Hi Edward. This post continues from: http://thread.gmane.org/gmane.science.nmr.relax.devel/6814
As I wrote in this post, the new user function: "relax_disp.r2eff_estimate()" gives freedom to the user to try other algorithms. Here scipy.optimize.leastsq which should be (or is) a well known option in the python community for minimisation. Did you find errors in MINPACK or in scipy ? Best Troels 2014-08-25 10:13 GMT+02:00 Edward d'Auvergne <edw...@nmr-relax.com>: > 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 _______________________________________________ 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
