Hi Edward,
Your description sounds very likely the cause of the problem, during
the time where no output is being produced, the computer gets
gradually more and more slow before finally giving up.
The error is reproducible such that I have tried it on a couple of
different machines and it has failed several times at the same stage.
The error messages tend to vary a little, however. Here are another 2
of the outputs given when the program has failed (I should clarify all
of these messages came from runs done on the same machine, and the
second was run with option "-d" but it hasn't helped very much):-
Simulation 492
Simulation 493
Simulation 494
Simulation 495
Simulation 496
Simulation 497
Simulation 498
Simulation 499
Simulation 500
Traceback (most recent call last):
File "/usr/local/relax-1.3.13/multi/uni_processor.py", line 136, in run
self.callback.init_master(self)
File "/usr/local/relax-1.3.13/multi/processor.py", line 263, in
default_init_m
aster
Traceback (most recent call last):
File "/usr/local/bin/relax", line 7, in <module>
relax.start()
File "/usr/local/relax-1.3.13/relax.py", line 100, in start
processor.run()
File "/usr/local/relax-1.3.13/multi/uni_processor.py", line 139, in run
self.callback.handle_exception(self, e)
File "/usr/local/relax-1.3.13/multi/processor.py", line 250, in
default_handle
_exception
traceback.print_exc(file=sys.stderr)
File "/usr/lib/python2.6/traceback.py", line 227, in print_exc
print_exception(etype, value, tb, limit, file)
File "/usr/lib/python2.6/traceback.py", line 125, in print_exception
print_tb(tb, limit, file)
File "/usr/lib/python2.6/traceback.py", line 69, in print_tb
line = linecache.getline(filename, lineno, f.f_globals)
File "/usr/lib/python2.6/linecache.py", line 14, in getline
lines = getlines(filename, module_globals)
File "/usr/lib/python2.6/linecache.py", line 40, in getlines
return updatecache(filename, module_globals)
File "/usr/lib/python2.6/linecache.py", line 136, in updatecache
lines = fp.readlines()
MemoryError
9203.219u 258.488s 8:05:09.46 32.5% 0+0k 90962440+0io 2215895pf+0w
------------------
Simulation 489
Simulation 490
Simulation 491
Simulation 492
Simulation 493
Simulation 494
Simulation 495
Simulation 496
Simulation 497
Simulation 498
Simulation 499
Simulation 500
debug> Execution lock: Release by 'script UI' ('script' mode).
debug> Execution lock: Release by 'script UI' ('script' mode).
Traceback (most recent call last):
File "/progs/Linux/bin/relax13", line 7, in <module>
relax.start()
File "/progs/relax-1.3.13/relax.py", line 100, in start
processor.run()
File "/progs/relax-1.3.13/multi/uni_processor.py", line 139, in run
self.callback.handle_exception(self, e)
File "/progs/relax-1.3.13/multi/processor.py", line 250, in
default_handle_exc
eption
traceback.print_exc(file=sys.stderr)
File "/usr/lib/python2.6/traceback.py", line 227, in print_exc
print_exception(etype, value, tb, limit, file)
MemoryError
8006.268u 542.873s 8:34:11.81 27.7% 0+0k 225824840+0io 6192344pf+0w
------------------
If the number of MC simulations is dropped even as little as 100, the
program finishes the fitting successfully, though I then get an error
message to do with the grace files (i've not been using them so I'm
not bothered about this though it will be of interest to you no
doubt):-
Data pipe 'final': The ts value of 2.6285e-08 is greater than
1.9714e-08, elimi
nating simulation 94 of spin system ':218@N'.
Data pipe 'final': The ts value of 2.6285e-08 is greater than
1.9714e-08, elimi
nating simulation 95 of spin system ':218@N'.
relax> monte_carlo.error_analysis(prune=0.0)
relax> results.write(file='results',
dir='/ld10c/home1/hugh/data/pgm298bq/relax/
final', compress_type=1, force=True)
Opening the file
'/ld10c/home1/hugh/data/pgm298bq/relax/final/results.bz2' for w
riting.
relax> grace.write(x_data_type='spin', y_data_type='s2', spin_id=None,
plot_data
='value', file='s2.agr',
dir='/ld10c/home1/hugh/data/pgm298bq/relax/final/grace'
, force=True, norm=False)
Opening the file
'/ld10c/home1/hugh/data/pgm298bq/relax/final/grace/s2.agr' for
writing.
relax> grace.write(x_data_type='spin', y_data_type='s2f', spin_id=None,
plot_dat
a='value', file='s2f.agr',
dir='/ld10c/home1/hugh/data/pgm298bq/relax/final/grac
e', force=True, norm=False)
Opening the file
'/ld10c/home1/hugh/data/pgm298bq/relax/final/grace/s2f.agr' for
writing.
relax> grace.write(x_data_type='spin', y_data_type='s2s', spin_id=None,
plot_dat
a='value', file='s2s.agr',
dir='/ld10c/home1/hugh/data/pgm298bq/relax/final/grac
e', force=True, norm=False)
Opening the file
'/ld10c/home1/hugh/data/pgm298bq/relax/final/grace/s2s.agr' for
writing.
relax> grace.write(x_data_type='spin', y_data_type='te', spin_id=None,
plot_data
='value', file='te.agr',
dir='/ld10c/home1/hugh/data/pgm298bq/relax/final/grace'
, force=True, norm=False)
Opening the file
'/ld10c/home1/hugh/data/pgm298bq/relax/final/grace/te.agr' for
writing.
relax> grace.write(x_data_type='spin', y_data_type='tf', spin_id=None,
plot_data
='value', file='tf.agr',
dir='/ld10c/home1/hugh/data/pgm298bq/relax/final/grace'
, force=True, norm=False)
Opening the file
'/ld10c/home1/hugh/data/pgm298bq/relax/final/grace/tf.agr' for
writing.
relax> grace.write(x_data_type='spin', y_data_type='ts', spin_id=None,
plot_data
='value', file='ts.agr',
dir='/ld10c/home1/hugh/data/pgm298bq/relax/final/grace'
, force=True, norm=False)
Opening the file
'/ld10c/home1/hugh/data/pgm298bq/relax/final/grace/ts.agr' for
writing.
relax> grace.write(x_data_type='spin', y_data_type='rex', spin_id=None,
plot_dat
a='value', file='rex.agr',
dir='/ld10c/home1/hugh/data/pgm298bq/relax/final/grac
e', force=True, norm=False)
Opening the file
'/ld10c/home1/hugh/data/pgm298bq/relax/final/grace/rex.agr' for
writing.
debug> Execution lock: Release by 'script UI' ('script' mode).
debug> Execution lock: Release by 'script UI' ('script' mode).
Traceback (most recent call last):
File "/ld10c/progs/relax-1.3.13/prompt/interpreter.py", line 383, in
exec_scri
pt
runpy.run_module(module, globals)
File "/usr/lib/python2.6/runpy.py", line 140, in run_module
fname, loader, pkg_name)
File "/usr/lib/python2.6/runpy.py", line 34, in _run_code
exec code in run_globals
File
"/ld10c/home1/hugh/data/pgm298bq/relax/dauvergne_protocol_lessMC.py", lin
e 216, in <module>
dAuvergne_protocol(pipe_name=name, diff_model=DIFF_MODEL,
mf_models=MF_MODEL
S, local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC,
min_algor=MIN_ALGOR, mc_s
im_num=MC_NUM, conv_loop=CONV_LOOP)
File "/ld10c/progs/relax-1.3.13/auto_analyses/dauvergne_protocol.py",
line 223
, in __init__
self.execute()
File "/ld10c/progs/relax-1.3.13/auto_analyses/dauvergne_protocol.py",
line 710
, in execute
self.write_results()
File "/ld10c/progs/relax-1.3.13/auto_analyses/dauvergne_protocol.py",
line 837
, in write_results
self.interpreter.grace.write(x_data_type='spin', y_data_type='rex',
file='re
x.agr', dir=dir, force=True)
File "/ld10c/progs/relax-1.3.13/prompt/grace.py", line 103, in write
grace.write(x_data_type=x_data_type, y_data_type=y_data_type,
spin_id=spin_i
d, plot_data=plot_data, file=file, dir=dir, force=force, norm=norm)
File "/ld10c/progs/relax-1.3.13/generic_fns/grace.py", line 366, in write
write_xy_header(sets=len(data[0]), file=file, data_type=[x_data_type,
y_data
_type], seq_type=seq_type, set_names=set_names, norm=norm)
File "/ld10c/progs/relax-1.3.13/generic_fns/grace.py", line 600, in
write_xy_h
eader
units = return_units(data_type[i])
File "/ld10c/progs/relax-1.3.13/specific_fns/model_free/main.py", line
2394, i
n return_units
raise RelaxNoSpinSpecError
RelaxNoSpinSpecError: RelaxError: The spin system must be specified.
3510.479u 20.741s 59:07.76 99.5% 0+0k 0+3368io 0pf+0w
------------------
Finally, this is the output from relax --info as requested:-
relax 1.3.13
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2011 the relax development team
This is free software which you are welcome to modify and redistribute
under the conditions of the
GNU General Public License (GPL). This program, including all
modules, is licensed under the GPL
and comes with absolutely no warranty. For details type 'GPL' within
the relax prompt.
Assistance in using the relax prompt and scripting interface can be
accessed by typing 'help' within
the prompt.
Processor fabric: Uni-processor.
Hardware information:
Machine: i686
Processor:
System information:
System: Linux
Release: 2.6.32-37-generic
Version: #81-Ubuntu SMP Fri Dec 2 20:35:14 UTC 2011
GNU/Linux version: Ubuntu 10.04 lucid
Distribution: Ubuntu 10.04 lucid
Full platform string:
Linux-2.6.32-37-generic-i686-with-Ubuntu-10.04-lucid
Software information:
Architecture: 32bit ELF
Python version: 2.6.5
Python branch: tags/r265
Python build: r265:79063, Apr 16 2010 13:09:56
Python compiler: GCC 4.4.3
Python implementation: CPython
Python revision: 79063
Numpy version: 1.3.0
Libc version: glibc 2.4
Python packages (most are optional):
Package Installed Version Path
minfx True Unknown
/ld10c/progs/relax-1.3.13/minfx
bmrblib True Unknown
/ld10c/progs/relax-1.3.13/bmrblib
numpy True 1.3.0
/usr/lib/python2.6/dist-packages/numpy
scipy True 0.7.0
/usr/lib/python2.6/dist-packages/scipy
wxPython False
mpi4py False
epydoc False
optparse True 1.5.3
/usr/lib/python2.6/optparse.pyc
readline True
/usr/lib/python2.6/lib-dynload/readline.so
profile True
/usr/lib/python2.6/profile.pyc
bz2 True
/usr/lib/python2.6/lib-dynload/bz2.so
gzip True
/usr/lib/python2.6/gzip.pyc
os.devnull True
/usr/lib/python2.6/os.pyc
Compiled relax C modules:
Relaxation curve fitting: True
------------------
Apologies for all the detail but I'm not really sure what to do here.
If it is the multi-processor part of it that is failing, is installing
relax 1.3.11 an option? I previously has 1.3.10 installed and the
commands seem to have changed quite a lot since then. What is your
opinion on the validity of error estimates based on 100 simulations?
Thanks
Hugh
On 5 March 2012 08:33, Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>
wrote:
Hi Hugh,
I'm pretty sure this error has not been encountered before. It at
least hasn't been reported. I've never seen anything close to this
before, but I would guess that this is an infinitely recursive
exception (the error is being caught but, in the process, the error
occurs again, being caught a second time, then the 3rd error occurs,
is caught a 3rd time, with this continuing until your computer runs
out of RAM and swap space and relax is killed by the operating
system). The error seems to occur within the error handing portion of
Gary Thompson's multi-processor framework (you are using the
uni-processor fabric of the framework here), so maybe Gary might know
a solution?
Is this error reproducible? For testing, can you drop the number of
Monte Carlo simulations down to say 5? Running relax with the debug
flag might also help:
$ relax --debug
or:
$ relax -d
Are you using the GUI or scripting user interface? The output of:
$ relax --info
might also be useful. As for your data set being too large, relax has
been used on much bigger systems before so this should not be an
issue. One last thing, would you be able to create a bug report for
this error (https://gna.org/bugs/?func=additem&group=relax)? All of
the info/log files can then be pasted/attached there, and it is a
useful future reference for anyone who encounters the same or a
similar bug.
Cheers,
Edward
On 2 March 2012 12:33, Hugh RW Dannatt <h.dannatt@xxxxxxxxxxxxxxx> wrote:
Dear All,
Having completed the fitting of 1 dataset without any problems, I am
now moving onto another. Everything has worked fine until I change the
DIFF_MODEL to "final" and try to run the program again to get error
estimates on my fitted parameters.
The program successfully re-opens all the results file and selects the
diffusion model. Then all 500 simulations are done without issue, but
as soon as the program has finished this, it stops outputting anything
to the screen for a long time (>12 hrs). During this time, the CPU and
Memory use is very high and the computer runs slowly. Eventually I get
a "Memory Error" and a whole load of messages outputted to the screen,
which I have pasted below. I should emphasize that all the stages of
running this program with different diffusion models have run fine,
and the computer I'm using is a relatively fast machine (dual core
Pentium 4, 2 GB RAM).
Has anyone had a similar problem? This dataset is larger than the
previous one which fit without issue (current one has 6 measurements
per 176 residues), but I can't imagine this being the cause of this
problem.
Thanks
Hugh
----
Simulation 485
Simulation 486
Simulation 487
Simulation 488
Simulation 489
Simulation 490
Simulation 491
Simulation 492
Simulation 493
Simulation 494
Simulation 495
Simulation 496
Simulation 497
Simulation 498
Simulation 499
Simulation 500
Traceback (most recent call last):
File "/progs/relax-1.3.13/multi/uni_processor.py", line 136, in run
self.callback.init_master(self)
File "/progs/relax-1.3.13/multi/processor.py", line 263, in
default_init_master
self.master.run()
File "/progs/relax-1.3.13/relax.py", line 171, in run
self.interpreter.run(self.script_file)
File "/progs/relax-1.3.13/prompt/interpreter.py", line 300, in run
return run_script(intro=self.__intro_string, local=locals(),
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script,
raise_relax_error=self.__raise_relax_error)
File "/progs/relax-1.3.13/prompt/interpreter.py", line 610, in
run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/progs/relax-1.3.13/prompt/interpreter.py", line 495, in
interact_script
exec_script(script_file, local)
File "/progs/relax-1.3.13/prompt/interpreter.py", line 383, in
exec_script
runpy.run_module(module, globals)
File "/usr/lib/python2.6/runpy.py", line 140, in run_module
fname, loader, pkg_name)
File "/usr/lib/python2.6/runpy.py", line 34, in _run_code
exec code in run_globals
File "/home1/hugh/data/pgm298bq/relax/dauvergne_protocol.py", line
216, in <module>
dAuvergne_protocol(pipe_name=name, diff_model=DIFF_MODEL,
mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS,
grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_sim_num=MC_NUM,
conv_loop=CONV_LOOP)
File "/progs/relax-1.3.13/auto_analyses/dauvergne_protocol.py", line
223, in __init__
Traceback (most recent call last):
File "/progs/Linux/bin/relax13", line 7, in <module>
relax.start()
File "/progs/relax-1.3.13/relax.py", line 100, in start
processor.run()
File "/progs/relax-1.3.13/multi/uni_processor.py", line 139, in run
self.callback.handle_exception(self, e)
File "/progs/relax-1.3.13/multi/processor.py", line 250, in
default_handle_exception
traceback.print_exc(file=sys.stderr)
File "/usr/lib/python2.6/traceback.py", line 227, in print_exc
print_exception(etype, value, tb, limit, file)
File "/usr/lib/python2.6/traceback.py", line 125, in print_exception
print_tb(tb, limit, file)
File "/usr/lib/python2.6/traceback.py", line 69, in print_tb
line = linecache.getline(filename, lineno, f.f_globals)
File "/usr/lib/python2.6/linecache.py", line 14, in getline
lines = getlines(filename, module_globals)
File "/usr/lib/python2.6/linecache.py", line 40, in getlines
return updatecache(filename, module_globals)
File "/usr/lib/python2.6/linecache.py", line 136, in updatecache
lines = fp.readlines()
MemoryError
9078.655u 666.933s 10:55:29.66 24.7% 0+0k 241482000+0io 6665721pf+0w
_______________________________________________
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--
Hugh Dannatt
PhD Student Researcher
Prof. Jon Waltho Lab
Department of Molecular Biology & Biotechnology
University of Sheffield
Firth Court
Western Bank
Sheffield
S10 2TN
0114 222 2729
Re: Problem during "final" run of d'Auvergne Protocol