I was able to get some more details about the problem by following your
suggestion to create a mini dataset.
First of all, the problem doesn't occur when using a single processor and
only occurs for DIFF_MODEL = 'sphere' when using mpirun.
I also didn't get the problem for mpirun when I used a subset of my data,
suggesting that the problem is with my input. I found an anomaly in my 500
MHz noe data that appears to be the culprit. Here is what that file looks
like for the subset that did cause a crash:
# Parameter description: The NOE.
# mol_name res_num res_name spin_num spin_name value
error
None 5 MET None None None
None
DesG 7 THR 15 N
0.718432367479729 0.0326572234546261
DesG 8 TYR 29 N
0.65401446462264 0.033499533240881
DesG 5 MET -1 N
-0.420574006604573 0.037900692900274
This happened because of how I loaded my spins. The pdb file I used is
missing the N-terminus, so I adding the MET using residue.create(res_num=5,
res_name='MET'), which I later realized should be residue.create(res_num=5,
res_name='MET',mol_name='DesG').
So now it's working for me. I have created bug report #21001 with relevant
files attached in case you want to track down the "bug" to prevent future
user error.
On Fri, Aug 2, 2013 at 8:12 AM, Edward d'Auvergne <edw...@nmr-relax.com>wrote:
> Hi Jack,
>
> Welcome to the relax mailing lists! Wow, it's rare to see bugs in the
> model-free part of relax nowadays! Though this problem has been seen
> before by Martin Ballaschk, see the thread at:
>
> http://thread.gmane.org/gmane.science.nmr.relax.user/1291
>
> The thread continues at:
>
> http://thread.gmane.org/gmane.science.nmr.relax.user/1312
>
> Unfortunately you will see that no solution was found in the end,
> apart from a problem with the input relaxation data. But you will see
> that the problem is identical to what you see. Would you be able to
> perform the checks I mention in my response at:
>
> http://thread.gmane.org/gmane.science.nmr.relax.user/1291/focus=1292
>
> If you can create a mini data set of 1 or 2 residues, as mentioned in
> that link, which reproduce the bug, I will then be able to add that to
> the relax test suite and eliminate the bug within a very short time.
> Files can be attached directly to your bug report
> (http://gna.org/bugs/?21001). With a good truncated data set and
> script, it usually takes me about 5-10 min to eliminate the bug. If I
> can replicate it, I can quickly eliminate it.
>
> Cheers,
>
> Edward
>
>
>
> On 1 August 2013 22:30, Jack Skinner <skinn...@uchicago.edu> wrote:
> > I am having a problem with the dauvergne_protocol.py script crashing
> when I
> > set DIFF_MODEL = 'sphere'
> > All other models run fine except for 'final', which complains about the
> > missing 'sphere' results.
> >
> > I am running this script with 8 processors using mpirun
> > mpirun -np 8 relax --multi='mpi4py' -n 7 --tee rnd2.log relax_rnd2.py
> >
> > The error message starts:
> > relax> grid_search(lower=None, upper=None, inc=11, constraints=True,
> > verbosity=1)
> >
> > Over-fit spin deselection:
> > No spins have been deselected.
> > Only diffusion tensor parameters will be used.
> > Parallelised diffusion tensor grid search.
> > Traceback (most recent call last):
> > File "/export/home/skinnerj/mypackages/relax-2.2.5/multi/processor.py",
> > line 479, in run
> > ...many lines that might not be helpful...
> > then:
> > Capturing_exception:
> > File "/export/home/skinnerj/mypackages/relax-2.2.5/multi/processor.py",
> > line 522, in run
> > command.run(self, completed)
> > File
> >
> "/export/home/skinnerj/mypackages/relax-2.2.5/specific_fns/model_free/multi_processor_commands.py",
> > line 129, in run
> > results = self.optimise()
> > File
> >
> "/export/home/skinnerj/mypackages/relax-2.2.5/specific_fns/model_free/multi_processor_commands.py",
> > line 175, in optimise
> > results = grid_point_array(func=self.mf.func, args=(),
> > points=self.opt_params.subdivision, verbosity=self.opt_params.verbosity)
> > File "/export/home/skinnerj/mypackages/relax-2.2.5/minfx/grid.py", line
> > 264, in grid_point_array
> > n = len(points[0])
> >
> > Nested Exception from sub processor
> > Rank: 1 Name: kff4-pid14220
> > Exception type: IndexError
> > Message: index out of bounds
> >
> >
> > Any suggestions will be appreciated. Thanks!
> >
> >
> > John "Jack" Skinner, Ph. D. | Postdoctoral Fellow | University of Chicago
> > Lab: 773.834.0658 | GCIS Room W107E, 929 E. 57th St. Chicago, IL 60637
> >
> > _______________________________________________
> > relax (http://www.nmr-relax.com)
> >
> > This is the relax-users mailing list
> > relax-users@gna.org
> >
> > 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-users
> >
>
--
John "Jack" Skinner, Ph. D. | Postdoctoral Fellow | University of Chicago
Lab: 773.834.0658 | GCIS Room W107E, 929 E. 57th St. Chicago, IL 60637
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