Re: Exception raised during black-box mf -- September 17, 2012 - 11:11

Hi Martin,

Would you be able to create a bug report for this problem?  The link
for this is https://gna.org/bugs/?func=additem&group=relax.  The error
message you are seeing is complicated because you appear to be running
in Gary's mpi4py multi-processor mode.  Could you also try in the
uni-processor mode and see if the error exists there as well?  The
traceback error messages from this mode are much easier to interpret.

Useful information for the bug report would be the command you typed
at the command line, the error message in multi- and uni-processor
modes, and the output of:

$ relax --info

It might be also useful if you came up with a mini dataset of only a
few spin systems together with a script which trigger the bug and then
to attach these to the bug report.  You can slightly randomise the
data if you wish to keep the results confidential.

Cheers,

Edward





On 14 September 2012 09:28, Martin Ballaschk <ballaschk@xxxxxxxxxxxxx> wrote:
> Hi Edward,
>
> I need a bit of help figuring out what was going wrong here. I started the 
> fully-automated protocol via the GUI in relax 2.1.0 (multi-processor).
>
> First, relax successfully fitted the local_tm:
>
> > relax> results.write(file='results', 
> > dir='/home/tron/relax-martin/b2m/local_tm/aic', compress_type=1, 
> > force=True)
> > Opening the file '/home/tron/relax-martin/b2m/local_tm/aic/results.bz2' 
> > for writing.
>
>
>
> Then, it started with the spherical diffusion tensor and raised the 
> following error message.
>
> > relax> pipe.create(pipe_name='sphere - mf (Thu Sep 13 15:47:14 2012)', 
> > pipe_type='mf', bundle='mf (Thu Sep 13 15:47:14 2012)')
> >
> > relax> results.read(file='results', 
> > dir='/home/tron/relax-martin/b2m/local_tm/aic')
> > Opening the file '/home/tron/relax-martin/b2m/local_tm/aic/results.bz2' 
> > for reading.
> >
> > relax> model_free.remove_tm(spin_id=None)
> >
> > relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0, 
> > angle_units='deg', param_types=0, spheroid_type=None, fixed=False)
> >
> > relax> fix(element='all_spins', fixed=True)
> >
> > relax> grid_search(lower=None, upper=None, inc=11, constraints=True, 
> > verbosity=1)
> >
> >
> > Over-fit spin deselection.
> >
> > Only diffusion tensor parameters will be used.
> > Parallelised diffusion tensor grid search.
> > Exception raised in thread.
> >
> > Traceback (most recent call last):
> >   File "/opt/relax-2.1.0/gui/analyses/execute.py", line 87, in run
> >     self.run_analysis()
> >   File "/opt/relax-2.1.0/gui/analyses/auto_model_free.py", line 803, in 
> > run_analysis
> >     dauvergne_protocol.dAuvergne_protocol(pipe_name=self.data.pipe_name, 
> > pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir, 
> > diff_model=self.data.global_models, mf_models=self.data.mf_models, 
> > local_tm_models=self.data.local_tm_models, grid_inc=self.data.inc, 
> > diff_tensor_grid_inc=self.data.diff_tensor_grid_inc, 
> > mc_sim_num=self.data.mc_sim_num, max_iter=self.data.max_iter, 
> > conv_loop=self.data.conv_loop)
> >   File "/opt/relax-2.1.0/auto_analyses/dauvergne_protocol.py", line 235, 
> > in __init__
> >     self.execute()
> >   File "/opt/relax-2.1.0/auto_analyses/dauvergne_protocol.py", line 619, 
> > in execute
> >     self.interpreter.grid_search(inc=inc)
> >   File "/opt/relax-2.1.0/prompt/uf_objects.py", line 219, in __call__
> >     self._backend(*new_args, **uf_kargs)
> >   File "/opt/relax-2.1.0/generic_fns/minimise.py", line 140, in grid_search
> >     grid_search(lower=lower, upper=upper, inc=inc, 
> > constraints=constraints, verbosity=verbosity)
> >   File "/opt/relax-2.1.0/specific_fns/model_free/mf_minimise.py", line 
> > 1493, in grid_search
> >     self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc, 
> > constraints=constraints, verbosity=verbosity, sim_index=sim_index)
> >   File "/opt/relax-2.1.0/specific_fns/model_free/mf_minimise.py", line 
> > 1817, in minimise
> >     processor.run_queue()
> >   File "/opt/relax-2.1.0/multi/processor.py", line 621, in run_queue
> >     self.run_command_queue(lqueue)
> >   File "/opt/relax-2.1.0/multi/processor.py", line 605, in 
> > run_command_queue
> >     result_queue.put(result)
> >   File "/opt/relax-2.1.0/multi/result_queue.py", line 90, in put
> >     super(Threaded_result_queue, self).put(job)
> >   File "/opt/relax-2.1.0/multi/result_queue.py", line 52, in put
> >     self.processor.process_result(job)
> >   File "/opt/relax-2.1.0/multi/multi_processor_base.py", line 123, in 
> > process_result
> >     result.run(self, memo)
> >   File "/opt/relax-2.1.0/multi/result_commands.py", line 141, in run
> >     raise self.exception
> > Capturing_exception:
> >
> > ------------------------------------------------------------------------------------------------------------------------
> >
> >   File "/opt/relax-2.1.0/multi/processor.py", line 521, in run
> >     command.run(self, completed)
> >   File 
> > "/opt/relax-2.1.0/specific_fns/model_free/multi_processor_commands.py", 
> > line 129, in run
> >     results = self.optimise()
> >   File 
> > "/opt/relax-2.1.0/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 "/opt/relax-2.1.0/minfx/grid.py", line 256, in grid_point_array
> >     n = len(points[0])
> >
> >
> > Nested Exception from sub processor
> > Rank: 1 Name: hyperion-pid7244
> > Exception type: IndexError
> > Message: index out of bounds
> >
> > ------------------------------------------------------------------------------------------------------------------------
>
>
>
> I'm not very good in reading these kinds of traceback error messages, and 
> in this case it's hard for me to see why the grid search failed.
>
> I noticed that my data are partly faulty: there is a single amino acid with 
> a HetNOE > 1. This is a artifact I have to look into yet, I suppose it is a 
> S/N problem of the original spectra (very weak peak?). Could that be the 
> reason for the exception?
>
> I'd be grateful if you could provide a bit of support (again).
>
> Cheers
> Martin
>
>
>
>
>
>
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