Hi Edward, Thank you for your suggestions. Unfortunately I am not in a position to answer many of your questions and so I will respond once I have had time to consult somebody with more understanding of our system. The behavior of the machine fits with your initial suggestion of a recursive exception, so monitoring the memory use during the analysis is definitely a good idea.
In the meantime I will try to remove the Monte Carlo commands from the dauvergne_protocol script and see what happens. Given that the error does not occur when the number of simulations is reduced I am confident that it is the simulations which are causing the error. I will get back to you on this. Unfortunately given the speed of the machine it is necessary to wait for one run to give an error before starting another, and this can take several hours! Hugh On 6 March 2012 17:39, Edward d'Auvergne <[email protected]> wrote: > According to http://en.wikipedia.org/wiki/Pentium_4, the dual-core > Pentium 4's should be 64-bit. Is there a reason why the computer is > running the 32-bit version of Ubuntu rather than the 64-bit version? > Is this running directly on the CPU or in a virtual machine? It could > be that you are simply limited to 4 Gb of total memory as this is a > 32-bit machine (2**32 is 4 Gb). Can you monitor relax at around > simulation 495 until the crash using top? Or maybe monitor the > virtual memory size with: > > $ grep VmSize /proc/xxxx/status > > replacing 'xxxx' with the PID of the relax process. > > Cheers, > > Edward > > > > > On 6 March 2012 17:59, Edward d'Auvergne <[email protected]> wrote: >> Ah, that's better. Well you have a total of 8 Gb of memory for relax >> to sit in, which is plenty for relax, so this is quite strange. I've >> loaded much more data than that before on systems with less total >> memory, and it hasn't been a problem. The Python MemoryError message >> appears to only occur once you have run out of total memory, and >> should kick in before the Linux OOM killer kills the program. Could >> there be any programs or settings limiting the amount of memory >> individual programs or users are allowed on your machine? If you run >> 'dmesg', is there anything at the end about memory issues? And does >> it always say "Simulation 500" followed by the Traceback messages? I >> wonder if this could be a memory corruption issue. This is quite a >> strange error. Do you have RAM testing programs available? >> >> For anther test, could you open 'auto_analyses/dauvergne_protocol.py' >> and delete the lines: >> >> # Simulations. >> self.interpreter.monte_carlo.setup(number=self.mc_sim_num) >> self.interpreter.monte_carlo.create_data() >> self.interpreter.monte_carlo.initial_values() >> self.interpreter.minimise(self.min_algor, >> func_tol=self.opt_func_tol, max_iterations=self.opt_max_iterations) >> self.interpreter.eliminate() >> self.interpreter.monte_carlo.error_analysis() >> >> With these removed, it will test if it the Monte Carlo simulations >> triggering the MemoryError. >> >> Cheers, >> >> Edward >> >> >> >> On 6 March 2012 17:43, Hugh RW Dannatt <[email protected]> wrote: >>> I certainly thought I had run it in the right directory, but having >>> done it again it has just outputted that info.py has been updated, so >>> perhaps not, my apologies! >>> >>> free -m gives the following output:- >>> >>> total used free shared buffers cached >>> Mem: 2011 1958 53 0 2 41 >>> -/+ buffers/cache: 1914 97 >>> Swap: 5889 927 4962 >>> >>> ----------- >>> >>> And relax -i gives the following:- >>> >>> >>> relax repository checkout >>> >>> Molecular dynamics by NMR data analysis >>> >>> Copyright (C) 2001-2006 Edward d'Auvergne >>> Copyright (C) 2006-2012 the relax development team >>> >>> This is free software which you are welcome to modify and redistribute >>> under the conditions of the >>> GNU General Public License (GPL). This program, including all >>> modules, is licensed under the GPL >>> and comes with absolutely no warranty. For details type 'GPL' within >>> the relax prompt. >>> >>> Assistance in using the relax prompt and scripting interface can be >>> accessed by typing 'help' within >>> the prompt. >>> >>> ImportError: relaxation curve fitting is unavailable, the >>> corresponding C modules have not been compiled. >>> >>> Processor fabric: Uni-processor. >>> >>> Hardware information: >>> Machine: i686 >>> Processor: >>> Endianness: little >>> >>> Total RAM size: 2011 Mb >>> Total swap size: 5889 Mb >>> >>> >>> Operating system information: >>> System: Linux >>> Release: 2.6.32-38-generic >>> Version: #83-Ubuntu SMP Wed Jan 4 11:13:04 UTC 2012 >>> GNU/Linux version: Ubuntu 10.04 lucid >>> Distribution: Ubuntu 10.04 lucid >>> Full platform string: >>> Linux-2.6.32-38-generic-i686-with-Ubuntu-10.04-lucid >>> >>> Python information: >>> Architecture: 32bit ELF >>> Python version: 2.6.5 >>> Python branch: tags/r265 >>> Python build: r265:79063, Apr 16 2010 13:09:56 >>> Python compiler: GCC 4.4.3 >>> Libc version: glibc 2.4 >>> Python implementation: CPython >>> Python revision: 79063 >>> Python executable: /usr/bin/python >>> Python flags: sys.flags(debug=0, py3k_warning=0, >>> division_warning=0, division_new=0, inspect=0, interactive=0, >>> optimize=0, dont_write_bytecode=0, no_user_site=0, no_site=0, >>> ignore_environment=0, tabcheck=0, verbose=0, unicode=0, >>> bytes_warning=0) >>> Python float info: >>> sys.floatinfo(max=1.7976931348623157e+308, max_exp=1024, >>> max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021, >>> min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.2204460492503131e-16, >>> radix=2, rounds=1) >>> Python module path: ['', '/home1/hugh/installs/relax-1.3', >>> '/home1/hugh/programs/mattfit', '/usr/lib/python2.6', >>> '/usr/lib/python2.6/plat-linux2', '/usr/lib/python2.6/lib-tk', >>> '/usr/lib/python2.6/lib-old', '/usr/lib/python2.6/lib-dynload', >>> '/usr/lib/python2.6/dist-packages', >>> '/usr/lib/python2.6/dist-packages/PIL', >>> '/usr/lib/python2.6/dist-packages/gst-0.10', >>> '/usr/lib/pymodules/python2.6', >>> '/usr/lib/python2.6/dist-packages/gtk-2.0', >>> '/usr/lib/pymodules/python2.6/gtk-2.0', >>> '/usr/local/lib/python2.6/dist-packages', >>> '/home1/hugh/installs/relax-1.3/extern/scientific_python/linux2'] >>> >>> Python packages (most are optional): >>> >>> Package Installed Version Path >>> minfx True Unknown >>> /usr/local/lib/python2.6/dist-packages/minfx >>> bmrblib False >>> numpy True 1.3.0 >>> /usr/lib/python2.6/dist-packages/numpy >>> scipy True 0.7.0 >>> /usr/lib/python2.6/dist-packages/scipy >>> wxPython False >>> mpi4py False >>> epydoc False >>> optparse True 1.5.3 >>> /usr/lib/python2.6/optparse.pyc >>> readline True >>> /usr/lib/python2.6/lib-dynload/readline.so >>> profile True >>> /usr/lib/python2.6/profile.pyc >>> bz2 True >>> /usr/lib/python2.6/lib-dynload/bz2.so >>> gzip True >>> /usr/lib/python2.6/gzip.pyc >>> os.devnull True >>> /usr/lib/python2.6/os.pyc >>> >>> Compiled relax C modules: >>> Relaxation curve fitting: False >>> >>> >>> ----------- >>> >>> Alas the computer is running extremely slowly so I expect I will get >>> the MemoryError at some point again. >>> >>> Cheers >>> >>> Hugh >>> >>> >>> >>> >>> On 6 March 2012 16:19, Edward d'Auvergne <[email protected]> wrote: >>>> Did you run 'svn up' in the base relax directory? And did you see a >>>> message that some files were updated? What happens if you type 'free >>>> -m' on your system? >>>> >>>> Cheers, >>>> >>>> Edward >>>> >>>> >>>> On 6 March 2012 15:59, Hugh RW Dannatt <[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 >>> >>> >>> >>> -- >>> 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
