Re: [bug #7296] Potential full analysis read problem -- October 05, 2006 - 17:22

Hi,

Unfortunately I have been unable to reproduce the bug.  I've used the
data that you attached Alex and modified the runner script to use both
my current copy of the 1.2 repository line and relax version 1.2.7 (as
your traceback message suggests that that was the version you were
using).  I also copied the full_analysis-oblate.py script to the local
tm script that 'runner' utilises and changed the self.diff_model
string to 'local_tm'.

When I run the 1.2.7 version it fails because of bug #7241
(https://gna.org/bugs/?7241).  When I run the 'runner' script using
the current 1.2 repository checkout, the script runs to completion
without problem.  I also tried the 1.3 repository line and it worked
fine as well.  Were you using the 1.2 repository line or version
1.2.7?  If you used the 1.2 line, is your copy up to date?  You may
already know this, and I doubt that is the issue, but to update your
checked out copy type the following in the base directory:

$ svn up

Could someone else attempt to reproduce this bug using Alex's test
data (http://gna.org/bugs/download.php?file_id=1369)?  This one has me
stumped!

Thanks,

Edward


On 10/4/06, Alex Hansen <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
> URL:
>   <http://gna.org/bugs/?7296>
>
>                  Summary: Potential full analysis read problem
>                  Project: relax
>             Submitted by: viochemist
>             Submitted on: Tuesday 10/03/2006 at 18:20
>                 Category: None
>                 Priority: 5 - Normal
>                 Severity: 4 - Important
>                   Status: None
>                  Privacy: Public
>              Assigned to: None
>          Originator Name:
>         Originator Email:
>              Open/Closed: Open
>                  Release: Repository: 1.2 line
>         Operating System: GNU/Linux
>
>     _______________________________________________________
>
> Details:
>
> I've run into a problem when running multiple iterations of the oblate
> scheme.  Granted, my RNA system is the exact oposite of oblate, but I don't
> know if that has anything to do with it.  I set up a script to run relax for
> 15 iterations and this is what happens (suppressing all but error messages):
>
> **The first ImportError is a good indication of what iteration is being run.
>
>
> ImportError: relaxation curve fitting is unavailible, try compiling the C
> modules.
>
> ImportError: relaxation curve fitting is unavailible, try compiling the C
> modules.
>
> ImportError: relaxation curve fitting is unavailible, try compiling the C
> modules.
> Traceback (most recent call last):
>   File "relax", line 458, in ?
>     Relax()
>   File "relax", line 170, in __init__
>     self.interpreter.run()
>   File "/local/home/viochem/relax_1.2.7/prompt/interpreter.py", line 213, in
> run
>     run_script(intro=self.relax.intro_string, local=self.local,
> script_file=self.relax.script_file, quit=1)
>   File "/local/home/viochem/relax_1.2.7/prompt/interpreter.py", line 388, in
> run_script
>     console.interact(intro, local, script_file, quit)
>   File "/local/home/viochem/relax_1.2.7/prompt/interpreter.py", line 340, in
> interact_script
>     execfile(script_file, local)
>   File "full_analysis-oblate.py", line 427, in ?
>     Main()
>   File "full_analysis-oblate.py", line 223, in __init__
>     self.multi_model()
>   File "full_analysis-oblate.py", line 419, in multi_model
>     minimise('newton', run=name)
>   File "/local/home/viochem/relax_1.2.7/prompt/minimisation.py", line 365, in
> minimise
>     self.relax.generic.minimise.minimise(run=run, min_algor=min_algor,
> min_options=min_options, func_tol=func_tol, grad_tol=grad_tol,
> max_iterations=max_iterations, constraints=constraints, scaling=scaling,
> print_flag=print_flag)
>   File "/local/home/viochem/relax_1.2.7/generic_fns/minimise.py", line 139,
> in minimise
>     minimise(run=run, min_algor=min_algor, min_options=min_options,
> func_tol=func_tol, grad_tol=grad_tol, max_iterations=max_iterations,
> constraints=constraints, scaling=scaling, print_flag=print_flag)
>   File "/local/home/viochem/relax_1.2.7/specific_fns/model_free.py", line
> 2367, in minimise
>     results = generic_minimise(func=self.mf.func, dfunc=self.mf.dfunc,
> d2func=self.mf.d2func, args=(), x0=self.param_vector, min_algor=min_algor,
> min_options=min_options, func_tol=func_tol, grad_tol=grad_tol,
> maxiter=max_iterations, A=A, b=b, full_output=1, print_flag=print_flag)
>   File "/local/home/viochem/relax_1.2.7/minimise/generic.py", line 397, in
> generic_minimise
>     results = method_of_multipliers(func=func, dfunc=dfunc, d2func=d2func,
> args=args, x0=x0, min_options=min_options, A=A, b=b, l=l, u=u, c=c, dc=dc,
> d2c=d2c, func_tol=func_tol, grad_tol=grad_tol, maxiter=maxiter,
> full_output=full_output, print_flag=print_flag)
>   File "/local/home/viochem/relax_1.2.7/minimise/method_of_multipliers.py",
> line 143, in method_of_multipliers
>     results = min.minimise()
>   File "/local/home/viochem/relax_1.2.7/minimise/method_of_multipliers.py",
> line 397, in minimise
>     results = self.generic_minimise(func=self.func_LA, dfunc=self.func_dLA,
> d2func=self.func_d2LA, args=self.args, x0=self.xk, min_algor=self.min_algor,
> min_options=self.min_options, func_tol=None, grad_tol=self.tk,
> maxiter=maxiter, full_output=1, print_flag=sub_print_flag,
> print_prefix="\t")
>   File "/local/home/viochem/relax_1.2.7/minimise/generic.py", line 328, in
> generic_minimise
>     results = newton(func=func, dfunc=dfunc, d2func=d2func, args=args, x0=x0,
> min_options=min_options, func_tol=func_tol, grad_tol=grad_tol,
> maxiter=maxiter, full_output=full_output, print_flag=print_flag,
> print_prefix=print_prefix)
>   File "/local/home/viochem/relax_1.2.7/minimise/newton.py", line 45, in
> newton
>     results = min.minimise()
>   File "/local/home/viochem/relax_1.2.7/minimise/base_classes.py", line 234,
> in minimise
>     self.new_param_func()
>   File "/local/home/viochem/relax_1.2.7/minimise/newton.py", line 167, in
> new_param_func
>     self.line_search()
>   File "/local/home/viochem/relax_1.2.7/minimise/base_classes.py", line 343,
> in backline
>     self.alpha, fc = backtrack(self.func, self.args, self.xk, self.fk,
> self.dfk, self.pk, a_init=self.a0)
> TypeError: unpack non-sequence
>
> ImportError: relaxation curve fitting is unavailible, try compiling the C
> modules.
> RelaxError: The file 'oblate/round_2/opt/results' does not exist.
>
> ImportError: relaxation curve fitting is unavailible, try compiling the C
> modules.
> RelaxError: The file 'oblate/round_2/opt/results' does not exist.
>
> ImportError: relaxation curve fitting is unavailible, try compiling the C
> modules.
> RelaxError: The file 'oblate/round_2/opt/results' does not exist.
>
> ImportError: relaxation curve fitting is unavailible, try compiling the C
> modules.
> RelaxError: The file 'oblate/round_2/opt/results' does not exist.
>
> ImportError: relaxation curve fitting is unavailible, try compiling the C
> modules.
> RelaxError: The file 'oblate/round_2/opt/results' does not exist.
>
> ImportError: relaxation curve fitting is unavailible, try compiling the C
> modules.
> RelaxError: The file 'oblate/round_2/opt/results' does not exist.
>
> ImportError: relaxation curve fitting is unavailible, try compiling the C
> modules.
> RelaxError: The file 'oblate/round_2/opt/results' does not exist.
>
> ImportError: relaxation curve fitting is unavailible, try compiling the C
> modules.
> RelaxError: The file 'oblate/round_2/opt/results' does not exist.
>
> ImportError: relaxation curve fitting is unavailible, try compiling the C
> modules.
> RelaxError: The file 'oblate/round_2/opt/results' does not exist.
>
> ImportError: relaxation curve fitting is unavailible, try compiling the C
> modules.
> RelaxError: The file 'oblate/round_2/opt/results' does not exist.
>
> ImportError: relaxation curve fitting is unavailible, try compiling the C
> modules.
> RelaxError: The file 'oblate/round_2/opt/results' does not exist.
>
> ImportError: relaxation curve fitting is unavailible, try compiling the C
> modules.
> RelaxError: The file 'oblate/round_2/opt/results' does not exist.
>
> ***************
>
>
> As can be seen, it runs the init and the first round, but upon reading the
> failing the second round all other rounds fail.  It would appear it's reading
> something in wrong from the first round output.  Am I wrong?
>
> Please let me know if any input info would be helpful.
>
> Alex Hansen
>
>
>
>
>
>
>
>
>
>
>
>
>
>     _______________________________________________________
>
> Reply to this item at:
>
>   <http://gna.org/bugs/?7296>
>
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