] 100 spins

[...] 3 sfrq

[...] ('sfrq: ', 600000000.0, 'number of cpmg frq', 15, array([ 2., 6., 10., 14., 18., 22., 26., 30., 34., 38., 42.,

[...] 46., 50., 54., 58.]))

[...] ('sfrq: ', 800000000.0, 'number of cpmg frq', 20, array([ 2., 6., 10., 14., 18., 22., 26., 30., 34., 38., 42.,

[...] 46., 50., 54., 58., 62., 66., 70., 74., 78.]))

[...] ('sfrq: ', 900000000.0, 'number of cpmg frq', 22, array([ 2., 6., 10., 14., 18., 22., 26., 30., 34., 38., 42.,

[...] 46., 50., 54., 58., 62., 66., 70., 74., 78., 82., 86.]))

[...] ('chi2 cluster:', 0.0)

[...]

[...] TRUNK

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1000 5.221 0.005 53.578 0.054 relax_disp.py:456(calc_CR72_chi2)

[...]

[...] BEFORE

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1000 14.871 0.015 43.084 0.043 relax_disp.py:494(calc_CR72_chi2)

[...]

[...] AFTER removing looping over exp and offset indicies. They are always 0.

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1000 12.831 0.013 38.248 0.038 relax_disp.py:494(calc_CR72_chi2)

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

[...] r23730 | tlinnet | 2014-06-08 13:14:38 +0200 (Sun, 08 Jun 2014) | 5 lines

[...]

[...] In profiling script, moved up the calculation of values one level.

[...]

[...] This is to better see the output of the profiling iterations for cr72.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23731 | tlinnet | 2014-06-08 19:48:23 +0200 (Sun, 08 Jun 2014) | 6 lines

[...]

[...] Fix for calculation of the larmor frequency per spin in profiling script.

[...]

[...] The frq loop should also be up-shifted.

[...] It was now extracted as 0.0.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23732 | tlinnet | 2014-06-08 19:48:25 +0200 (Sun, 08 Jun 2014) | 7 lines

[...]

[...] Re-inserted safety checks in lin/dispersion/cr72.py file.

[...]

[...] This is re-inserted for the rank_1 cases.

[...]

[...] This makes the unit-tests pass again.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23733 | tlinnet | 2014-06-08 19:48:27 +0200 (Sun, 08 Jun 2014) | 8 lines

[...]

[...] Important fix for extracting the correct shape to create new arrays.

[...]

[...] If using just one field, or having the same number of dispersion points, the shape would extend to the dispersion number.

[...] It would report [ei][si][mi][oi][di] when calling ndarray.shape.

[...]

[...] Shape always has to be reported as: [ei][si][mi][oi].

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23734 | tlinnet | 2014-06-08 19:48:29 +0200 (Sun, 08 Jun 2014) | 3 lines

[...]

[...] Made it easier to switch between single and cluster reporting in profiling script.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23735 | tlinnet | 2014-06-08 19:48:31 +0200 (Sun, 08 Jun 2014) | 9 lines

[...]

[...] Important fix for the creation of the multi dimensional pA numpy array.

[...]

[...] It should be created as numpy.zeros([ei][si][mi][oi]) instead of numpy.ones([ei][si][mi][oi]).

[...]

[...] This allows for rapid testing of all dimensions with np.allclose(pA, numpy.ones(dw.shape)).

[...] pA can have missing filled out values, when the number of dispersion points are different

[...] per spectrometer frequency.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23736 | tlinnet | 2014-06-08 19:48:33 +0200 (Sun, 08 Jun 2014) | 18 lines

[...]

[...] Added unit tests demonstrating edge cases 'no Rex' failures of the model 'CR72 full', for a clustered multi dimensional calculation.

[...]

[...] This is implemented for one field.

[...]

[...] 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,

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23737 | tlinnet | 2014-06-08 19:48:35 +0200 (Sun, 08 Jun 2014) | 7 lines

[...]

[...] Re-implemented safety checks in lib/dispersion/cr72.py.

[...]

[...] This is now implemented for both rank-1 float array and of higher dimensions.

[...]

[...] This makes the unit tests pass for multi dimensional computing.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23738 | tlinnet | 2014-06-08 19:48:37 +0200 (Sun, 08 Jun 2014) | 17 lines

[...]

[...] Added unit tests demonstrating edge cases 'no Rex' failures of the model 'CR72 full', for a clustered multi dimensional calculation.

[...]

[...] This is implemented for three fields.

[...]

[...] 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,

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23739 | tlinnet | 2014-06-08 19:48:38 +0200 (Sun, 08 Jun 2014) | 5 lines

[...]

[...] Changed that special numpy structure is also created for "CR72".

[...]

[...] This makes most system tests pass.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23740 | tlinnet | 2014-06-08 22:22:22 +0200 (Sun, 08 Jun 2014) | 5 lines

[...]

[...] Critical fix for the slicing of values in target function.

[...]

[...] This makes system test: Relax_disp.test_sod1wt_t25_to_cr72 pass.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23741 | tlinnet | 2014-06-08 22:22:24 +0200 (Sun, 08 Jun 2014) | 6 lines

[...]

[...] Added self.has_missing keyword in initialization of the Dispersion class.

[...]

[...] This is to test once, per spin or cluster.

[...] This saves a looping over the dipsersion points, when collection the data.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23742 | tlinnet | 2014-06-08 22:22:26 +0200 (Sun, 08 Jun 2014) | 6 lines

[...]

[...] Created multi dimensional error and value numpy arrays.

[...]

[...] This is to calculate the chi2 sum much faster.

[...] Reordered the loop over missing data points, so it is only iniatiated if missing points is detected.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

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

[...] r24654 | bugman | 2014-07-22 18:52:58 +0200 (Tue, 22 Jul 2014) | 118 lines

[...]

[...] Merged revisions 23745-23752,23754-23758 via svnmerge from

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

[...]

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

[...] r23745 | tlinnet | 2014-06-08 23:44:44 +0200 (Sun, 08 Jun 2014) | 8 lines

[...]

[...] Swith the looping from spin->frq to frq->spin.

[...]

[...] Since the number of dispersion points are the same for all spins, this

[...] allows to move the calculation of pA and kex array one level up.

[...]

[...] This saves alot of computation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23746 | tlinnet | 2014-06-08 23:44:45 +0200 (Sun, 08 Jun 2014) | 3 lines

[...]

[...] Changed all the creation of special numpy arrays to be of float64 type.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23747 | tlinnet | 2014-06-08 23:54:41 +0200 (Sun, 08 Jun 2014) | 5 lines

[...]

[...] Moved the data filling of special numpy array errors and values, to initialization of Dispersion class.

[...]

[...] These values does not change, and can safely be stored outside.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23748 | tlinnet | 2014-06-08 23:56:36 +0200 (Sun, 08 Jun 2014) | 3 lines

[...]

[...] Just a tiny little more speed, by removing temporary storage of chi2 calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23749 | tlinnet | 2014-06-09 00:09:59 +0200 (Mon, 09 Jun 2014) | 25 lines

[...]

[...] Changed all calls to numpy np.X functions to just the numpy function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

[...]

[...] Timing is now showing, 17% loss per single spin, but but 277 % gain on 100 spin.

[...] 3 fields, 1000 iterations.

[...] 1 spin

[...] 1 0.000 0.000 0.677 0.677 :1()

[...] 1 0.001 0.001 0.677 0.677 pf:419(single)

[...] 1000 0.002 0.000 0.671 0.001 pf:405(calc)

[...] 1000 0.009 0.000 0.669 0.001 relax_disp.py:979(func_CR72_full)

[...] 1000 0.102 0.000 0.655 0.001 relax_disp.py:507(calc_CR72_chi2)

[...] 1003 0.160 0.000 0.365 0.000 cr72.py:101(r2eff_CR72)

[...] 23029 0.188 0.000 0.188 0.000 {numpy.core.multiarray.array}

[...] 4003 0.119 0.000 0.182 0.000 numeric.py:1862(allclose)

[...]

[...] 100 spin

[...] 1 0.000 0.000 19.783 19.783 :1()

[...] 1 0.002 0.002 19.783 19.783 pf:441(cluster)

[...] 1000 0.004 0.000 19.665 0.020 pf:405(calc)

[...] 1000 0.013 0.000 19.661 0.020 relax_disp.py:979(func_CR72_full)

[...] 1000 6.541 0.007 19.634 0.020 relax_disp.py:507(calc_CR72_chi2)

[...] 916108 11.127 0.000 11.127 0.000 {numpy.core.multiarray.array}

[...] 1300 1.325 0.001 2.026 0.002 cr72.py:101(r2eff_CR72)

[...] 4300 0.495 0.000 0.634 0.000 numeric.py:1862(allclose)

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

[...] r23750 | tlinnet | 2014-06-09 00:49:14 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Removed unused import of numpy.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23751 | tlinnet | 2014-06-09 00:49:15 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Changed all calls to numpy np.X functions to just the numpy function in lib/dispersion/cr72.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23752 | tlinnet | 2014-06-09 00:49:18 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Removed unused import of numpy.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23754 | tlinnet | 2014-06-09 19:46:17 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Made copies of numpy arrays instead of creating from new.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23755 | tlinnet | 2014-06-09 19:46:19 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Added a self.frqs_a as a multidimensional numpy array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23756 | tlinnet | 2014-06-09 19:46:20 +0200 (Mon, 09 Jun 2014) | 3 lines

[...]

[...] Small fix for the indicies to the errors and values numpy array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23757 | tlinnet | 2014-06-09 19:46:22 +0200 (Mon, 09 Jun 2014) | 5 lines

[...]

[...] Lowered the number of iterations to the profiling scripts.

[...]

[...] This is to use the profiling script as bug finder.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23758 | tlinnet | 2014-06-09 19:46:25 +0200 (Mon, 09 Jun 2014) | 7 lines

[...]

[...] Moved the calculation of dw_frq out of spin and spectrometer loop.

[...]

[...] This is done by having a special 1/0 spin numpy array, which turns on or off the values in the numpy array multiplication.

[...]

[...] The multiplication needs to first axis expand dw, and then tile the arrays according to the numpy structure.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

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

[...] r24655 | bugman | 2014-07-22 18:56:51 +0200 (Tue, 22 Jul 2014) | 543 lines

[...]

[...] Merged revisions 23760-23770,23787-23789,23791-23806,23813-23855 via svnmerge from

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

[...]

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

[...] r23760 | tlinnet | 2014-06-10 01:01:49 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Moved the calculation of pA and kex out off all loopes.

[...]

[...] This was done by having two special 1/0 spin structure arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23761 | tlinnet | 2014-06-10 01:01:51 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Removed dw_frq_a numpy array, as it was not necessary.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23762 | tlinnet | 2014-06-10 01:01:53 +0200 (Tue, 10 Jun 2014) | 6 lines

[...]

[...] Removed all looping over spin and spectrometer frequency.

[...]

[...] This is the last loop!

[...] Wuhu.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23763 | tlinnet | 2014-06-10 01:01:55 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Reordered arrays for beauty of code.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23764 | tlinnet | 2014-06-10 01:01:57 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Made the back_calc array be initiated as copy of the values array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23765 | tlinnet | 2014-06-10 01:01:59 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Small edit to profiling script, to help bug finding.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23766 | tlinnet | 2014-06-10 01:02:00 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Fixed that arrays are correctly initiated with one or zero values.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23767 | tlinnet | 2014-06-10 01:02:02 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Very important fix, for only replacing part of data array which have Nan values.

[...]

[...] Before, all values were replaced, which was wrong.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23768 | tlinnet | 2014-06-10 01:02:04 +0200 (Tue, 10 Jun 2014) | 8 lines

[...]

[...] Needed to increase the relative tolerance when testing if pA array is 1.

[...]

[...] Now system test Relax_disp.test_hansen_cpmg_data_missing_auto_analysis passes.

[...]

[...] Also added some comments lines, to prepare for mask replace of values.

[...] For example if only some of etapos values should be replaced.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23769 | tlinnet | 2014-06-10 01:02:06 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Restored profiling script to normal.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23770 | tlinnet | 2014-06-10 01:21:14 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Made the logic and comments much clearer about how to reshape, expand axis, and tile numpy arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23787 | tlinnet | 2014-06-10 16:51:30 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Removed line "# -*- coding: utf-8 -*-" which was automatically inserted by new python code editor.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23788 | tlinnet | 2014-06-10 16:51:33 +0200 (Tue, 10 Jun 2014) | 10 lines

[...]

[...] Implemented a masked array search for where "missing" array is equal 1.

[...]

[...] This makes it possible to replace all values with this mask, from the value array.

[...]

[...] This eliminates the last loops over the missing values.

[...]

[...] It took over 4 hours to figure out, that the mask should be called with mask.mask,

[...] to return the same fulls structure,

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23789 | tlinnet | 2014-06-10 16:51:35 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Yet another small improvement for the profiling script.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23791 | tlinnet | 2014-06-10 18:40:55 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Removed the multi dimensional structure of pA.

[...]

[...] pA is not multi-dimensional, and can just be multiplied with numpy arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23792 | tlinnet | 2014-06-10 18:40:59 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Fix for testing of pA in lib function, when pA is just float.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23793 | tlinnet | 2014-06-10 18:41:01 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Modified unit tests, so pA is sent to target function as float instead of array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23794 | tlinnet | 2014-06-10 18:41:03 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Removed the multi dimensional structure of kex.

[...]

[...] kex is not multi-dimensional, and can just be multiplied with numpy arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23795 | tlinnet | 2014-06-10 18:41:05 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Fix for testing of kex in lib function, when kex is just float.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23796 | tlinnet | 2014-06-10 18:41:06 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Modified unit tests, so kex is sent to target function as float instead of array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23797 | tlinnet | 2014-06-10 18:41:08 +0200 (Tue, 10 Jun 2014) | 10 lines

[...]

[...] Important fix for replacing values if eta_pos > 700 is violated.

[...]

[...] This fixes systemtest: Relax_disp.test_sod1wt_t25_to_cr72, which failed after making kex to a numpy float.

[...]

[...] The trick is to make a numpy mask which stores the position where to replace the values.

[...] Then replace the values just before last return.

[...]

[...] This makes sure, that not all values are changed.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23798 | tlinnet | 2014-06-10 18:41:10 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Increased the kex speed to 1e7 in clustered unit tests cases.

[...]

[...] This is to demonstrate where there will be no excange.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23799 | tlinnet | 2014-06-10 18:54:28 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Added a multi-dimensional numpy array chi2 value calculation function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23800 | tlinnet | 2014-06-10 18:54:31 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Called the newly created chi2 function to calculate for multi dimensional numpy arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23801 | tlinnet | 2014-06-10 19:11:07 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Renamed chi2_ND to chi2_rankN.

[...]

[...] This is a better name for representing multiple axis calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23802 | tlinnet | 2014-06-10 20:58:15 +0200 (Tue, 10 Jun 2014) | 5 lines

[...]

[...] Made special ei, si, mi, and oi numpy structure array.

[...]

[...] This is for rapid speed-up of numpy array creation in target function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23803 | tlinnet | 2014-06-10 20:58:19 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Code clean-up in lib function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23804 | tlinnet | 2014-06-10 20:58:22 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Replace np.tile with tile.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23805 | tlinnet | 2014-06-10 20:58:24 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Replaced self.spins_a with self.disp_struct.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23806 | tlinnet | 2014-06-10 21:06:12 +0200 (Tue, 10 Jun 2014) | 3 lines

[...]

[...] Removed un-used self structures in __init__of class.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23813 | tlinnet | 2014-06-11 08:28:25 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Made iinitialisation structures for dw.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23814 | tlinnet | 2014-06-11 08:28:27 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Initial try to reshape dw faster.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23815 | tlinnet | 2014-06-11 08:40:38 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Switched to use self.ei, self.si, self.mi, self.oi, self.di.

[...]

[...] This is for better reading of code.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23816 | tlinnet | 2014-06-11 08:40:40 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Comment out the sys.exit(), which would make the code fail for wrong calculation of dw.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23817 | tlinnet | 2014-06-11 08:46:00 +0200 (Wed, 11 Jun 2014) | 7 lines

[...]

[...] Copied profiling script for CPMG model CR72 to R1rho DPL94 model.

[...]

[...] The framework of the script will be the same, but the data a little different.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23818 | tlinnet | 2014-06-11 10:08:02 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Started converting profiling script to DPL94.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23819 | tlinnet | 2014-06-11 10:08:05 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Replaced self.(ei,si,mi,oi,di) with self.(NE,NS,NM,NO,ND).

[...]

[...] These numbers represents the maximum number of dimensions, instead of index.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23820 | tlinnet | 2014-06-11 10:08:06 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Added the ei index, when creating the first dw_mask.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23821 | tlinnet | 2014-06-11 10:08:08 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Reordered how the structures dw init structures are created.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23822 | tlinnet | 2014-06-11 10:08:10 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Clearing the dw_struct before calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23823 | tlinnet | 2014-06-11 10:16:27 +0200 (Wed, 11 Jun 2014) | 8 lines

[...]

[...] Started using the new way of constructing dw.

[...]

[...] This is for running system tests.

[...]

[...] Note, somewhere in the dw array, the frequencies will be different between the two implementations.

[...] But apparently, this does not matter.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23824 | tlinnet | 2014-06-11 10:46:42 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Inserted temporary method to switch for profiling.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23825 | tlinnet | 2014-06-11 10:46:44 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] First try to speed-up the old dw structure calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23826 | tlinnet | 2014-06-11 13:12:12 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Simplified calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23827 | tlinnet | 2014-06-11 13:12:14 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Yet another try to implement a fast dw structure method.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23828 | tlinnet | 2014-06-11 13:12:16 +0200 (Wed, 11 Jun 2014) | 6 lines

[...]

[...] Implemented the fastest way to calculate the dw structure.

[...]

[...] This uses the numpy ufunc multiply.outer function to create the outer array, and then multiply

[...] with the frqs_structure.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23829 | tlinnet | 2014-06-11 13:12:18 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Renamed dw temporary structure to generic structure.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23830 | tlinnet | 2014-06-11 13:12:20 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Restructured the calculation of R20A and R20B to the most efficient way.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23831 | tlinnet | 2014-06-11 13:12:21 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Made the lib/cr72.py to a numpy multi dimensional numpy array calculation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23832 | tlinnet | 2014-06-11 14:05:35 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Changed the catching when dw is zero, to use masked array.

[...]

[...] Implemented backwards compability with unit tests.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23833 | tlinnet | 2014-06-11 14:05:37 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Bugfix for testing if kex is zero.

[...]

[...] It was tested if kex was equal 1.0.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23834 | tlinnet | 2014-06-11 14:54:37 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Implemented masked replacement if fact is less that 1.0.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23835 | tlinnet | 2014-06-11 14:55:31 +0200 (Wed, 11 Jun 2014) | 1 line

[...]

[...] Replaced isnan mask with function that catches all invalid values.

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

[...] r23836 | tlinnet | 2014-06-11 14:55:32 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Clean up of comment lines.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23837 | tlinnet | 2014-06-11 14:55:34 +0200 (Wed, 11 Jun 2014) | 8 lines

[...]

[...] Removed the masked replacement if fact is less than 1.0.

[...]

[...] This is very strange, but otherwise system test:

[...] Relax_disp.test_hansen_cpmg_data_missing_auto_analysis

[...]

[...] would fail.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23838 | tlinnet | 2014-06-11 15:09:01 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Removed the slow allclose() function to test if R20A and R20B is equal.

[...]

[...] It is MUCH faster to just subtract and check sum is not 0.0.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23839 | tlinnet | 2014-06-11 15:25:32 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Replaced the temporary variable R2eff with back_calc, and used numpy subtract to speed up.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23840 | tlinnet | 2014-06-11 15:25:34 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Made the lib function into a pure numpy array calculation.

[...]

[...] This requires, that r20a, r20b and dw has same dimension as the dispersion points.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23841 | tlinnet | 2014-06-11 15:25:36 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Changes too unit tests, so data is sent to target function in numpy array format.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23842 | tlinnet | 2014-06-11 16:19:10 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Removed an the creation of a unnessary structure bu using numpy multiply.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23843 | tlinnet | 2014-06-11 16:19:12 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Moved the mask which finds where to replace values into the _init_ function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23844 | tlinnet | 2014-06-11 16:43:17 +0200 (Wed, 11 Jun 2014) | 7 lines

[...]

[...] Replaced the multiplcation with the disp structure, to a replacement with a mask.

[...]

[...] My timings are varying at my computer, so results are within the very same timing.

[...]

[...] But for reading the code, having two masks, is essential better.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23845 | tlinnet | 2014-06-11 17:09:23 +0200 (Wed, 11 Jun 2014) | 14 lines

[...]

[...] Merged revisions 23743 via svnmerge from

[...] svn+ssh://tlinnet@svn.gna.org/svn/relax/trunk

[...]

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

[...] r23743 | tlinnet | 2014-06-08 22:42:55 +0200 (Sun, 08 Jun 2014) | 6 lines

[...]

[...] Updated profiling text for CR72 model.

[...]

[...] Now it is tested for 3 fields.

[...]

[...] This is related to:

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

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

[...] r23846 | tlinnet | 2014-06-11 17:14:09 +0200 (Wed, 11 Jun 2014) | 25 lines

[...]

[...] Reverted r23845-r23844 as this was using a wrong commit message.

[...]

[...] The command used was:

[...] svn merge -r23845:23844 .

[...]

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

[...] r23845 | tlinnet | 2014-06-11 17:09:23 +0200 (Wed, 11 Jun 2014) | 14 lines

[...]

[...] Merged revisions 23743 via svnmerge from

[...] svn+ssh://tlinnet@svn.gna.org/svn/relax/trunk

[...]

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

[...] r23743 | tlinnet | 2014-06-08 22:42:55 +0200 (Sun, 08 Jun 2014) | 6 lines

[...]

[...] Updated profiling text for CR72 model.

[...]

[...] Now it is tested for 3 fields.

[...]

[...] This is related to:

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

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

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

[...] r23847 | tlinnet | 2014-06-11 17:15:03 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Copied profiling script for CR72 to B14 model.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23848 | tlinnet | 2014-06-11 19:37:37 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Modified profiling script for the B14 model.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23849 | tlinnet | 2014-06-11 19:37:40 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Modified model B14 lib file to faster numpy multidimensional mode.

[...]

[...] The implementations comes almost directly from the CR72 model file.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23850 | tlinnet | 2014-06-11 19:37:42 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Reverted the use of the mask "mask_set_blank".

[...]

[...] It did not work, and many system tests started failing.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23851 | tlinnet | 2014-06-11 19:37:43 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Changed the target function to handle the B14 model for faster numpy computation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23852 | tlinnet | 2014-06-11 19:37:45 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Changed unit test for B14 to match numpy input requirement.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23853 | tlinnet | 2014-06-11 20:43:45 +0200 (Wed, 11 Jun 2014) | 5 lines

[...]

[...] Added additional tests in b14, when math errors can occur.

[...]

[...] This is very easy with a conditional masked search in arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23854 | tlinnet | 2014-06-11 20:43:47 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Comment fix for finding when E0 is above 700 in lib function of B14.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23855 | tlinnet | 2014-06-11 20:47:29 +0200 (Wed, 11 Jun 2014) | 3 lines

[...]

[...] Removed use of "asarray", since the variables are already arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

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

[...] r24656 | bugman | 2014-07-22 19:04:10 +0200 (Tue, 22 Jul 2014) | 615 lines

[...]

[...] Merged revisions 23864-23877,23880,23888-23934,23937-23942,23946 via svnmerge from

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

[...]

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

[...] r23864 | tlinnet | 2014-06-12 12:12:58 +0200 (Thu, 12 Jun 2014) | 14 lines

[...]

[...] Changed target function for model CR72.

[...]

[...] To CR72 is now also the input of the parameters of R20A, R20B and dw.

[...] dw is tested for zero, to return flat lines.

[...] It is faster to search in the smaller numpy array, than the 5 dimensional dw array.

[...]

[...] This is for speed-up.

[...]

[...] R20A and R20B is also subtracted, to see if the full model should be used.

[...] In the same way, it is faster to subtract the smaller array.

[...]

[...] These small tricks are expected to give 5-10 pct. speeed-up.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23865 | tlinnet | 2014-06-12 12:12:59 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Made the lib function of CR72 accept the R20A, R20B and dw of the original array.

[...]

[...] This is for speed-up.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23866 | tlinnet | 2014-06-12 12:13:01 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Changed unit-tests, to send in the original R20A, R20B and dw_orig to the testing of the lib function CR72.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23867 | tlinnet | 2014-06-12 12:13:03 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Changed profiling script to send R20A, R20B and dw, as original parameters to the lib function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23868 | tlinnet | 2014-06-12 12:23:18 +0200 (Thu, 12 Jun 2014) | 11 lines

[...]

[...] Changed target function for model B14.

[...]

[...] To B14 now also send the input of the original parameters dw.

[...] dw is tested for zero, to return flat lines.

[...] It is faster to search in the smaller numpy array, than the 5 dimensional dw array.

[...]

[...] This is for speed-up.

[...]

[...] These small tricks are expected to give 5-10 pct. speeed-up.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23869 | tlinnet | 2014-06-12 12:23:20 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Made the lib function of B14 accept dw of the original array.

[...]

[...] This is for speed-up.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23870 | tlinnet | 2014-06-12 12:23:21 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Changed unit-tests, to send in the original dw_orig to the testing of the lib function B14.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23871 | tlinnet | 2014-06-12 12:23:23 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Changed profiling script to send dw as original parameters to the lib function B14.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23872 | tlinnet | 2014-06-12 12:31:42 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Copied profiling script for CR72 model to TSMFK01 model.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23873 | tlinnet | 2014-06-12 13:18:56 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Indention fix in cr72.py and b14.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23874 | tlinnet | 2014-06-12 13:18:58 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Modified profiling script to be used for model TSMFK01.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23875 | tlinnet | 2014-06-12 13:19:00 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Modified target function for model TSMFK01, to send in dw as original parameter.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23876 | tlinnet | 2014-06-12 13:19:02 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Modified lib function for model TSMFK01 to accept dw_orig as input and replaced functions to find math domain errors into maske replacements.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23877 | tlinnet | 2014-06-12 13:19:04 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Made unit tests for model TSMFK01 send in R20A and dw as a numpy array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23880 | tlinnet | 2014-06-12 13:56:12 +0200 (Thu, 12 Jun 2014) | 32 lines

[...]

[...] Large increase in speed for model TSMFK01 by changing target functions to use multidimensional numpy arrays in calculation.

[...]

[...] This is done by restructuring data into multidimensional arrays of dimension [NE][NS][NM][NO][ND], which are

[...] number of spins, number of magnetic field strength, number of offsets, maximum number of dispersion point.

[...]

[...] The speed comes from using numpy ufunc operations.

[...]

[...] The new version is 2.4X as fast per spin calculation, and 54X as fast for clustered analysis.

[...]

[...] The different in timings for 3 spectrometer frequencies, calculated for 1 spin or 100 clustered spins with 1000 iterations are:

[...]

[...] ----

[...] VERSION 3.2.2

[...] ----

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 0.262 0.262 :1()

[...] 100 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 25.391 25.391 :1()

[...] ----

[...] New version

[...] ---

[...]

[...] 1 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 0.111 0.111 :1()

[...] 100 spin:

[...] ncalls tottime percall cumtime percall filename:lineno(function)

[...] 1 0.000 0.000 0.468 0.468 :1()

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23888 | tlinnet | 2014-06-12 20:07:59 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Replacing math domain checking in model DPL94, with masked array replacement.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23889 | tlinnet | 2014-06-12 20:08:01 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Fix for import missing error in lib function dpl94.

[...]

[...] Needed to import numpy any() function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23890 | tlinnet | 2014-06-12 20:08:03 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] First try to speed up model DPL94.

[...]

[...] This has not succeded, since systemtest: Relax_disp.test_dpl94_data_to_dpl94 sti?\195?\131ll fails.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23891 | tlinnet | 2014-06-12 20:08:06 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Trying to move some of the structures into its own part.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23892 | tlinnet | 2014-06-12 20:08:08 +0200 (Thu, 12 Jun 2014) | 7 lines

[...]

[...] Fix for forgetting to multiply frqs to power 2.

[...]

[...] This was found by inspecting all print out before and after implementation.

[...]

[...] New implementation of DPL94 now passes all system and unit tests.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23893 | tlinnet | 2014-06-12 20:08:10 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Moved the expansion of the R1 structure out of the for loops.

[...]

[...] This is to speed-up the _init_ of the class of the target function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23894 | tlinnet | 2014-06-12 20:35:04 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Moved the packing of errors and values out of for loop in the _init_ class of target function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23895 | tlinnet | 2014-06-12 20:35:06 +0200 (Thu, 12 Jun 2014) | 5 lines

[...]

[...] Moved the multi dimensional expansion of inv_relax_times out of for loop.

[...]

[...] This can be done for all structures, which does not have missing points.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23896 | tlinnet | 2014-06-12 20:35:08 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] For inv_relax_times, expanded one axis, and tiled up to NR spins, before reshaping and blowing up to full structure.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23897 | tlinnet | 2014-06-12 20:35:10 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Moved the expansion of frqs out of for loops.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23898 | tlinnet | 2014-06-12 23:11:38 +0200 (Thu, 12 Jun 2014) | 3 lines

[...]

[...] Documentation fix for description of input arrays to lib functions.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23899 | tlinnet | 2014-06-13 07:20:57 +0200 (Fri, 13 Jun 2014) | 3 lines

[...]

[...] Converted TAP03 model to use multi dimensional numpy arrays.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r23900 | tlinnet | 2014-06-13 07:21:00 +0200 (Fri, 13 Jun 2014) | 3 lines

[...]

[...] Made dw in unit tests of TAP03 be of numpy array.

[...]

[...] Task #7807 (https://gna.org/task/index.php?78

(Browse SVN revision 24670)

Merged revisions 24362-24364,24510,24612-24615,24619-24637,24641-24648,24650 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_spin_speed

........
r24362 | bugman | 2014-06-30 10:41:27 +0200 (Mon, 30 Jun 2014) | 10 lines

Created a master profiling script for comparing the speed between different dispersion models.

This is similar to the disp_profile_all.py script except it only operates on a single relax version.
The output is then simply the timings, with statistics, of the calculation time for 100 function
calls for 100 spins (either 10,000 function calls for single spins or 100 function calls for the
cluster of 100 spins).

The output of the script for the current disp_spin_speed branch code has also been added.
........
r24363 | tlinnet | 2014-06-30 11:48:47 +0200 (Mon, 30 Jun 2014) | 5 lines

Critical fix for the recalculation of tau cpmg, when plotting for numerical models.

The interpolated dispersion points with tau_cpgm was calculated with frq, instead of cmpg_frq.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24364 | bugman | 2014-06-30 12:20:31 +0200 (Mon, 30 Jun 2014) | 7 lines

The new dispersion model profiling master script now includes links to the relax wiki.

The models are no longer presented by name but rather by the relax wiki links for each model (see
http://wiki.nmr-relax.com/Category:Relaxation_dispersion for all these links). This is to improve
the Google rank of the relax wiki, as these links may appear in a number of locations.
........
r24510 | bugman | 2014-07-10 12:04:53 +0200 (Thu, 10 Jul 2014) | 6 lines

Removal of many unused imports in the disp_spin_speed branch.

These were detected using the devel_scripts/find_unused_imports.py script which uses pylint to find
all unused imports. The false positives also present in the trunk were ignored.
........
r24612 | tlinnet | 2014-07-22 15:16:47 +0200 (Tue, 22 Jul 2014) | 13 lines

Reverted r24339 as relax dependency of numpy is now 1.6 where the "out" argument is available.

The command used was:
svn merge -r24339:r24338 .

.....
r24339 | tlinnet | 2014-06-27 12:58:29 +0200 (Fri, 27 Jun 2014) | 3 lines

Added a list of systemtests to skip, if numpy "out" argument is not available.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

[...] .....

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

[...] r24613 | tlinnet | 2014-07-22 15:23:47 +0200 (Tue, 22 Jul 2014) | 13 lines

[...]

[...] Reverted r24336 as relax dependency of numpy is now 1.6 where the "einsum" function is available.

[...]

[...] The command used was:

[...] svn merge -r24336:r24335 .

[...]

[...] .....

[...] r24336 | tlinnet | 2014-06-27 12:58:22 +0200 (Fri, 27 Jun 2014) | 3 lines

[...]

[...] Added to target function that experiment_type_setup() should not be initiated, if numpy.einsum is missing.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

[...] .....

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

[...] r24614 | tlinnet | 2014-07-22 15:27:44 +0200 (Tue, 22 Jul 2014) | 18 lines

[...]

[...] Reverted r24337 as relax dependency of numpy is now 1.6 where the "out" argument is available.

[...]

[...] The command used was:

[...] svn merge -r24337:r24336 .

[...]

[...] .....

[...] r24337 | tlinnet | 2014-06-27 12:58:24 +0200 (Fri, 27 Jun 2014) | 8 lines

[...]

[...] Added a numpy "out" argument check to dep_check.py.

[...]

[...] This is for checking the out argument of:

[...] numpy.multiply

[...] numpy.add

[...] numpy.subtract

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

[...] .....

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

[...] r24615 | tlinnet | 2014-07-22 15:35:16 +0200 (Tue, 22 Jul 2014) | 13 lines

[...]

[...] Reverted r24323 as relax dependency of numpy is now 1.6 where "einsum" function is available.

[...]

[...] The command used was:

[...] svn merge -r24323:r24322 .

[...]

[...] .....

[...] r24323 | tlinnet | 2014-06-25 19:31:40 +0200 (Wed, 25 Jun 2014) | 3 lines

[...]

[...] Implemented a dependency check for numpy einsum, so relax can still start.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

[...] .....

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

[...] r24619 | tlinnet | 2014-07-22 16:51:26 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/b14.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24620 | tlinnet | 2014-07-22 16:51:28 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/cr72.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24621 | tlinnet | 2014-07-22 16:51:30 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/dpl94.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24622 | tlinnet | 2014-07-22 16:51:32 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/lm63_3site.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24623 | tlinnet | 2014-07-22 16:51:33 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/lm63.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24624 | tlinnet | 2014-07-22 16:51:35 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/m61b.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24625 | tlinnet | 2014-07-22 16:51:37 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/m61.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24626 | tlinnet | 2014-07-22 16:51:38 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/matrix_exponential.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24627 | tlinnet | 2014-07-22 16:51:40 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/mp05.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24628 | tlinnet | 2014-07-22 16:51:42 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/ns_cpmg_2site_expanded.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24629 | tlinnet | 2014-07-22 16:51:44 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/ns_cpmg_2site_star.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24630 | tlinnet | 2014-07-22 16:51:46 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/ns_mmq_2site.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24631 | tlinnet | 2014-07-22 16:51:48 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/ns_mmq_3site.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24632 | tlinnet | 2014-07-22 16:51:50 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/ns_r1rho_2site.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24633 | tlinnet | 2014-07-22 16:51:51 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/ns_r1rho_3site.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24634 | tlinnet | 2014-07-22 16:51:53 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/tap03.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24635 | tlinnet | 2014-07-22 16:51:55 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/tp02.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24636 | tlinnet | 2014-07-22 16:51:57 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of lib/dispersion/two_point.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24637 | tlinnet | 2014-07-22 16:51:59 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Code validation of target_functions/relax_disp.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24641 | tlinnet | 2014-07-22 17:53:38 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Removal of space after for loop in target_functions/relax_disp.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24642 | tlinnet | 2014-07-22 17:53:40 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Copyright time extension for lib/dispersion/tsmfk01.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24643 | tlinnet | 2014-07-22 17:53:42 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] More removal of space after for loop in target_functions/relax_disp.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24644 | tlinnet | 2014-07-22 17:53:43 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] For model ns mmq 3site, moved the parameter conversion of dw_AB from target function to lib function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24645 | tlinnet | 2014-07-22 17:53:45 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Removed chi sum initialisation in func_ns_mmq_2site() as this is not used.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24646 | tlinnet | 2014-07-22 17:53:47 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Documentation fix for the get_back_calc() function in target_function/relax_disp.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24647 | tlinnet | 2014-07-22 17:56:23 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Removed unnecessary repetitive calculation of kex**2 in model DPL94.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24648 | tlinnet | 2014-07-22 18:08:22 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] API documentation fixes, where a "\" is the last character on the line. There should be a space " ", ending this characater.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24650 | tlinnet | 2014-07-22 18:21:20 +0200 (Tue, 22 Jul 2014) | 3 lines

[...]

[...] Comment space fixing in target_functions/relax_disp.py.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...]

[...]

(Browse SVN revision 24664)

Merged revisions 24265-24266,24270-24278,24280-24283,24285-24308,24315,24319-24320 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/branches/disp_spin_speed

........
r24265 | tlinnet | 2014-06-24 10:43:06 +0200 (Tue, 24 Jun 2014) | 3 lines

Modified profiling script for NS R1rho 3site, to be functional.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24266 | tlinnet | 2014-06-24 10:46:17 +0200 (Tue, 24 Jun 2014) | 3 lines

Modified profiling script for ns r1rho 3site linear to be functional.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24270 | tlinnet | 2014-06-24 11:15:43 +0200 (Tue, 24 Jun 2014) | 3 lines

Removed un-used imports in profiling scripts for NS r1rho 3site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24271 | bugman | 2014-06-24 13:46:59 +0200 (Tue, 24 Jun 2014) | 6 lines

Added a relaxation dispersion model profiling log file for relax version 3.1.3 vs. 3.1.2 vs. 3.1.1.

This is the output from the dispersion model profiling master script. It shows that there are no
major speed differences between these relax versions.
........
r24272 | bugman | 2014-06-24 13:52:19 +0200 (Tue, 24 Jun 2014) | 5 lines

Added the system information printout to the dispersion model profiling master script output.

This is for the log files comparing one version of relax to the previous version.
........
r24273 | tlinnet | 2014-06-24 14:17:59 +0200 (Tue, 24 Jun 2014) | 3 lines

Added profiling script for model mmq cr72,

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24274 | tlinnet | 2014-06-24 14:18:03 +0200 (Tue, 24 Jun 2014) | 5 lines

Fix for the replacement value for invalid values in model MMQ CR72.

The value was set to use r20, but should instead be 1e100.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.
........
r24275 | tlinnet | 2014-06-24 14:20:31 +0200 (Tue, 24 Jun 2014) | 3 lines

[...] Copied profiling script from mmq cr72, to ns mmq 2site and 3site.

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

[...] r24276 | tlinnet | 2014-06-24 14:22:23 +0200 (Tue, 24 Jun 2014) | 3 lines

[...]

[...] Copied profiling script to ns mmq 3site linear.

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

[...] r24277 | tlinnet | 2014-06-24 14:32:23 +0200 (Tue, 24 Jun 2014) | 3 lines

[...]

[...] Implemented profiling script for NS MMQ 2SITE.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24278 | tlinnet | 2014-06-24 14:46:29 +0200 (Tue, 24 Jun 2014) | 3 lines

[...]

[...] Implemented profiling script for ns mmq 3site and 3site linear.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24280 | tlinnet | 2014-06-24 14:58:07 +0200 (Tue, 24 Jun 2014) | 3 lines

[...]

[...] Speeded up model NS CPMG 2site star, by moving the forming of the propagator matrix out of the for loops, and preform it.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24281 | bugman | 2014-06-24 15:04:47 +0200 (Tue, 24 Jun 2014) | 6 lines

[...]

[...] Added a relaxation dispersion model profiling log file for relax version 3.1.4 vs. 3.1.3.

[...]

[...] This is the output from the dispersion model profiling master script. It shows that there are no

[...] speed differences.

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

[...] r24282 | tlinnet | 2014-06-24 15:27:51 +0200 (Tue, 24 Jun 2014) | 3 lines

[...]

[...] Speeded up ns mmq 2site, by moving the forming of evolution matrix out of the for loops, and preform it.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24283 | tlinnet | 2014-06-24 15:36:01 +0200 (Tue, 24 Jun 2014) | 3 lines

[...]

[...] Speeded up ns mmq 3site, by moving the forming of evolution matrix out of the for loops, and preform it.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24285 | bugman | 2014-06-24 16:30:19 +0200 (Tue, 24 Jun 2014) | 6 lines

[...]

[...] Added a relaxation dispersion model profiling log file for relax version 3.1.5 vs. 3.1.4.

[...]

[...] This is the output from the dispersion model profiling master script. It shows that there are no

[...] speed differences.

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

[...] r24286 | tlinnet | 2014-06-24 16:35:01 +0200 (Tue, 24 Jun 2014) | 3 lines

[...]

[...] Speeded up ns r1rho 2site, by preforming the evolution matrices, and the M0 matrix in the init part of the target function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24287 | tlinnet | 2014-06-24 16:35:05 +0200 (Tue, 24 Jun 2014) | 3 lines

[...]

[...] Speeded up ns r1rho 3site, by preforming the evolution matrices, and the M0 matrix in the init part of the target function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24288 | bugman | 2014-06-24 17:06:45 +0200 (Tue, 24 Jun 2014) | 6 lines

[...]

[...] Expanded the dispersion model profiling master script to cover all the new profiling scripts.

[...]

[...] This includes all 3-site and MMQ models. The list is now complete and covers all models. The only

[...] model not included in 'M61 skew' which has redundant parameters and is not optimisable anyway.

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

[...] r24289 | bugman | 2014-06-24 17:47:53 +0200 (Tue, 24 Jun 2014) | 7 lines

[...]

[...] Added a relaxation dispersion model profiling log file for relax version 3.1.6 vs. 3.1.5.

[...]

[...] This is the output from the dispersion model profiling master script. It shows that there are

[...] almost no speed differences, except for a slight decrease in speed in the 'CR72 full' model for

[...] single spins.

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

[...] r24290 | tlinnet | 2014-06-25 02:14:22 +0200 (Wed, 25 Jun 2014) | 3 lines

[...]

[...] Split systemtest test_tp02_data_to_ns_r1rho_2site into a setup and test part.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24291 | tlinnet | 2014-06-25 02:14:29 +0200 (Wed, 25 Jun 2014) | 3 lines

[...]

[...] Implemented a clustered version of systemtest test_tp02_data_to_ns_r1rho_2site.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24292 | tlinnet | 2014-06-25 02:14:32 +0200 (Wed, 25 Jun 2014) | 6 lines

[...]

[...] Inserted an extremely interesting development in NS R1rho 2site.

[...]

[...] If one do a transpose of M0, one can calculate all the matrix evolutions in the start via numpy einsum.

[...] Since M0 is in higher a dimensions, one should not do a numpy transpose, but swap/roll the outer M0 6x1 axis.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24293 | tlinnet | 2014-06-25 02:14:34 +0200 (Wed, 25 Jun 2014) | 5 lines

[...]

[...] Shortened the code dramatically for NS R1rho 2site.

[...]

[...] It is possible to calculate all in "one" go, after having the trasposer/rolled-back M0 magnetization.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24294 | tlinnet | 2014-06-25 02:14:36 +0200 (Wed, 25 Jun 2014) | 7 lines

[...]

[...] Speeded up the code of NS r1rho 2site.

[...]

[...] This was essential done to numpy einsum, and doing the dot operations in multiple dimensions.

[...] It was though necessary to realize, that to do the proper dot product operations, the outer two

[...] axis if M0 should be swapped, by rolling the outer axis one back.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24295 | tlinnet | 2014-06-25 02:14:38 +0200 (Wed, 25 Jun 2014) | 7 lines

[...]

[...] Speeded up the code of NS r1rho 3site.

[...]

[...] This was essential done to numpy einsum, and doing the dot operations in multiple dimensions.

[...] It was though necessary to realize, that to do the proper dot product operations, the outer two

[...] axis if M0 should be swapped, by rolling the outer axis one back.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24296 | tlinnet | 2014-06-25 02:14:40 +0200 (Wed, 25 Jun 2014) | 3 lines

[...]

[...] Removed un-used import of rollaxis in ns r1rho 2site.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24297 | tlinnet | 2014-06-25 02:14:42 +0200 (Wed, 25 Jun 2014) | 5 lines

[...]

[...] For model NS CPMG 2site 3d, the M0 matrix was preformed for higher dimensionality in init of target function.

[...]

[...] The transposes/rolled axis versions was also initiated.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24298 | tlinnet | 2014-06-25 02:14:43 +0200 (Wed, 25 Jun 2014) | 5 lines

[...]

[...] Swapped the dot product position, when propagating the magnetisation in model NS CPMG 2site 3D.

[...]

[...] This it to try to align to same method as in NS R1rho 2site.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24299 | tlinnet | 2014-06-25 02:14:45 +0200 (Wed, 25 Jun 2014) | 3 lines

[...]

[...] Lowered the looping in NS CPMG 2site 3D, by preforming the inital dot product.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24300 | tlinnet | 2014-06-25 02:14:46 +0200 (Wed, 25 Jun 2014) | 3 lines

[...]

[...] Speeded up ns cpmg 2site 3d, by preforming the magnetisation.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24301 | tlinnet | 2014-06-25 02:14:48 +0200 (Wed, 25 Jun 2014) | 23 lines

[...]

[...] Got rid of the inner evolution of the magnetization.

[...]

[...] If the looping over the number of CPMG elements is given by the index l, and the initial magnetization has

[...] been formed, then the number of times for propagation of magnetization is l = power_si_mi_di-1.

[...] If the magnetization matrix "Mint" has the index Mint_(i,k) and the evolution matrix has the index Evol_(k,j), i=1, k=7, j=7

[...] then the dot product is given by: Sum_{k=1}^{k} Mint_(1,k) * Evol_(k,j) = D_(1, j).

[...] The numpy einsum formula for this would be: einsum('ik,kj -> ij', Mint, Evol)

[...]

[...] Following evolution will be: Sum_{k=1}^{k} D_(1, j) * Evol_(k,j) = Mint_(1,k) * Evol_(k,j) * Evol_(k,j).

[...] We can then realize, that the evolution matrix can be raised to the power l. Evol_P = Evol**l.

[...] It will then be: einsum('ik,kj -> ij', Mint, Evol_P)

[...]

[...] - Get which power to raise the matrix to.

[...] l = power_si_mi_di-1

[...]

[...] - Raise the square evolution matrix to the power l.

[...] evolution_matrix_T_pwer_i = matrix_power(evolution_matrix_T_i, l)

[...]

[...] Mint_T_i = dot(Mint_T_i, evolution_matrix_T_pwer_i)

[...] or

[...] Mint_T_i = einsum('ik,kj -> ij', Mint_T_i, evolution_matrix_T_pwer_i)

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24302 | tlinnet | 2014-06-25 02:14:50 +0200 (Wed, 25 Jun 2014) | 10 lines

[...]

[...] Tried to implement using lib.linear_algebra.matrix_power.square_matrix_power instead of matrix_power from numpy in NS CPMG 2site 3d.

[...]

[...] Strangely, then systemtest:

[...] test_hansen_cpmg_data_to_ns_cpmg_2site_3D_full

[...]

[...] starts to fail!

[...]

[...] This is very weird.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24303 | tlinnet | 2014-06-25 02:14:52 +0200 (Wed, 25 Jun 2014) | 5 lines

[...]

[...] Changes to unit test of NS CPMG 2site 3D.

[...]

[...] This is after the new initiated M0 matrix in init of target function.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24304 | tlinnet | 2014-06-25 03:41:00 +0200 (Wed, 25 Jun 2014) | 3 lines

[...]

[...] Double speed in NS CPMG 2site star, after using numpy.linalg.matrix_power instead of the lib version in relax.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24305 | tlinnet | 2014-06-25 03:41:02 +0200 (Wed, 25 Jun 2014) | 3 lines

[...]

[...] Triple speed in NS MMQ 2site, after using numpy.linalg.matrix_power instead of the lib version in relax.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24306 | tlinnet | 2014-06-25 03:41:04 +0200 (Wed, 25 Jun 2014) | 13 lines

[...]

[...] Small fix for making sure that power is a integer in ns mmq 2site.

[...]

[...] Following system tests was failing.

[...] - Relax_disp.test_korzhnev_2005_15n_dq_data

[...] - Relax_disp.test_korzhnev_2005_15n_sq_data

[...] - Relax_disp.test_korzhnev_2005_15n_zq_data

[...] - Relax_disp.test_korzhnev_2005_1h_sq_data

[...] - Relax_disp.test_korzhnev_2005_all_data

[...] - Relax_disp.test_korzhnev_2005_all_data_disp_speed_bug

[...]

[...] They should already be integers, but is now solved.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24307 | tlinnet | 2014-06-25 03:41:05 +0200 (Wed, 25 Jun 2014) | 3 lines

[...]

[...] Comment and spell fixing in NS CPMG 2site 3d.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24308 | tlinnet | 2014-06-25 03:41:07 +0200 (Wed, 25 Jun 2014) | 3 lines

[...]

[...] Triple speed in NS MMQ 3site, after using numpy.linalg.matrix_power instead of the lib version in relax.

[...]

[...] Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

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

[...] r24315 | bugman | 2014-06-25 13:23:16 +0200 (Wed, 25 Jun 2014) | 9 lines

[...]

[...] Updated the dispersion model profiling comparison of the disp_spin_speed branch vs. relax-3.2.2.

[...]

[...] This is for the current revision r24314 and now includes all dispersion models. This shows the

[...] large speed increases in the numeric and MMQ models recently obtained.

[...]

[...] Note that something went wrong with the 'NS CPMG 2-site 3D full' model for the clustered analysis,

[...] most times were around 24 seconds except for the first which was strangely 292 seconds.

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

[...] r24319 | bugman | 2014-06-25 17:04:00 +0200 (Wed, 25 Jun 2014) | 7 lines

[...]

[...] Updated the relaxation dispersion model profiling log file for relax version 3.2.2 vs. 3.2.1.

[...]

[...] This adds the MMQ and 3-site models to the log file. The new information shows that there was a 4.2

[...] times speed up for the 'MMQ CR72' model between these two relax versions, both for single spins and

[...] clustered spins, a much greater improvement than any other of the models.

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

[...] r24320 | bugman | 2014-06-25 17:08:54 +0200 (Wed, 25 Jun 2014) | 7 lines

[...]

[...] Removed the now redundant disp_profile_all_3.2.2.table.txt dispersion model profiling table.

[...]

[...] As the dispersion model profiling master script now covers all dispersion models, the output from

[...] this script produces this table exactly. Therefore the end of the log files saved from running this

[...] script contains this table.

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

[...]

[...]

(Browse SVN revision 24662)