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
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