mailRe: Problem during "final" run of d'Auvergne Protocol


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Posted by Edward d'Auvergne on March 06, 2012 - 17:59:
Ah, that's better.  Well you have a total of 8 Gb of memory for relax
to sit in, which is plenty for relax, so this is quite strange.  I've
loaded much more data than that before on systems with less total
memory, and it hasn't been a problem.  The Python MemoryError message
appears to only occur once you have run out of total memory, and
should kick in before the Linux OOM killer kills the program.  Could
there be any programs or settings limiting the amount of memory
individual programs or users are allowed on your machine?  If you run
'dmesg', is there anything at the end about memory issues?  And does
it always say "Simulation 500" followed by the Traceback messages?  I
wonder if this could be a memory corruption issue.  This is quite a
strange error.  Do you have RAM testing programs available?

For anther test, could you open 'auto_analyses/dauvergne_protocol.py'
and delete the lines:

            # Simulations.
            self.interpreter.monte_carlo.setup(number=self.mc_sim_num)
            self.interpreter.monte_carlo.create_data()
            self.interpreter.monte_carlo.initial_values()
            self.interpreter.minimise(self.min_algor,
func_tol=self.opt_func_tol, max_iterations=self.opt_max_iterations)
            self.interpreter.eliminate()
            self.interpreter.monte_carlo.error_analysis()

With these removed, it will test if it the Monte Carlo simulations
triggering the MemoryError.

Cheers,

Edward



On 6 March 2012 17:43, Hugh RW Dannatt <h.dannatt@xxxxxxxxxxxxxxx> wrote:
I certainly thought I had run it in the right directory, but having
done it again it has just outputted that info.py has been updated, so
perhaps not, my apologies!

free -m gives the following output:-

           total       used       free     shared    buffers     cached
Mem:          2011       1958         53          0          2         41
-/+ buffers/cache:       1914         97
Swap:         5889        927       4962

-----------

And relax -i gives the following:-


                                   relax repository checkout

                            Molecular dynamics by NMR data analysis

                           Copyright (C) 2001-2006 Edward d'Auvergne
                       Copyright (C) 2006-2012 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.

ImportError: relaxation curve fitting is unavailable, the
corresponding C modules have not been compiled.

Processor fabric:  Uni-processor.

Hardware information:
  Machine:                 i686
  Processor:
  Endianness:              little

  Total RAM size:          2011 Mb
  Total swap size:         5889 Mb


Operating system information:
  System:                  Linux
  Release:                 2.6.32-38-generic
  Version:                 #83-Ubuntu SMP Wed Jan 4 11:13:04 UTC 2012
  GNU/Linux version:       Ubuntu 10.04 lucid
  Distribution:            Ubuntu 10.04 lucid
  Full platform string:
Linux-2.6.32-38-generic-i686-with-Ubuntu-10.04-lucid

Python 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
  Libc version:            glibc 2.4
  Python implementation:   CPython
  Python revision:         79063
  Python executable:       /usr/bin/python
  Python flags:            sys.flags(debug=0, py3k_warning=0,
division_warning=0, division_new=0, inspect=0, interactive=0,
optimize=0, dont_write_bytecode=0, no_user_site=0, no_site=0,
ignore_environment=0, tabcheck=0, verbose=0, unicode=0,
bytes_warning=0)
  Python float info:
sys.floatinfo(max=1.7976931348623157e+308, max_exp=1024,
max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021,
min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.2204460492503131e-16,
radix=2, rounds=1)
  Python module path:      ['', '/home1/hugh/installs/relax-1.3',
'/home1/hugh/programs/mattfit', '/usr/lib/python2.6',
'/usr/lib/python2.6/plat-linux2', '/usr/lib/python2.6/lib-tk',
'/usr/lib/python2.6/lib-old', '/usr/lib/python2.6/lib-dynload',
'/usr/lib/python2.6/dist-packages',
'/usr/lib/python2.6/dist-packages/PIL',
'/usr/lib/python2.6/dist-packages/gst-0.10',
'/usr/lib/pymodules/python2.6',
'/usr/lib/python2.6/dist-packages/gtk-2.0',
'/usr/lib/pymodules/python2.6/gtk-2.0',
'/usr/local/lib/python2.6/dist-packages',
'/home1/hugh/installs/relax-1.3/extern/scientific_python/linux2']

Python packages (most are optional):

Package              Installed       Version         Path
minfx                True            Unknown
/usr/local/lib/python2.6/dist-packages/minfx
bmrblib              False
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: False


-----------

Alas the computer is running extremely slowly so I expect I will get
the MemoryError at some point again.

Cheers

Hugh




On 6 March 2012 16:19, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
Did you run 'svn up' in the base relax directory?  And did you see a
message that some files were updated?  What happens if you type 'free
-m' on your system?

Cheers,

Edward


On 6 March 2012 15:59, Hugh RW Dannatt <h.dannatt@xxxxxxxxxxxxxxx> wrote:
Okay, made those changes, and it is now running. Thanks.

I've run "svn up" and got the message " Skipped '.' ", which I guess I
can ignore.

Output of relax -i:-

                                    relax repository checkout

                             Molecular dynamics by NMR data analysis

                            Copyright (C) 2001-2006 Edward d'Auvergne
                        Copyright (C) 2006-2012 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.

ImportError: relaxation curve fitting is unavailable, the
corresponding C modules have not been compiled.

Processor fabric:  Uni-processor.

Hardware information:
   Machine:                 i686
   Processor:
   Endianness:              little

Operating system information:
   System:                  Linux
   Release:                 2.6.32-38-generic
   Version:                 #83-Ubuntu SMP Wed Jan 4 11:13:04 UTC 2012
   GNU/Linux version:       Ubuntu 10.04 lucid
   Distribution:            Ubuntu 10.04 lucid
   Full platform string:
Linux-2.6.32-38-generic-i686-with-Ubuntu-10.04-lucid

Python 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
   Libc version:            glibc 2.4
   Python implementation:   CPython
   Python revision:         79063
   Python executable:       /usr/bin/python
   Python flags:            sys.flags(debug=0, py3k_warning=0,
division_warning=0, division_new=0, inspect=0, interactive=0,
optimize=0, dont_write_bytecode=0, no_user_site=0, no_site=0,
ignore_environment=0, tabcheck=0, verbose=0, unicode=0,
bytes_warning=0)
   Python float info:
sys.floatinfo(max=1.7976931348623157e+308, max_exp=1024,
max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021,
min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.2204460492503131e-16,
radix=2, rounds=1)
   Python module path:      ['', '/home1/hugh/installs/relax-1.3',
'/home1/hugh/programs/mattfit', '/usr/lib/python2.6',
'/usr/lib/python2.6/plat-linux2', '/usr/lib/python2.6/lib-tk',
'/usr/lib/python2.6/lib-old', '/usr/lib/python2.6/lib-dynload',
'/usr/lib/python2.6/dist-packages',
'/usr/lib/python2.6/dist-packages/PIL',
'/usr/lib/python2.6/dist-packages/gst-0.10',
'/usr/lib/pymodules/python2.6',
'/usr/lib/python2.6/dist-packages/gtk-2.0',
'/usr/lib/pymodules/python2.6/gtk-2.0',
'/usr/local/lib/python2.6/dist-packages',
'/home1/hugh/installs/relax-1.3/extern/scientific_python/linux2']

Python packages (most are optional):

Package              Installed       Version         Path
minfx                True            Unknown
/usr/local/lib/python2.6/dist-packages/minfx
bmrblib              False
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: False

---------

Hugh




On 6 March 2012 14:54, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
Oh, that's a recent change as well.  There are a few changes in the
main line which will require small changes to the relax input scripts.
 I have standardised the value.set and related user functions across
the different analysis types.  The 'bond_length' parameter needs to be
replaced with 'r'.  You might encounter a few of these:

   'bond_length' -> 'r'
   'heteronucleus' -> 'heteronuc_type'
   'proton' -> 'proton_type'

I think that's all you'll need to modify in the script, the rest
should be internally handled within relax.

As for the memory error, I have updated the relax information print
out to show more details.  Could you run 'svn up' and resend the
output of 'relax -i'?

Cheers,

Edward



On 6 March 2012 15:29, Hugh RW Dannatt <h.dannatt@xxxxxxxxxxxxxxx> wrote:
Thanks for that, relax does now open properly. However, I now get the
following error when trying to run the dauvergne_protocol.py script:-

relax> relax_data.read(ri_id='NOE_600', ri_type='NOE',
frq=600133000.0, file='noe_600', dir=None, spin_id_col=None,
mol_name_col=None, res_num_col=1, res_name_col=None,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4,
sep=None, spin_id=None)
Opening the file 'noe_600' for reading.

relax> value.set(val=1.0200000000000001e-10, param='bond_length', 
spin_id=None)
debug> Execution lock:  Release by 'script UI' ('script' mode).
Traceback (most recent call last):
 File "/home1/hugh/installs/relax-1.3/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
205, in <module>
   value.set(1.02 * 1e-10, 'bond_length')
 File "/home1/hugh/installs/relax-1.3/prompt/value.py", line 239, in set
   value.set(val=val, param=param, spin_id=spin_id)
 File "/home1/hugh/installs/relax-1.3/generic_fns/value.py", line 356, 
in set
   set_param_values(param=param, value=val, spin_id=spin_id, 
force=force)
 File "/home1/hugh/installs/relax-1.3/specific_fns/model_free/main.py",
line 2316, in set_param_values
   raise RelaxError("The parameter '%s' is unknown." % mf_params[i])
RelaxError: RelaxError: The parameter 'bond_length' is unknown.



Hugh



On 6 March 2012 13:43, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
Ok, the message is taking longer than normal to appear.  The float128
problem was a recent change in relax.  I had just forgotten that
float128 is absent from 32-bit numpy.  So on your machine you have no
access to such high precision values.  This is only a problem if you
do your own code and analysis development within relax, as no part of
relax currently uses float128.

Regards,

Edward



On 6 March 2012 14:34, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
Hi Hugh,

Just quickly, I fixed the float128 import problem.  See my commit
message at 
https://mail.gna.org/public/relax-commits/2012-03/msg00025.html
(you might have to wait a few min for the post to be archived and the
link to work).  Just type 'svn up' and the problem will be gone.  I'll
look at the other problem now.

Regards,

Edward


On 6 March 2012 14:19, Hugh RW Dannatt <h.dannatt@xxxxxxxxxxxxxxx> 
wrote:
Hi Edward,

I have removed the suggested files from uni_processor.py and the 
error
given is below:-

Simulation 495
Simulation 496
Simulation 497
Simulation 498
Simulation 499
Simulation 500
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 135, 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
230, in __init__
   status.exec_lock.release()
MemoryError
3171.454u 7.344s 53:10.23 99.6% 0+0k 16400+0io 14pf+0w

---------------

At the same time (as the computer hangs for hours each time I try to
test this), I thought I would try to run the most up-to-date of 
relax,
but this has proved problematic. We have installed subversion and
downloaded the latest repository as you described. We then had to
install "minfx" which was not required for the release version 
1.3.13.
Is this correct?

After this, when trying to run relax, arg_check.py returns an error
trying to import "float128" from numpy. It may be that we are running
an old version, I will look into this this afternoon.

Hugh



On 6 March 2012 12:04, Edward d'Auvergne <edward@xxxxxxxxxxxxx> 
wrote:
One other point is that I've recently been working on cleaning up,
simplifying, and fixing a few IO stream bugs the multi-processor
package in the 1.3 line of the relax repository since I tagged and
released the 1.3.13 version.  So there is a slight chance that I may
accientally have fixed the problem already.  But you'll need to 
check
out the most up to date repository code with the subversion program 
to
test this.

Regards,

Edward


On 6 March 2012 12:58, Edward d'Auvergne <edward@xxxxxxxxxxxxx> 
wrote:
Actually, looking the code, it appears as though the 
multi-processor
error handling is failing.  Which means that there are probably two
bugs here.  One is causing the program to fail, the second in the
multi-processor error handling is causing the memory error, hiding 
the
frist problem.  Could you replace the run() function in
multi/uni_processor.py code?  The original code should be:

   def run(self):
       try:
           self.pre_run()
           self.callback.init_master(self)
           self.post_run()
       except Exception, e:
           self.callback.handle_exception(self, e)

Could you replace it with:

   def run(self):
       self.pre_run()
       self.callback.init_master(self)
       self.post_run()

and see what the error message is?  If what I said above is 
correct,
then this should uncover the first bug (which then triggers the
second).  By the way, how long does it take to test this problem?

Cheers,

Edward



On 6 March 2012 12:49, Edward d'Auvergne <edward@xxxxxxxxxxxxx> 
wrote:
Hi,

Thank you for all the details.  That really helps in narrowing 
down
the bug!  From all the info, the bug is without doubt within the
multi-processor package.  Cheers.  If you have a little time, we 
can
work together and fix this.  The changes/fixes will go into the
repository version, so you'll need a copy of that for testing.  
Do you
have the subversion program installed?  If so, you can obtain the 
most
up to date copy from the repository by typing:

$ svn co svn://svn.gna.org/svn/relax/1.3 relax-1.3

or if this doesn't work:

$ svn co http://svn.gna.org/svn/relax/1.3 relax-1.3

If you already have a checked out copy, you can update to the 
newest
copy by typing:

$ svn up

I'll look at the second bug you've identifed later.  It would be
appreciated if you created a second bug report for that problem 
too.
I would not recommend reverting to earlier relax versions due to 
the
number of bug fixes and other problems solved since then.  This 
should
not affect the model-free results, but the bugs could bite 
elsewhere.
Hopefully I can fix this problem quickly.

Cheers,

Edward


P. S.  For reference, the bug report is 
https://gna.org/bugs/?19528.



On 6 March 2012 12:18, Hugh RW Dannatt 
<h.dannatt@xxxxxxxxxxxxxxx> wrote:
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

_______________________________________________
relax (http://nmr-relax.com)

This is the relax-users mailing list
relax-users@xxxxxxx

To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-users



--
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



--
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



--
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

_______________________________________________
relax (http://nmr-relax.com)

This is the relax-users mailing list
relax-users@xxxxxxx

To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-users



--
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



--
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



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