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
