Hi Ed, WOW ! I noticed the differences for local parameters between the two versions, but never tested a completed diffusion tensor optimization... The differences are huge ! They're so big that users should probably tell which version they used when publishing... i.e. ModelFree-4.20-Portland or ModelFree-4.20-gcc...
Also, maybe you're right, maybe the speed is not the best test for quality here... What do you think about simply printing a few lines summarising the text below in the user manual, hence in the code as some comments ? Ciao Séb Edward d'Auvergne wrote: > Hi, > > I've noticed this difference too. But I think I'm too much of a > Fortran sceptic! A long time ago, I went through the Modelfree4 > source code with a fine toothed comb and found 4 bugs in there. A few > of these were code issues which had no effect on the Portland compiler > (well the compilation part anyway) but was causing gcc to complain > loudly. Rightfully so as there was an undeclared variable used as a > counter in a loop - it's value was garbage. One of the bugs was a > problem with the Levenberg-Marquardt algorithm and that, together with > the other problems found in: > > d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR > dynamic models I. Minimisation algorithms and their performance within > the model-free and Brownian rotational diffusion spaces. J. Biomol. > NMR, 40(2), 107-119. (http://dx.doi.org/10.1007/s10858-007-9214-2) > > was the reason for Modelfree 4.20 to be released. The other bugs > caught by gcc, and the undeclared variable were the reason for > Modelfree 4.16 > (http://cpmcnet.columbia.edu/dept/gsas/biochem/labs/palmer/software/modelfree.html). > So I'm not sure if the speed of the two binaries is the best measure > of quality. It could be that the Portland version is faster due to a > bug. Or that the gcc one is slower due to higher precision. Who > knows? > > I'm not sure how we could advise the user. Maybe a print out at the > start of palmer.execute()? I think it would be best to advise the > user to only use Modelfree4 as a test and that it should be compared > to the much higher precision - hence slower - relax results. It might > also be worth stating that the Portland and gcc versions give > different results. Eg in the system test I created for it, one finds > the diffusion tensors: > > gcc: > tm = 8.964 > Dratio = 1.324 > theta = -52.070 > phi = 2.377 > > Portland: > tm = 8.443 > Dratio = 1.053 > theta = 68.864 > phi = 73.913 > > There is no glide or reflection symmetry here, so the results are > quite different. > > Regards, > > Edward > > _______________________________________________ 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
