Re: Exception raised during black-box mf -- September 27, 2012 - 16:17

Hi Edward, dear list readers,

turns out I made a mistake while importing the relaxation data. When I let 
relax read the correct data sets, everything works just fine.

Cheers,
Martin


On 17.09.2012, at 23:49, Martin Ballaschk <ballaschk@xxxxxxxxxxxxx> wrote:

> Hi Edward,
>
> a similar message pops up also when running relax in single-processor mode. 
>
> As soon as I'm back in Berlin I will try to make a minimal data set and 
> post the required info with the bug report. 
>
> Thanks for your support
>
> Cheers
> Martin 
>
>
>
> Am 17.09.2012 um 11:10 schrieb "Edward d'Auvergne" <edward@xxxxxxxxxxxxx>:
>
> > 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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