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