Re: full_analysis.py -- November 22, 2006 - 17:03

Hi Sebastien,

This is just a follow up query from an old post.  Did your
calculations using the new model-free optimisation protocol
implemented in the 'full_analysis.py' script eventually finish?  If
so, did it take much longer than a week?

Cheers,

Edward



On 10/17/06, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> Hi all !
>
> Thanks for sending me your comments and feelings...
>
> Here is an update of my benchmarks. Times are not precise though... only
> approximations based on a rapid lookup of the time stamps for my log
> files and outputs.
>
> All machine are x86 from Dell and run under Gentoo Linux
> (http://www.gentoo.org/)
>
> Computers
> Processor                                                         Memory
> =========
> ================================================================  ========
> Pelican    Intel Pentium4
> 3.20GHz                                            2.0 Go
> Pigeon     Intel Pentium4
> 3.20GHz                                            1.0 Go
> Hibou      Intel Xeon CPU 2.80GHz (x2 CPU, relax always using only one
> CPU)  2.0 Go
>
>
> Diffusion model    Round    Machine          Time      Time_for_opt/
> ===============    =====    =============    =======   =============
> local_tm           ---      Pelican          15h00
> --------------------------------------------------------------------
> sphere MII         init    Pelican            0h10
>                       1    Pelican           42h00     31h00
>                       2    Pelican           23h00     21h00
>                       3    Pelican           18h00     16h00
>                       4    Pelican
>
> prolate MIII       init    Hibou              0h20
>                       1    Hibou             76h00     74h00
>                       2    Hibou             44h00     39h00
>                       3    Hibou
>
> oblate MIV         init    Hibou              0h20
>                       1    Hibou             76h00     75h00
>                       2    Hibou             44h00     40h00
>                       3    Hibou
>
> ellipsoid MV       init    Pigeon             1h00
>                       1    Pigeon            75h00     74h00
>                       2    Pigeon            31h00     27h00
>                       3    Pigeon            20h00     17h00
>                       4    Pigeon
> --------------------------------------------------------------------
>
> So, it seems the behaviour is normal with the processing times getting
> shorter as the optimization proceeds... Maybe the first runs were long
> because of my errors on the NOEs being too small (I think they could be
> too underestimated because, with the traditional approach used in
> ModelFree -- the approach from Mandel et al., 1995 -- I can select only
> ~20% of residues for model 1 (and almost no residues in subsequent
> models) under an axially symmetric diffusion tensor...
>
> Also, the fitted values seem reasonable.
>
> Anyway, it seems I'll get optimized models soon and then I could look at
> them and maybe exclude models 6 to 9 if I find them irrelevant... Let's
> see !
>
> A question, however... Is it normal that the X2 in the opt directories
> as the same value for every residue (for example in the file
> ellipsoid/round_3/opt/results.bz2) ? Is it the global X2 ?
>
> Thanks !!
>
>
> Sébastien :)