Interesting. I'm guessing it's alright to optimize the different models at the same time on different CPUs since models II-V can be done in any order. Is there a way to specify use of another CPU on a parallel processor machine, or should I just run relax on other machines?
Tyler Quoting Edward d'Auvergne <[EMAIL PROTECTED]>: > 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
