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, <tlin...@nmr-relax.com> 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-comm...@gna.org > > 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 _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org 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-devel
