Hi, Thanks for the info! I now won't bug you about creating bug reports and will save myself some time not trying to debug the problem.
Cheers, Edward On 27 September 2012 16:17, Martin Ballaschk <[email protected]> wrote: > 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 _______________________________________________ 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
