Hi Ed !
I ran the problematic models (m5, m6, m7, m8) and they all seem to work
fine... Now, models m0 to m9 all run successfully. Thanks for solving this
issue !
...
However, I also tried the some local_tm models and got an error with model
tm2 (after the command "relax> monte_carlo.error_analysis(run='tm2',
prune=0.0)") which is different from the error encountered in bug 11004.
=============================================================
File "/home/semor/packages/relax-1.2/relax", line 454, in ?
Relax()
File "/home/semor/packages/relax-1.2/relax", line 166, in __init__
self.interpreter.run()
File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 216, in
run
run_script(intro=self.relax.intro_string, local=self.local,
script_file=self.relax.script_file, quit=1)
File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 391, in
run_script
console.interact(intro, local, script_file, quit)
File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 343, in
interact_script
execfile(script_file, local)
File "./model2_tm", line 42, in ?
monte_carlo.error_analysis(name)
File "/home/semor/packages/relax-1.2/prompt/monte_carlo.py", line 145, in
error_analysis
self.__relax__.generic.monte_carlo.error_analysis(run=run, prune=prune)
File "/home/semor/packages/relax-1.2/generic_fns/monte_carlo.py", line
240, in error_analysis
sd = sqrt(sd / (float(n) - 1.0))
ZeroDivisionError: float division
=============================================================
Maybe important for diagnostic is the many many lines like :
=============================================================
The local tm parameter of 2.0000000000000002e-07 is greater than
5.0000000000000004e-08, eliminating spin system 103 ASN of the run 'tm2
=============================================================
encountered during model-free models elimination ("eliminate(run='tm2',
function=None, args=None)"). The problem is probably due to the
underestimation of the correlation time causing the ts values to rise
artefactully (like you pointed in your previous mail of the same thread).
However, relax shouldn't break and should be able to continue after such a
problem.
Note also that this problem does not arise for models tm0, tm1, tm3, tm4
and tm9 (I haven't had time yet to run the models tm5 to tm8).
Do you have an idea about the reason for this new bug..?
Should I submit a new bug report for this issue ?
Thanks !
Séb :)
Edward d'Auvergne wrote:
Hi,
I've fixed this bug, although I think other issues will arise. From
the attached 'tail_1000_lines_log_model_5' file, it looks pretty
obvious that the global correlation time of 6.7 ns used in the script
is an underestimation. The result is all the ts values are absorbing
this underestimation causing them to shoot up to values slower than
the global tumbling. Of course it could be another issue causing the
large ts values. Anyway, I have a feeling that this issue may cause
other bugs to be uncovered in relax. Seb, could you test to see if
the 1.2 line now works?
Cheers,
Edward
On Fri, Feb 8, 2008 at 1:31 AM, Sébastien Morin
<NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
URL:
<http://gna.org/bugs/?11004>
Summary: Model elimination
Project: relax
Submitted by: semor
Submitted on: Thursday 02/07/2008 at 19:31
Category: relax's source code
Severity: 3 - Normal
Priority: 5 - Normal
Status: None
Privacy: Public
Assigned to: None
Originator Name:
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Release: Repository: 1.2 line
Operating System: GNU/Linux
_______________________________________________________
Details:
Hi,
I recently got into a small problem related to model elimination, I think.
The relax version used was 1.2 from the repository (r4938).
The script used consisted of minimizing one model-free model, doing Monte
Carlo simulations, eliminating bad simulations and calculating errors (just
as in the sample script on page 30, section 6.2.1, of the manual, v1.2.11,
see attached file for an example with model 5).
R1s, R2s and NOEs were available from 2 magnetic fields for most residues,
some of which only had data from 1 magnetic field. For some models
(5,6,7,8),
model elimination eliminated lots of simulations... When reaching the
'monte_carlo.error_analysis' call, relax crashed (the saved state just
after
the eliminate() call, just before relax crashing, is available at :
http://maple.rsvs.ulaval.ca/users/semor/tmp/save_after_eliminate.bz2) with
the following error :
==============================================================
relax> monte_carlo.error_analysis(run='m5', prune=0.0)
Traceback (most recent call last):
File "/home/semor/packages/relax-1.2/relax", line 454, in ?
Relax()
File "/home/semor/packages/relax-1.2/relax", line 166, in __init__
self.interpreter.run()
File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 216, in
run
run_script(intro=self.relax.intro_string, local=self.local,
script_file=self.relax.script_file, quit=1)
File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 391, in
run_script
console.interact(intro, local, script_file, quit)
File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 343, in
interact_script
execfile(script_file, local)
File "./model_5.py", line 43, in ?
monte_carlo.error_analysis(name)
File "/home/semor/packages/relax-1.2/prompt/monte_carlo.py", line 145, in
error_analysis
self.__relax__.generic.monte_carlo.error_analysis(run=run, prune=prune)
File "/home/semor/packages/relax-1.2/generic_fns/monte_carlo.py", line 220,
in error_analysis
Xav = Xsum / float(n)
ZeroDivisionError: float division
==============================================================
It seems 'n' was zero for at least one residue...
Thanks for help with this !
Séb
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Thursday 02/07/2008 at 19:31 Name: model_5.py Size: 1kB By: semor
<http://gna.org/bugs/download.php?file_id=3760>
_______________________________________________________
Reply to this item at:
<http://gna.org/bugs/?11004>
_______________________________________________
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Re: [bug #11004] Model elimination