Hi, 14 rounds of that length is quite normal. See Seb's post at https://mail.gna.org/public/relax-users/2006-11/msg00015.html for typical details. Actually, all the posts in the thread starting at https://mail.gna.org/public/relax-users/2006-11/msg00014.html could be useful. You can make this as fast as Art Palmer's Modelfree program (http://cpmcnet.columbia.edu/dept/gsas/biochem/labs/palmer/software/modelfree.html), but I can also modify Modelfree to be almost as slow as relax. relax will always be a little slower than Modelfree as the model-free code is in numpy which is slower than Modelfree's FORTRAN. Converting this relax code will speed relax up a bit. But, anyway, the major timing difference you see if running the 2 programs on default settings is due to an absolutely massive difference in optimization precision. For details please see d'Auvergne, E. J. and Gooley, P. R. 2008a (http://www.nmr-relax.com/refs.html).
Regards, Edward On Fri, Oct 31, 2008 at 5:47 PM, Tyler Reddy <[EMAIL PROTECTED]> wrote: > I'm on the 14th round of 'prolate' optimization at several hours per round. I > guess I'll have to try and get errors a different way as we discussed for this > to be reasonable in relax. > > Tyler > > > > Quoting Edward d'Auvergne <[EMAIL PROTECTED]>: > >> Hi, >> >> You'll need to update using: >> >> $ svn up >> >> then install as root/administrator by typing (assuming python is >> installed as root): >> >> $ python setup.py install >> >> in the minfx base directory. Then the crash shouldn't happen. If it >> does still have problems, it would be worth reporting it to the minfx >> mailing lists (https://gna.org/mail/?group=minfx). A bug report for >> minfx can be submitted at >> https://gna.org/bugs/?func=additem&group=minfx. >> >> As for this taking a long time to optimise, that is because of the >> convoluted, very tight optimisation space. You can decrease the >> max_iter value from 1e7 in the minimise() user function at the start >> to to maybe 1e5, but this should not be done at the end of the >> analysis. I would say though that all these problems will go away >> with a better error analysis in the R2 curve-fitting. >> >> Regards, >> >> Edward >> >> >> >> On Mon, Oct 27, 2008 at 12:48 AM, Tyler Reddy <[EMAIL PROTECTED]> wrote: >>> I used subversion to update minfx, but I'm still having the problem >>> (unless I >>> need to delete the old minfx, or does the nested update automatically 'take >>> over' in this case?). >>> >>> The calculation certainly goes a lot longer now than it did before, but >>> at k=312 >>> it crashes out with the same traceback. Another possibility is that >>> I have to >>> delete all the local_tm and sphere folders and just start from scratch >>> with the >>> new minfx, though I'm not sure that makes sense. >>> >>> Tyler >>> >>> >>> Quoting Edward d'Auvergne <[EMAIL PROTECTED]>: >>> >>>> Right, I've fixed the bug in the minfx repository. It will take me a >>>> while to release minfx 1.0.2 but using subversion you can get the >>>> changes immediately. Note that as this space is so warped, >>>> optimisation of this model will take a long, long time! >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> On Fri, Oct 24, 2008 at 10:40 PM, Edward d Auvergne >>>> <[EMAIL PROTECTED]> wrote: >>>>> >>>>> Update of bug #12499 (project relax): >>>>> >>>>> Status: Confirmed => Fixed >>>>> Open/Closed: Open => Closed >>>>> >>>>> _______________________________________________________ >>>>> >>>>> Follow-up Comment #5: >>>>> >>>>> This problem has been fixed in the minfx project >>>>> (https://gna.org/projects/minfx/), in the bug report >>>>> https://gna.org/bugs/?12501. >>>>> >>>>> _______________________________________________________ >>>>> >>>>> Reply to this item at: >>>>> >>>>> <http://gna.org/bugs/?12499> >>>>> >>>>> _______________________________________________ >>>>> Message sent via/by Gna! >>>>> http://gna.org/ >>>>> >>>>> >>>> >>> >>> >>> >>> >>> _______________________________________________ >>> relax (http://nmr-relax.com) >>> >>> This is the relax-devel mailing list >>> [email protected] >>> >>> 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://nmr-relax.com) >> >> This is the relax-devel mailing list >> [email protected] >> >> 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://nmr-relax.com) > > This is the relax-devel mailing list > [email protected] > > 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://nmr-relax.com) This is the relax-devel mailing list [email protected] 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
