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 _______________________________________________ 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
