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" <[email protected]>: > 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
