Hi Troels, You should note that the 20x speed up is due to the change in optimisation algorithm rather than scipy vs. minfx vs. MINPACK. The reason I wrote minfx is that I started with scipy optimisation but found all implemented algorithms contained fatal bugs. This was not fixed for years after I reported it, and I don't know if the code had changed since 2003 when I looked into it. Anyway a scipy optimisation solution is incompatible with the minfx optimisation solution in relax. If you derive and code the gradients into relax, then you can use the minfx LM algorithm as a solution. Regards, Edward On 25 August 2014 01:08, <tlinnet@xxxxxxxxxxxxx> wrote:
Author: tlinnet Date: Mon Aug 25 01:08:44 2014 New Revision: 25228 URL: http://svn.gna.org/viewcvs/relax?rev=25228&view=rev Log: Further improved the profiling of relax curve fit. This profiling shows, that Python code is about twice as slow as the C code implemented. But it also shows that optimising with scipy.optimize.leastsq is 20 X faster. It also gives reasonable error values. Combining a function for a linear fit to guess the initial values, together with scipy optimise, will be an extreme time win for estimating R2eff values fast. A further test would be to use relax Monte-Carlo simulations for say 1000-2000 iterations, and compare to the errors extracted from estimated covariance. Added: trunk/test_suite/shared_data/curve_fitting/profiling/relax_fit.py Modified: trunk/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: trunk/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py?rev=25228&r1=25227&r2=25228&view=diff Added: trunk/test_suite/shared_data/curve_fitting/profiling/relax_fit.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/curve_fitting/profiling/relax_fit.py?rev=25228&view=auto _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@xxxxxxx To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits