On 12 October 2015 at 09:04, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > On 11 October 2015 at 19:32, Sze Chan <samuelsw.c...@mail.utoronto.ca> wrote: >> Hello, >> >> >> While I was setting up my modelfree analysis in the GUI automated protocol , >> I received the error in the controller: >> >> >> RelaxWarning: comparison to `None` will result in an elementwise object >> comparison in the future. >> >> >> After loading my data, setting dipolar interactions, setting CSA relaxations >> and setting the isotopes but before execution of the analysis. >> >> >> I'm not sure what happened to cause the warning, but when the modelfree >> analysis is running, each successive round of optimization in each model >> does not compare to the previous round, instead it would always compare each >> optimized chi-square value to 'none' such as in round 21 of the oblate model: >> >> >> Storing the optimisation results for the spin >> '#LARA_N_term_no_helixFH_reg_mol24:358@N', the optimised chi-squared value >> is lower than the current value (283.50425283 < None). >> >> >> Even though I'm guessing it should refer to a previously optimised value? >> >> >> During the analysis it would go through the default 30 rounds of >> optimisation for each global model but not reach convergence. >> >> >> I was wondering how I can remedy this or at least create a log file so I can >> make my problem more clear. > > Hi Sam, > > I would suggest running relax with these options: > > $ relax --gui --log relax_warning.log --traceback > > This will start the GUI, send all output into a 'relax_warning.log' > file, and produce highly detailed RelaxError and RelaxWarning messages > pointing to the exact place in the code where the problem occurred. > Then exit relax once this warning first occurs (using kill if > necessary). > > Which version of relax are you using by the way? And which numpy > version? The RelaxWarning message you see is either due to Python or > numpy (specifically using newer versions). I have seen it many times > before, and I try to avoid it in the code where possible. Strangely I > have never seen this one before. The relax test suite tests the full > automated dauvergne_protocol analysis, including multiple rounds of > optimisation and convergence tests. And for each relax release I run > the full test suite on Python version 2.5, 2.6, 2.7, 3.0, 3.1, 3.2, > 3.3, and 3.4 (and now 3.5). Because the test suite has not replicated > the problem you see, maybe it has something to do with numpy. Anyway, > I look forward to seeing the traceback on that RelaxWarning, and maybe > the output of 'relax -i'. If you'd like to attach files, then please > create a bug report and attach the file to the report ( > https://gna.org/bugs/?func=additem&group=relax ).
Hi Sam, Thanks for creating the bug report ( https://gna.org/bugs/?23933 ). From this I can see that the RelaxWarning is not the problem, but rather this: """ relax> relax_data.read(ri_id='R1_600_2', ri_type='R1', frq=600402816.0, file='C:\\Users\\Sam Chan\\Desktop\\r1_600.txt', 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=2, error_col=3, sep=None, spin_id='@N*') Opening the file 'C:\\Users\\Sam Chan\\Desktop\\r1_600.txt' for reading. Traceback (most recent call last): File "C:\relax\gui\wizards\wiz_objects.py", line 166, in _apply self.exec_status = self.on_execute() File "C:\relax\gui\uf_objects.py", line 917, in on_execute return_status = self.execute(self.name, **kargs) File "C:\relax\gui\uf_objects.py", line 839, in execute return_status = interpreter.apply(uf, *args, **kwds) File "C:\relax\gui\interpreter.py", line 109, in apply fn(*args, **kwds) File "C:\relax\pipe_control\relax_data.py", line 920, in read pack_data(ri_id, ri_type, frq, values, errors, mol_names=mol_names, res_nums=res_nums, res_names=res_names, spin_nums=spin_nums, spin_names=spin_names, spin_id=spin_id) File "C:\relax\pipe_control\relax_data.py", line 767, in pack_data if ids: NameError: global name 'ids' is not defined """ Did you see this error in the GUI? To help debug this, I was wondering if you could attach a shortened version of the r1_600.txt file (truncated to 1 or 2 residues, but still enough to trigger the error). I could then use this to create a new system or GUI test to catch the problem. That will allow me to come up with a fix in normally a few minutes. Oh, you may have seen that I just released relax 4.0.0, the first of the 4 series ( http://wiki.nmr-relax.com/Relax_4.0.0 ). However this problem you see will still be present. Cheers, Edward _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org 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
