Re: [bug #11004] Model eliminationRe: [bug #11004] Model elimination|
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> _______________________________________________ Message sent via/by Gna! http://gna.org/ |