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 <skinnerj@xxxxxxxxxxxx> 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
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Re: crash during multi-processor grid search for 'sphere' model