Hi Nick, >From the relax printouts you gave in the mail, I can see that the problem lies much higher up in the analysis. I can see that for all diffusion tensors, only round 2 was reached. This is nowhere near enough number of iterations for the analysis to reach the global optimisation+model selection minimum. See figure 2 of d'Auvergne and Gooley, 2008b (http://dx.doi.org/10.1007/s10858-007-9213-3) for the iterative protocol concept and how many rounds you should expect and the d'Auvergne and Gooley 2007 (http://dx.doi.org/10.1039/b702202f) paper for the description of what a combined optimisation+model selection minimum for a model-free analysis is.
I'm pretty sure that if the iterative procedure for each diffusion tensor to find the global combined optimisation+model selection minimum is completed, that the chi-squared value would significantly decrease and hence the final AIC model selection between diffusion tensors will produce quite a different result. The completion of the iterations should also eliminate a lot of artificial motions in the system (see the above papers for details). Do you know why only 2 iterations for each diffusion tensor was completed? Regards, Edward P. S. The RelaxError is another problem which may disappear when the iterative procedure is completed. This is thoroughly tested in the relax test suite, so I think this is a corner case problem triggered by another problem higher up in the analysis. You would normally never encounter this. On 23 September 2012 18:37, Nicolas Doucet <[email protected]> wrote: > Edward, > > It seems we finally got around the relax halting problem but unfortunately I > don’t know how! Logging didn’t affect anything but our last couple of trials > worked fine and this sudden stop of relax could not be reproduced. Hopefully > it’s not a failing hardware problem like you suggested. I haven't gotten to > it yet but will definitely run relax on another workstation to rule this > out. > > In any case, we re-ran each DIFF_MODEL and they all completed without > halting. Still, we get the same error when trying the final run: > > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > relax> value.set(val=-0.00017199999999999998, param='csa', spin_id='@N') > > relax> pipe.create(pipe_name='local_tm - mf (Sat Sep 22 16:54:58 2012)', > pipe_type='mf', bundle='mf (Sat Sep 22 16:54:58 2012)') > > relax> results.read(file='results', > dir='/home/dgagne/nmrdata2/DG12-116_15SEP2012_ModelFree_Analysis_of_ECP_Free_Form/dauvergne_protocol_final/local_tm/aic') > Opening the file > '/home/dgagne/nmrdata2/DG12-116_15SEP2012_ModelFree_Analysis_of_ECP_Free_Form/dauvergne_protocol_final/local_tm/aic/results.bz2' > for reading. > > relax> pipe.create(pipe_name='sphere - mf (Sat Sep 22 16:54:58 2012)', > pipe_type='mf', bundle='mf (Sat Sep 22 16:54:58 2012)') > > relax> results.read(file='results', > dir='/home/dgagne/nmrdata2/DG12-116_15SEP2012_ModelFree_Analysis_of_ECP_Free_Form/dauvergne_protocol_final/sphere/round_2/opt') > Opening the file > '/home/dgagne/nmrdata2/DG12-116_15SEP2012_ModelFree_Analysis_of_ECP_Free_Form/dauvergne_protocol_final/sphere/round_2/opt/results.bz2' > for reading. > > relax> pipe.create(pipe_name='prolate - mf (Sat Sep 22 16:54:58 2012)', > pipe_type='mf', bundle='mf (Sat Sep 22 16:54:58 2012)') > > relax> results.read(file='results', > dir='/home/dgagne/nmrdata2/DG12-116_15SEP2012_ModelFree_Analysis_of_ECP_Free_Form/dauvergne_protocol_final/prolate/round_2/opt') > Opening the file > '/home/dgagne/nmrdata2/DG12-116_15SEP2012_ModelFree_Analysis_of_ECP_Free_Form/dauvergne_protocol_final/prolate/round_2/opt/results.bz2' > for reading. > > relax> pipe.create(pipe_name='oblate - mf (Sat Sep 22 16:54:58 2012)', > pipe_type='mf', bundle='mf (Sat Sep 22 16:54:58 2012)') > > relax> results.read(file='results', > dir='/home/dgagne/nmrdata2/DG12-116_15SEP2012_ModelFree_Analysis_of_ECP_Free_Form/dauvergne_protocol_final/oblate/round_2/opt') > Opening the file > '/home/dgagne/nmrdata2/DG12-116_15SEP2012_ModelFree_Analysis_of_ECP_Free_Form/dauvergne_protocol_final/oblate/round_2/opt/results.bz2' > for reading. > > relax> pipe.create(pipe_name='ellipsoid - mf (Sat Sep 22 16:54:58 2012)', > pipe_type='mf', bundle='mf (Sat Sep 22 16:54:58 2012)') > > relax> results.read(file='results', > dir='/home/dgagne/nmrdata2/DG12-116_15SEP2012_ModelFree_Analysis_of_ECP_Free_Form/dauvergne_protocol_final/ellipsoid/round_2/opt') > Opening the file > '/home/dgagne/nmrdata2/DG12-116_15SEP2012_ModelFree_Analysis_of_ECP_Free_Form/dauvergne_protocol_final/ellipsoid/round_2/opt/results.bz2' > for reading. > > relax> model_selection(method='AIC', modsel_pipe='final - mf (Sat Sep 22 > 16:54:58 2012)', bundle='mf (Sat Sep 22 16:54:58 2012)', pipes=['local_tm - > mf (Sat Sep 22 16:54:58 2012)', 'sphere - mf (Sat Sep 22 16:54:58 2012)', > 'prolate - mf (Sat Sep 22 16:54:58 2012)', 'oblate - mf (Sat Sep 22 16:54:58 > 2012)', 'ellipsoid - mf (Sat Sep 22 16:54:58 2012)']) > AIC model selection. > > Global model - all diffusion tensor parameters and spin specific model-free > parameters. > Data pipe Num_params_(k) Num_data_sets_(n) Chi2 > Criterion > local_tm - mf (Sat Sep 22 16:54:58 2012) 233 678 > 374948.04349 375414.04349 > sphere - mf (Sat Sep 22 16:54:58 2012) 150 678 > 379689.20076 379989.20076 > prolate - mf (Sat Sep 22 16:54:58 2012) 155 678 > 379992.81969 380302.81969 > oblate - mf (Sat Sep 22 16:54:58 2012) 158 678 > 379741.98189 380057.98189 > ellipsoid - mf (Sat Sep 22 16:54:58 2012) 161 678 > 379888.19715 380210.19715 > The model from the data pipe 'local_tm - mf (Sat Sep 22 16:54:58 2012)' has > been selected. > > relax> monte_carlo.setup(number=500) > > > relax> monte_carlo.create_data(method='back_calc') > RelaxError: The specific model has not been selected or set up. > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > We went back to each individual DIFF_MODEL logs to figure out whether > irregularities could be observed. Here is what shows up in each individual > run (sphere, oblate, etc.) for each individual spin (we have 133 different > @N spins in this pdb file, a few of those we listed in the 'unresolved' > file): > > Fitting to spin '#2KB5_mol1:4@N' > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Cannot run a grid search on a model with zero parameters, directly > calculating the function value. > Storing the optimisation results, the optimised chi-squared value is lower > than the current value (6753.10859718 < None). > > The following message then appears: > > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > relax> minimise(min_algor='newton', line_search=None, hessian_mod=None, > hessian_type=None, func_tol=1e-25, grad_tol=None, max_iter=10000000, > constraints=True, scaling=True, verbosity=1) > > > Over-fit spin deselection. > > Only the model-free parameters for single spins will be used. > > > Fitting to spin '#2KB5_mol1:4@N' > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Cannot run optimisation on a model with zero parameters, directly > calculating the function value. > > Parameter values: [] > Function value: 6701.4699098031615 > Iterations: 0 > Function calls: 1 > Gradient calls: 0 > Hessian calls: 0 > Warning: No optimisation > > Storing the optimisation results, the optimised chi-squared value is lower > than the current value (6701.4699098 < None). > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > Thanks again for your input. > > Nick > > -- > Nicolas Doucet > Assistant Professor > INRS - Institut Armand-Frappier > University of Quebec > Institut Pasteur International Network > 531 Boulevard des Prairies > Laval (Quebec) H7V 1B7 CANADA > Phone: (450) 687-5010 #4212 > Fax: (450) 686-5501 > Email: [email protected] > Web: http://www.profs.inrs.ca/ndoucet/ > -- > > > > On 2012-09-21, at 9:48 AM, Edward d'Auvergne <[email protected]> wrote: > > Hi, > > I'll answer below: > > On Friday, 21 September 2012, Doucet, Nicolas <[email protected]> > wrote: >> Edward, >> >> Using all the relaxation .out files previously created by relax in one >> single directory including the pdb and the dauvergne_protocol.py script, we >> simply ran the following command as you previously suggested: >> >> $ relax --log log dauvergne_protocol.py > > I would recommend, simply as a test, to run relax without logging: > > $ relax dauvergne_protocol.py > > >> We ran it twice identically except for the following selections: >> >> 1- With "res_name_col=3", "spin_num_col=4" >> 2- With "res_name_col-None", "spin_num_col=None" > > I'm guessing that the minus is a typo here. If you have the residue number, > the name is not essential. And if you have a unique spin name, then a spin > number is not essential. > > >> In both cases the results are identical and yield the same warnings: >> >> 1- We see "Over-fit spin deselection" when "grid_search" is starting. > > From your log file, I can see that protons are deselected - this is normal > as you are looking at nitrogen relaxation rather than proton relaxation. > > >> 2- We always see the string "RelaxWarning: The spin '#2KB5_mol1:123@N' has >> been deselected because of missing relaxation data". > > How many data points do you have for this residue 123 nitrogen? > > >> 3- In "fitting to spin (Grid search)", "fk" values are identical in both >> runs. >> 4- In "fitting to spin (Grid search)", the output message is the >> following: "Storing the optimisation results, the optimised chi-squared >> value is lower than the current value (12620.7348396 < None)". Is this what >> one would expect to see? > > This is normal. This message makes more sense in the multiple-processor > mode whereby the grid search is broken into pieces and each processor > produces this message or the alternative saying that the chi-squared value > is higher. > > >> Still, the major issue is the halting of relax in the middle of the tm8 >> grid search. I will try to install relax 2.1.1 on a 64-bit dual processor >> later today and run everything again. > > This is strange! Maybe without the logging you will see more. Otherwise > type 'dmesg' and see if the OS system log says more. I really have only > seen such problems on failing hardware. But as this occurs in the same > place each time, there must be some other problem! Your ram size of 3 Gb > (https://gna.org/bugs/?20177) should be sufficient. We need to get to the > bottom of this problem. > > Regards, > > Edward > > >> Nick >> >> -- >> Nicolas Doucet >> Assistant Professor >> INRS - Institut Armand-Frappier >> University of Quebec >> Institut Pasteur International Network >> 531 Boulevard des Prairies >> Laval (Quebec) H7V 1B7 CANADA >> Phone: (450) 687-5010 #4212 >> Fax: (450) 686-5501 >> Email: [email protected] >> Web: http://www.profs.inrs.ca/ndoucet/ >> -- >> >> >> >> -----Original Message----- >> From: [email protected] on behalf of Edward d'Auvergne >> Sent: Fri 9/21/2012 4:35 AM >> To: Doucet, Nicolas >> Cc: [email protected] >> Subject: Re: Final model-free run with dauvergne_protocol.py >> >> Hi Nick, >> >> How did you run relax? Could you copy and paste the entire command >> used? This will help me work out if you are using Gary Thompson's >> multiprocessor and how IO redirection is occurring. Do you get the >> same messages without IO redirection? It is quite peculiar that relax >> just stops like that without giving any output. I have seen this >> before, but it was due to a dying CPU (or harddrive, I don't remember >> exactly). I would guess that without the multiprocessor or IO >> redirection, you should see a much more informative error message. >> >> Cheers, >> >> Edward >> >> >> >> On 20 September 2012 21:33, Nicolas Doucet <[email protected]> >> wrote: >>> Edward, >>> >>> We started the dauvergne_protocol.py again from scratch and we do see a >>> few >>> warning messages in the initial local_tm run. Here is what we see right >>> before each tm grid search (the example is from the log file for tm0): >>> >>> relax> pipe.copy(pipe_from='origin - mf (Tue Sep 18 14:19:13 2012)', >>> pipe_to='tm0 - mf (Tue Sep 18 14:19:13 2012)', bundle_to='mf (Tue Sep 18 >>> 14:19:13 2012)') >>> >>> relax> pipe.switch(pipe_name='tm0 - mf (Tue Sep 18 14:19:13 2012)') >>> >>> relax> model_free.select_model(model='tm0', spin_id=None) >>> >>> relax> grid_search(lower=None, upper=None, inc=11, constraints=True, >>> verbosity=1) >>> >>> >>> Over-fit spin deselection. >>> >>> RelaxWarning: The spin '#2KB5_mol1:2@N' has been deselected because of >>> missing relaxation data. >>> RelaxWarning: The spin '#2KB5_mol1:3@N' has been deselected because of >>> missing relaxation data. >>> RelaxWarning: The spin '#2KB5_mol1:4@H' has been deselected because of an >>> absence of relaxation mechanisms. >>> RelaxWarning: The spin '#2KB5_mol1:4@H' has been deselected because of >>> missing relaxation data. >>> RelaxWarning: The spin '#2KB5_mol1:5@H' has been deselected because of an >>> absence of relaxation mechanisms. >>> RelaxWarning: The spin '#2KB5_mol1:5@H' has been deselected because of >>> missing relaxation data. >>> RelaxWarning: The spin '#2KB5_mol1:6@H' has been deselected because of an >>> absence of relaxation mechanisms. >>> RelaxWarning: The spin '#2KB5_mol1:6@H' has been deselected because of >>> missing relaxation data. >>> RelaxWarning: The spin '#2KB5_mol1:7@H' has been deselected because of an >>> absence of relaxation mechanisms. >>> RelaxWarning: The spin '#2KB5_mol1:7@H' has been deselected because of >>> missing relaxation data. >>> RelaxWarning: The spin '#2KB5_mol1:8@H' has been deselected because of an >>> absence of relaxation mechanisms. >>> RelaxWarning: The spin '#2KB5_mol1:8@H' has been deselected because of >>> missing relaxation data. >>> RelaxWarning: The spin '#2KB5_mol1:9@H' has been deselected because of an >>> absence of relaxation mechanisms. >>> RelaxWarning: The spin '#2KB5_mol1:9@H' has been deselected because of >>> missing relaxation data. >>> RelaxWarning: The spin '#2KB5_mol1:10@H' has been deselected because of >>> an >>> absence of relaxation mechanisms. >>> RelaxWarning: The spin '#2KB5_mol1:10@H' has been deselected because of >>> missing relaxation data. >>> RelaxWarning: The spin '#2KB5_mol1:11@H' has been deselected because of >>> an >>> absence of relaxation mechanisms. >>> RelaxWarning: The spin '#2KB5_mol1:11@H' has been deselected because of >>> missing relaxation data. >>> RelaxWarning: The spin '#2KB5_mol1:12@H' has been deselected because of >>> an >>> absence of relaxation mechanisms. >>> RelaxWarning: The spin '#2KB5_mol1:12@H' has been deselected because of >>> missing relaxation data. >>> RelaxWarning: The spin '#2KB5_mol1:13@H' has been deselected because of >>> an >>> absence of relaxation mechanisms. >>> RelaxWarning: The spin '#2KB5_mol1:13@H' has been deselected because of >>> missing relaxation data. >>> RelaxWarning: The spin '#2KB5_mol1:14@H' has been deselected because of >>> an >>> absence of relaxation mechanisms. >>> RelaxWarning: T > > > > _______________________________________________ > 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
