Re: Problem during "final" run of d'Auvergne Protocol -- March 16, 2012 - 17:30

Hi Edward,

Just confirming that this has indeed fixed the problem. Thank you very much.

Hugh



On 15 March 2012 19:25, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> Ok, I think I have fixed the problem.  You'll either need a new
> release of relax, when I make one, or the subversion copy of the main
> 1.3 line of relax for this.  If you would like the changes without
> waiting for a new release of relax, the new code can be checked out
> 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, try typing:
>
> $ svn up
>
> This requires installation of the subversion program
> (http://subversion.tigris.org/).
>
> Regards,
>
> Edward
>
>
> On 15 March 2012 19:19, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> > Hi,
> >
> > I'm debugging this right now.  From what I can see, the
> > multi-processor code is clearly at fault.  The issue is in the
> > generic_fns/minimise.py file and the lines:
> >
> >    # Get the Processor box singleton (it contains the Processor instance).
> >    processor_box = Processor_box()
> >
> >    # Execute the queued elements.
> >    processor_box.processor.run_queue()
> >
> > This is repeated twice, but the problem is in the minimise() function.
> >  The problem is that the run_queue() call causes all the calculations
> > to execute.  Prior to this, all calculations will be queued up, either
> > on the multi-processor or uni-processor stack.  Previously, each
> > calculation was being executed serially, i.e. one after the other.
> >
> > The serial calculations are not a problem as, at the end of each, the
> > Python garbage collector would destroy all the data structures used by
> > that calculation, freeing up the memory.  But with the multi-processor
> > code, this memory-freeing operation can only occur at the end of all
> > calculations.  The merger of the multi-processor relax branch
> > eliminated the serial calculations.  The solution I am working on is
> > shifting the run_queue() call higher up into the model-free code.
> > That is so the calculations for each Monte Carlo simulation is run
> > serially.  The parallelisation occurs at the residue level, not the
> > Monte Carlo simulation level.  Say there are 200 residues, then I am
> > aiming at having only 200 calculations queued at once (there is one
> > per spin), rather than 200 * 500 = 100,000 calculations queued.
> >
> > I am in the testing phase, so I have to make sure my fix doesn't break
> > any other parts of relax.  But you can test it youself if you like.
> > You can delete all of the 'processor_box' lines from the
> > generic_fns/minimise.py file.  Then at the very end of the
> > specific_fns/model_free/mf_minimise.py file, the last lines should
> > look like:
> >
> >
> >            # Pass in the data and optimisation parameters.
> >            command.store_data(deepcopy(data_store), deepcopy(opt_params))
> >
> >            # Set up the model-free memo and add it to the processor queue.
> >            memo = MF_memo(model_free=self,
> > model_type=data_store.model_type, spin=spin, sim_index=sim_index,
> > scaling=scaling, scaling_matrix=data_store.scaling_matrix)
> >            processor.add_to_queue(command, memo)
> >
> >        # Get the Processor box singleton (it contains the Processor 
> > instance).
> >        processor_box = Processor_box()
> >
> >        # Execute the queued elements.
> >        processor_box.processor.run_queue()
> >
> > This fix is temporary and incomplete, but might just solve your
> > problem.  With these changes, my testing indicates that virtual memory
> > usage drops from 1871 Mb down to 648 Mb!  I will continue with the
> > testing, and hopefully tomorrow I should have a permanent fix for you.
> >
> > Regards,
> >
> > Edward
> >
> >
> >
> >
> > On 15 March 2012 18:46, Hugh RW Dannatt <h.dannatt@xxxxxxxxxxxxxxx> wrote:
> > > This is really encouraging, thank you for your continued interest! I'm
> > > intrigued as to why this has not been seen before, do you have any
> > > feeling for this? It doesn't seem like this is a particularly large
> > > data set.
> > >
> > > Unfortunately running 450 sims seems to have succumbed as well, so I
> > > will try your temporary fix and await something more permenant.
> > >
> > > Cheers
> > >
> > > Hugh
> > >
> > >
> > >
> > > On 15 March 2012 17:25, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> > > > Hi,
> > > >
> > > > Using this results file, I can reproduce the problem.  Well, I can at
> > > > least see where the problem is.  Running on my machine, a 64-bit
> > > > laptop, the total memory usage (virtual memory) reaches 1871 Mb.  As
> > > > my laptop only has 2 Gb of RAM, this results in a lot of swapping to
> > > > calculate the parameter errors but it does not cause the crashes you
> > > > are seeing.  The swapping is a very, very slow process and the relax
> > > > CPU usage is almost 0% during this time.  You can see this in the
> > > > program top whereby memory is switching between 'RES' and 'SWAP'.  So
> > > > I see the same memory and CPU usage that you reported.  For the
> > > > testing, I am running the simple script:
> > > >
> > > > -----
> > > > state.load('results')
> > > > fix('diff')
> > > >
> > > > # Simulations.
> > > > monte_carlo.setup(number=500)
> > > > monte_carlo.create_data()
> > > > monte_carlo.initial_values()
> > > > minimise('newton', max_iterations=1)
> > > > eliminate()
> > > > monte_carlo.error_analysis()
> > > >
> > > > # Create results files and plots of the data.
> > > > state.save('mc', force=True)
> > > > -----
> > > >
> > > > On your 32-bit systems, this might be too much memory usage.  I'm not
> > > > sure why relax is using so much memory at this stage.  You don't have
> > > > much control of memory in the Python programming language which make
> > > > things more difficult.  But I'll have a look and see if I can decrease
> > > > the memory footprint.  Thanks for sending the results file, this
> > > > should allow me to fix, or at least minimise this problem.
> > > >
> > > > Cheers,
> > > >
> > > > Edward
> > > >
> > > >
> > > > P. S.  If you are desparate to get results out, you might be able to
> > > > avoid running out of memory by running your computer with the minimum
> > > > number of programs running.  You could switch to a VT (Ctrl-Alt-F1)
> > > > and run 'init 3' as root.  This will kill X and all X programs.  You
> > > > could then run relax in the terminal.  This might just give you enough
> > > > memory to survive.  Otherwise, you could wait until I have some fixes.
> > > >
> > > >
> > > >
> > > > On 15 March 2012 17:11, Hugh RW Dannatt <h.dannatt@xxxxxxxxxxxxxxx> 
> > > > wrote:
> > > > > Hi Edward,
> > > > >
> > > > > Attached is the results.bz2 file from ellipsoid/round_14/opt/.
> > > > >
> > > > > I will try to see what happens if I set the number of simulations at 
> > > > > 450.
> > > > >
> > > > > Hugh
> > > > >
> > > > >
> > > > >
> > > > > On 15 March 2012 11:14, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> > > > > > Hi,
> > > > > >
> > > > > > This is a very perculiar problem.  As I cannot reproduce it, I can
> > > > > > only guess what is going on.  How big is the results.bz2 file for the
> > > > > > final round of the selected diffusion tensor?  Maybe if you send it in
> > > > > > a private mail, I could then try to replicate the problem on a 32-bit
> > > > > > virtual machine image.  That way I'd be able to chase down the source
> > > > > > of the problem.  It could be the RAM, the virtual memory on 32-bit,
> > > > > > the operating system, the specific python version, or relax.  Although
> > > > > > I am pretty sure that the problem lies outside of relax, it would be
> > > > > > good to track down which exact operation down to the source code line
> > > > > > number in relax is triggering the problem.  That way I might be able
> > > > > > to come up with some tricks for minimising the memory usage.  For a
> > > > > > temporary alternative, maybe you could try 450 simulations to see if
> > > > > > you can get the results out.  The results would be less precise, but
> > > > > > still reasonable.  I'm not sure if the results would be reasonable if
> > > > > > you decreased the number much lower than that though.
> > > > > >
> > > > > > In the mean time, I might try to look into minimising memory usage at
> > > > > > the Monte Carlo simulation optimisation stage.  Your results file
> > > > > > would also significantly help in optimisating this.
> > > > > >
> > > > > > Regards,
> > > > > >
> > > > > > Edward
> > > > > >
> > > > > >
> > > > > >
> > > > > > On 14 March 2012 18:41, Hugh RW Dannatt <h.dannatt@xxxxxxxxxxxxxxx> 
> > > > > > wrote:
> > > > > > > Hi Edward,
> > > > > > >
> > > > > > > A couple of comments - as I've said before this problem occurs on the
> > > > > > > 3 different machines that I have tried it on, so I don't think that
> > > > > > > any memory corruption or other computer-specific issues are the cause
> > > > > > > of this. You mentioned our running on the 32-bit version of the OS, I
> > > > > > > guess this is because we have various machines (some new, some old)
> > > > > > > networked together all running the same system. Perhaps some of the
> > > > > > > older machines can't handle the 64-bit version.
> > > > > > >
> > > > > > > I tried decreasing the number of MC simulations to 250, and
> > > > > > > surprisingly this works! Dissatisfying a solution as it may be, just a
> > > > > > > quick fix for me as I need to start writing my thesis v. soon, is
> > > > > > > there a way of running this twice, loading in both sets of simulations
> > > > > > > and doing the error analysis on the combined back-calculated datasets?
> > > > > > > I have only run relax using dauvergne_protocol so I may need guiding
> > > > > > > through this!
> > > > > > >
> > > > > > > For a more proper fix, I have monitored the memory usage in top, as
> > > > > > > you suggested. The CPU usage during the minimisations is 100%, and the
> > > > > > > memory usage slowly climbs to, eg. 11% by sim 200, 22% by sim 500. At
> > > > > > > this point, the memory usage increases at about triple the rate it was
> > > > > > > doing during the minimisations, up to a point that depends on how many
> > > > > > > simulations have been done - 18% if 100 sims, 33% if 200, etc. If the
> > > > > > > program is not destined to crash (no. of sims < 250), at this stage
> > > > > > > the CPU usage is still 100% and stays very high until the program
> > > > > > > finishes. As soon as the program enters the "MC sim elimination" phase
> > > > > > > the memory usage stops rising and stays constant until the program has
> > > > > > > finished. If I set the no. of sims to 500, the memory usage following
> > > > > > > minimisation of all 500 simulations increases until it gets to ~90%
> > > > > > > where it fluctuates between 87-91% for a long time until eventually
> > > > > > > the program crashes. Crucially, during this time the CPU usage is
> > > > > > > almost nothing. At no point does the program enter the elimination
> > > > > > > phase, so something is clearly happening at the end of the
> > > > > > > minimisation - and the rising memory usage even when the no. of sims
> > > > > > > is low would also suggest this.
> > > > > > >
> > > > > > > This result is backed up by the behavior of the program when lines of
> > > > > > > dauvergne_protocol.py in auto_analyses are commented out. If you
> > > > > > > comment out the entire MC simulation part, the program works fine.
> > > > > > > Additionally, removal of the self.interpreter.eliminate(),
> > > > > > > self.interpreter.monte_carlo.error_analysis(), or final
> > > > > > > self.write_results() lines (individually or at the same time) are
> > > > > > > insufficient to rescue the program. Only if the
> > > > > > > self.interpreter.minimise command (and therefore the subsequent lines
> > > > > > > concerning MC simulations) are commented out does the program finish.
> > > > > > > So, as I said above, it is something taking place at the end of the
> > > > > > > minimisation which is causing the problem.
> > > > > > >
> > > > > > > Below is the output if only the self.interpreter.eliminate() line is 
> > > > > > > removed:-
> > > > > > >
> > > > > > > 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 "/home1/hugh/installs/relax-1.3/multi/uni_processor.py", line 
> > > > > > > 136, in run
> > > > > > > Traceback (most recent call last):
> > > > > > >  File "/home1/hugh/installs/relax-1.3/relax", line 7, in <module>
> > > > > > >    relax.start()
> > > > > > >  File "/home1/hugh/installs/relax-1.3/relax.py", line 103, in start
> > > > > > >    processor.run()
> > > > > > >  File "/home1/hugh/installs/relax-1.3/multi/uni_processor.py", line 
> > > > > > > 139, in run
> > > > > > >    self.callback.handle_exception(self, e)
> > > > > > >  File "/home1/hugh/installs/relax-1.3/multi/__init__.py", line 227,
> > > > > > > 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
> > > > > > > 2745.731u 413.433s 5:12:02.27 16.8%     0+0k 169003312+64io 
> > > > > > > 4488658pf+0w
> > > > > > >
> > > > > > > --------
> > > > > > >
> > > > > > > If both the self.interpreter.eliminate() and
> > > > > > > self.interpreter.monte_carlo.error_analysis() lines are removed:-
> > > > > > >
> > > > > > > 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 "/home1/hugh/installs/relax-1.3/multi/uni_processor.py", line 
> > > > > > > 136, in run
> > > > > > >  File "/home1/hugh/installs/relax-1.3/multi/__init__.py", line 240,
> > > > > > > in default_init_master
> > > > > > >  File "/home1/hugh/installs/relax-1.3/relax.py", line 174, in run
> > > > > > >  File "/home1/hugh/installs/relax-1.3/prompt/interpreter.py", line 
> > > > > > > 300, in run
> > > > > > >  File "/home1/hugh/installs/relax-1.3/prompt/interpreter.py", line
> > > > > > > 610, in run_script
> > > > > > >  File "/home1/hugh/installs/relax-1.3/prompt/interpreter.py", line
> > > > > > > 495, in interact_script
> > > > > > >  File "/home1/hugh/installs/relax-1.3/prompt/interpreter.py", line
> > > > > > > 383, in exec_script
> > > > > > >  File "/usr/lib/python2.6/runpy.py", line 140, in run_module
> > > > > > >  File "/usr/lib/python2.6/runpy.py", line 34, in _run_code
> > > > > > >  File "/home1/hugh/data/pgm298bq/relax/dauvergne_protocol_repos.py",
> > > > > > > line 216, in <module>
> > > > > > >  File 
> > > > > > > "/home1/hugh/installs/relax-1.3/auto_analyses/dauvergne_protocol.py",
> > > > > > > line 223, in __init__
> > > > > > >  File 
> > > > > > > "/home1/hugh/installs/relax-1.3/auto_analyses/dauvergne_protocol.py",
> > > > > > > line 701, in execute
> > > > > > >  File "/home1/hugh/installs/relax-1.3/prompt/minimisation.py", line
> > > > > > > 294, in minimise
> > > > > > >  File "/home1/hugh/installs/relax-1.3/generic_fns/minimise.py", line
> > > > > > > 221, in minimise
> > > > > > >  File "/home1/hugh/installs/relax-1.3/multi/uni_processor.py", line
> > > > > > > 149, in run_queue
> > > > > > >  File 
> > > > > > > "/home1/hugh/installs/relax-1.3/specific_fns/model_free/multi_processor_commands.py",
> > > > > > > line 130, in run
> > > > > > >  File 
> > > > > > > "/home1/hugh/installs/relax-1.3/specific_fns/model_free/multi_processor_commands.py",
> > > > > > > line 113, in optimise
> > > > > > >  File "/usr/local/lib/python2.6/dist-packages/minfx/generic.py", line
> > > > > > > 321, in generic_minimise
> > > > > > >  File "/usr/local/lib/python2.6/dist-packages/minfx/newton.py", line
> > > > > > > 44, in newton
> > > > > > >  File "/usr/local/lib/python2.6/dist-packages/minfx/base_classes.py",
> > > > > > > line 271, in minimise
> > > > > > >  File "/usr/local/lib/python2.6/dist-packages/minfx/newton.py", line
> > > > > > > 215, in update_newton
> > > > > > >  File "/home1/hugh/installs/relax-1.3/maths_fns/mf.py", line 925, in 
> > > > > > > d2func_mf
> > > > > > >  File "/home1/hugh/installs/relax-1.3/maths_fns/jw_mf.py", line 2309,
> > > > > > > in calc_S2_te_d2jw_dte2
> > > > > > > Traceback (most recent call last):
> > > > > > >  File "/home1/hugh/installs/relax-1.3/relax", line 7, in <module>
> > > > > > >    relax.start()
> > > > > > >  File "/home1/hugh/installs/relax-1.3/relax.py", line 103, in start
> > > > > > >    processor.run()
> > > > > > >  File "/home1/hugh/installs/relax-1.3/multi/uni_processor.py", line 
> > > > > > > 139, in run
> > > > > > >    self.callback.handle_exception(self, e)
> > > > > > >  File "/home1/hugh/installs/relax-1.3/multi/__init__.py", line 227,
> > > > > > > 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 126, in print_exception
> > > > > > >    lines = format_exception_only(etype, value)
> > > > > > > MemoryError
> > > > > > > 2702.244u 398.632s 5:12:15.23 16.5%     0+0k 165775728+64io 
> > > > > > > 4501002pf+0w
> > > > > > >
> > > > > > > ------------
> > > > > > >
> > > > > > > And finally if the self.interpreter.eliminate(),
> > > > > > > self.interpreter.monte_carlo.error_analysis(), and final
> > > > > > > self.write_results() lines are all removed:-
> > > > > > >
> > > > > > > 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):
> > > > > > > Traceback (most recent call last):
> > > > > > >  File "/home1/hugh/installs/relax-1.3/relax", line 7, in <module>
> > > > > > >    relax.start()
> > > > > > >  File "/home1/hugh/installs/relax-1.3/relax.py", line 103, in start
> > > > > > >    processor.run()
> > > > > > >  File "/home1/hugh/installs/relax-1.3/multi/uni_processor.py", line 
> > > > > > > 139, in run
> > > > > > >    self.callback.handle_exception(self, e)
> > > > > > >  File "/home1/hugh/installs/relax-1.3/multi/__init__.py", line 227,
> > > > > > > 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)
> > > > > > > MemoryError
> > > > > > > 2684.091u 374.487s 5:00:55.96 16.9%     0+0k 163383960+64io 
> > > > > > > 4258400pf+0w
> > > > > > >
> > > > > > > -----------
> > > > > > >
> > > > > > > If there are any other tests you would like me to do then let me know
> > > > > > > but as I've said this is rather time consuming! I hope this helps.
> > > > > > >
> > > > > > > Hugh
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On 7 March 2012 11:33, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> > > > > > > > Hi,
> > > > > > > >
> > > > > > > > This is a very difficult problem to debug, as it currently appears to
> > > > > > > > be triggered outside of relax.  For another test, could you remove 
> > > > > > > > the
> > > > > > > > lines:
> > > > > > > >
> > > > > > > >            # Write the final results.
> > > > > > > >            ##########################
> > > > > > > >
> > > > > > > >            # Create results files and plots of the data.
> > > > > > > >            self.write_results()
> > > > > > > >
> > > > > > > > after the Monte Carlo simulation user function calls in the
> > > > > > > > auto_analyses/dauvergne_protocol.py module and retest?  The strange
> > > > > > > > thing is that it is printing out simulation number 500, which should
> > > > > > > > mean that the simulation code has terminated.  But it hasn't printed
> > > > > > > > out the results.write user function message, which means that it
> > > > > > > > hasn't even started to create the results file (well, thats what the
> > > > > > > > above check tests).  If this is the case, the error occurs precisely
> > > > > > > > between the self.interpreter.monte_carlo.error_analysis() and
> > > > > > > > self.write_results() in the analysis, and not during the simulations
> > > > > > > > or results file creation.  But the strange thing is that relax is
> > > > > > > > doing absolutely nothing at that point!
> > > > > > > >
> > > > > > > > Another test for this would be to load your molecule twice, but as 
> > > > > > > > two
> > > > > > > > different molecules, and duplicate all the relaxation data loading,
> > > > > > > > effectively doubling your data size, and seeing if relax dies at
> > > > > > > > around simulation number 250.  If it is the Monte Carlo code causing
> > > > > > > > the problem of running out of memory, then you should not be able to
> > > > > > > > reach simulation 500.  But that is only if the problem is relax using
> > > > > > > > too much memory, which needs to be checked via top, etc.  Hopefully 
> > > > > > > > we
> > > > > > > > can get to the bottom of this problem and design a work around.
> > > > > > > >
> > > > > > > > Another interesting test would be to deactive your swap partition (as
> > > > > > > > system administrator) and re-run relax.  The command 'free -m' should
> > > > > > > > show that the swap size is zero or non-existant.  This will cut the
> > > > > > > > amount of virtual memory available, hopefully triggering the
> > > > > > > > MemoryError prior to simulation 500.  The slowing down of your
> > > > > > > > computer towards the end is caused by Linux heavily swapping out 
> > > > > > > > relax
> > > > > > > > from RAM to the swap partition and back again, so if you have no 
> > > > > > > > swap,
> > > > > > > > this slow down will be avoided.  That should speed up the process.
> > > > > > > > Another speed up would be to change line 701 of
> > > > > > > > auto_analyses/dauvergne_protocol.py from:
> > > > > > > >
> > > > > > > >            self.interpreter.minimise(self.min_algor,
> > > > > > > > func_tol=self.opt_func_tol, max_iterations=self.opt_max_iterations)
> > > > > > > >
> > > > > > > > to
> > > > > > > >
> > > > > > > >            self.interpreter.minimise(self.min_algor,
> > > > > > > > func_tol=self.opt_func_tol, max_iterations=3, constraints=False)
> > > > > > > >
> > > > > > > > This will massively speed up the simulations, though the resultant
> > > > > > > > errors will be underestimated.  This is no issue for these tests
> > > > > > > > though.
> > > > > > > >
> > > > > > > > Regards,
> > > > > > > >
> > > > > > > > Edward
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > On 7 March 2012 11:46, Hugh RW Dannatt <h.dannatt@xxxxxxxxxxxxxxx> 
> > > > > > > > wrote:
> > > > > > > > > Hi Edward,
> > > > > > > > >
> > > > > > > > > Haven't yet asked your questions on our set-up, but I have run 
> > > > > > > > > another
> > > > > > > > > couple of tests if I remove the Monte Carlo simulation commands from
> > > > > > > > > the dauvergne_protocol.py in auto_analyses then the program runs 
> > > > > > > > > fine
> > > > > > > > > without any problems at all. If I leave those commands in, the error
> > > > > > > > > message I get with the repository version of the program is below:-
> > > > > > > > >
> > > > > > > > > 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 "/home1/hugh/installs/relax-1.3/multi/uni_processor.py", line 
> > > > > > > > > 136, in run
> > > > > > > > > Traceback (most recent call last):
> > > > > > > > >  File "/home1/hugh/installs/relax-1.3/relax", line 7, in <module>
> > > > > > > > >    relax.start()
> > > > > > > > >  File "/home1/hugh/installs/relax-1.3/relax.py", line 103, in start
> > > > > > > > >    processor.run()
> > > > > > > > >  File "/home1/hugh/installs/relax-1.3/multi/uni_processor.py", line 
> > > > > > > > > 139, in run
> > > > > > > > >    self.callback.handle_exception(self, e)
> > > > > > > > >  File "/home1/hugh/installs/relax-1.3/multi/__init__.py", line 227,
> > > > > > > > > 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
> > > > > > > > > 8539.337u 606.393s 10:03:45.92 25.2%    0+0k 247727448+0io 
> > > > > > > > > 7012268pf+0w
> > > > > > > > >
> > > > > > > > > ----------
> > > > > > > > >
> > > > > > > > > Hugh
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > On 6 March 2012 17:47, Hugh RW Dannatt <h.dannatt@xxxxxxxxxxxxxxx> 
> > > > > > > > > wrote:
> > > > > > > > > > Hi Edward,
> > > > > > > > > >
> > > > > > > > > > Thank you for your suggestions. Unfortunately I am not in a 
> > > > > > > > > > position
> > > > > > > > > > to answer many of your questions and so I will respond once I have 
> > > > > > > > > > had
> > > > > > > > > > time to consult somebody with more understanding of our system. The
> > > > > > > > > > behavior of the machine fits with your initial suggestion of a
> > > > > > > > > > recursive exception, so monitoring the memory use during the 
> > > > > > > > > > analysis
> > > > > > > > > > is definitely a good idea.
> > > > > > > > > >
> > > > > > > > > > In the meantime I will try to remove the Monte Carlo commands from 
> > > > > > > > > > the
> > > > > > > > > > dauvergne_protocol script and see what happens. Given that the 
> > > > > > > > > > error
> > > > > > > > > > does not occur when the number of simulations is reduced I am
> > > > > > > > > > confident that it is the simulations which are causing the error. I
> > > > > > > > > > will get back to you on this. Unfortunately given the speed of the
> > > > > > > > > > machine it is necessary to wait for one run to give an error before
> > > > > > > > > > starting another, and this can take several hours!
> > > > > > > > > >
> > > > > > > > > > Hugh
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > On 6 March 2012 17:39, Edward d'Auvergne <edward@xxxxxxxxxxxxx> 
> > > > > > > > > > wrote:
> > > > > > > > > > > According to http://en.wikipedia.org/wiki/Pentium_4, the dual-core
> > > > > > > > > > > Pentium 4's should be 64-bit.  Is there a reason why the computer 
> > > > > > > > > > > is
> > > > > > > > > > > running the 32-bit version of Ubuntu rather than the 64-bit 
> > > > > > > > > > > version?
> > > > > > > > > > > Is this running directly on the CPU or in a virtual machine?  It 
> > > > > > > > > > > could
> > > > > > > > > > > be that you are simply limited to 4 Gb of total memory as this is 
> > > > > > > > > > > a
> > > > > > > > > > > 32-bit machine (2**32 is 4 Gb).  Can you monitor relax at around
> > > > > > > > > > > simulation 495 until the crash using top?  Or maybe monitor the
> > > > > > > > > > > virtual memory size with:
> > > > > > > > > > >
> > > > > > > > > > > $ grep VmSize /proc/xxxx/status
> > > > > > > > > > >
> > > > > > > > > > > replacing 'xxxx' with the PID of the relax process.
> > > > > > > > > > >
> > > > > > > > > > > Cheers,
> > > > > > > > > > >
> > > > > > > > > > > Edward
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > On 6 March 2012 17:59, Edward d'Auvergne <edward@xxxxxxxxxxxxx> 
> > > > > > > > > > > wrote:
> > > > > > > > > > > > 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
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > --
> > > > > > > > > > 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
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > 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