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 <[email protected]> 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 > > > > > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-users mailing list > [email protected] > > 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 _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list [email protected] 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
