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 <[email protected]> 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" <[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
