Re: full_analysis.py -- November 23, 2006 - 09:18

Hi,

In response to your query about convergence of the new model-free
optimisation protocol (full_analysis.py), I have added a function to
that script which will run the three tests - identical chi2, identical
model-free models, and identical diffusion tensor and model-free
parameter values.  If you use this modified script, it will tell you
exactly when convergence has occured.

The improved 'full_analysis.py' script is currently only located
within the Subversion repository (http://svn.gna.org/viewcvs/relax/).
There are two ways to get this script.  The first is to install svn
and checkout the stable 1.2 line from the repository.  The other
option is to follow the given link, into the 1.2 repository line, and
then download it directly.

Cheers,

Edward


On 11/23/06, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> Hi !
>
> For my model-free analysis, it finally converged.
>
> However, when I first tried the final optimization, it didn't work
> because of bug 7616 (I think)... I'm about to try that final
> optimization again since I had to work on other things for the last few
> weeks...
>
> In summary, it took, for my 271 residue (220 residues with data at three
> fields) :
>
> 1. local_tm : 15 hours on a Intel Pentium 4 CPU 3.20GHz (2MB L3cache)
>
> 2. sphere : 153h (~6 days) before convergence on a Intel Pentium 4 CPU
> 3.20GHz (2MB L3cache)
>
> 3. prolate : 244h (~10 days) before convergence on a Intel Xeon CPU 2.80GHz
>
> 4. oblate : 234h (~10 days) before convergence on a Intel Xeon CPU 2.80GHz
>
> 5. ellipsoid : 215h (~9 days) before convergence on a Intel Pentium 4
> CPU 3.20GHz
>
> Total (without the final optimization) with 4 CPU : ~10 days which is
> better than I thought... (In fact, it converged before I noticed since I
> wasn't looking at the results so much because I had several projects at
> the same time).
>
> Please see the file readme.txt to get detailed info about the CPUs and
> also detailed times for the different optimization steps. As I told, it
> converged before I stopped doing iterations and I made a lot of runs for
> nothing especially for the sphere and ellipsoid diffusion tensors...
>
> So, a question here, is looking at X2 convergence enough to say an
> optimization converged or must I look at detailed individual parameters ?
>
> Thanks !
>
>
> Séb :)
>
>
>
> Voici les fichiers input :
> ==========================
>
> 500_NOE.in.min
> 500_R1.in.min
> 500_R2.in.min
>
> 600_NOE.in.min
> 600_R1.in.min
> 600_R2.in.min
>
> 800_NOE.in.min
> 800_R1.in.min
> 800_R2.in.min
>
> PSE-4_start22_rotate-pdbinertia_axial-600.pdb
>
>
>
> Computers
> ===================
> Pelican :       1 CPU -> Intel Pentium 4 CPU 3.20GHz
>                          L1 data cache : 8KB
>                          L2 unified cache : 512KB
>                          L3 unified cache : 2MB
>
> Pigeon  :       1 CPU -> Intel Pentium 4 CPU 3.20GHz
>                          L1 data cache : 8KB
>                          L2 unified cache : 512KB
>
> Hibou   :       2 CPU -> Intel Xeon CPU 2.80GHz
>                          L1 data cache : 8KB
>                          L2 unified cache : 512KB
>
> Modèle          Round   Machine         Durée   X2              Convergence 
> ?
> ============    =====   =============   ======= =============   =============
> local_tm        ---     Pelican         15h00
> -----------------------------------------------
> sphere MII      init    Pelican          0h10
>                  1      Pelican         42h00   7718.74681973
>                  2      Pelican         23h00   7533.93421105
>                  3      Pelican         18h00   7512.54761496
>                  4      Pelican         31h00   7514.7552298
>                  5      Pelican         19h00   7515.04861607
>                  6      Pelican          7h00   7525.64668195
>                  7      Pelican         13h00   7516.27057309
>                  8      Pelican          3h00   7516.27057309   Convergence
>                  9      Pelican          3h00   7516.27057309   Convergence-2
>                 10      Pelican          3h00   7516.27057309   Convergence-3
>                 11      Pelican          3h00   7516.27057309   Convergence-4
>                 12      Pelican          5h00   7516.27057309   Convergence-5
>                 13      Pelican          3h00   7516.27057309   Convergence-6
>                 14      Pelican          3h00   7516.27057309   Convergence-7
>                 15      Pelican          3h00   7516.27057309   Convergence-8
>                 16      Pelican          3h00   7516.27057309   Convergence-9
>                 17      Pelican          5h00   7516.27057309   Convergence-10
>                 18      Pelican          3h00   7516.27057309   Convergence-11
>                 19      Pelican          3h00   7516.27057309   Convergence-12
>                 20      Pelican          4h00   7516.27057309   Convergence-13
>                 21      Pelican          4h00   7516.27057309   Convergence-14
>
> prolate MIII    init    Hibou            0h20
>                  1      Hibou           75h00   7337.50825218
>                  2      Hibou           44h00   7116.88659287
>                  3      Hibou           32h00   7102.52111138
>                  4      Hibou           23h00   7081.39916081
>                  5      Hibou           17h00   7084.09742106
>                  6      Hibou           16h00   7089.93520425
>                  7      Hibou           22h00   7088.84030659
>                  8      Hibou           15h00   7086.72261677
>                  9      Hibou            5h00   7086.72261677   Convergence
>                 10      Hibou            3h00   7086.72261677   Convergence-2
>                 11      Hibou            4h00   7086.72261677   Convergence-3
>
> oblate MIV      init    Hibou            0h20
>                  1      Hibou           75h00   7612.76117331
>                  2      Hibou           44h00   7374.16115094
>                  3      Hibou           23h00   7351.41096494
>                  4      Hibou           40h00   7313.90788663
>                  5      Hibou           19h00   7311.26394344
>                  6      Hibou           12h00   7312.89980682
>                  7      Hibou           21h00   7310.50446393
>                  8      Hibou            6h00   7310.50446393   Convergence
>                  9      Hibou            5h00   7310.50446393   Convergence-2
>                 10      Hibou            5h00   7310.50446393   Convergence-3
>
> ellipsoid MV    init    Pigeon           1h00
>                  1      Pigeon          75h00   7318.54929865
>                  2      Pigeon          31h00   7062.93677664
>                  3      Pigeon          20h00   7044.01927992
>                  4      Pigeon          21h00   7030.85159805
>                  5      Pigeon           9h00   7027.99439236
>                  6      Pigeon          18h00   7029.89513108
>                  7      Pigeon          14h00   7027.60385085
>                  8      Pigeon          14h00   7026.60491212
>                  9      Pigeon          12h00   7022.72611396
>                 10      Pigeon           4h00   7022.72611396   Convergence
>                 11      Pigeon           4h00   7022.72611396   Convergence-2
>                 12      Pigeon           4h00   7022.72611396   Convergence-3
>                 13      Pigeon           4h00   7022.72611396   Convergence-4
>                 14      Pigeon           4h00   7022.72611396   Convergence-5
>                 15      Pigeon           5h00   7022.72611396   Convergence-6
>                 16      Pigeon           4h00   7022.72611396   Convergence-7
>                 17      Pigeon           4h00   7022.72611396   Convergence-8
> -----------------------------------------------
> final           init    Pelican         short   Failed because of bug 7616...