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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]>
>>>>>>> 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 <[email protected]>
>>>>>>>> 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 <[email protected]>
>>>>>>>>> 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
>>>>>>>>>> [email protected]
>>>>>>>>>>
>>>>>>>>>> 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
> [email protected]
>
> 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
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