Hi,
I'll answer below:
On Friday, 21 September 2012, Doucet, Nicolas <
Nicolas.Doucet@xxxxxxxxxxx> 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:
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> Web:
http://www.profs.inrs.ca/ndoucet/> --
>
>
>
> -----Original Message-----
> From:
edward.dauvergne@xxxxxxxxx on behalf of Edward d'Auvergne
> Sent: Fri 9/21/2012 4:35 AM
> To: Doucet, Nicolas
> Cc:
relax-users@xxxxxxx> 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 <
nicolas.doucet@xxxxxxxxxxx> 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
Re: Final model-free run with dauvergne_protocol.py