Re: crash during multi-processor grid search for 'sphere' modelRe: crash during multi-processor grid search for 'sphere' modelHi Jack, I would be quite interested in finally squashing this bug! Some type of RelaxWarning or RelaxError would need to be shown instead - the error message you saw should never be seen. For the mini dataset of 3-4 residues, would you have those files still? Would it be possible to create a tar or zip file with all 6 truncated relaxation data sets, your script which triggers the error, and the PDB file (also truncated)? Coud you put all of these together in a special directory, and run relax once more and make sure the problem occurs, delete the local_tm directory and anything else created by running relax, and then archive that directory and attach it to https://gna.org/bugs/?21001. Cheers! Unfortunately the file you attached last time is not enough for me to reproduce the bug. If I can unpack one archive, run relax and instantly see the bug, that would be very much appreciated. Thank you, Edward On 2 August 2013 18:44, Jack Skinner <skinnerj@xxxxxxxxxxxx> wrote:
I was able to get some more details about the problem by following your suggestion to create a mini dataset. First of all, the problem doesn't occur when using a single processor and only occurs for DIFF_MODEL = 'sphere' when using mpirun. I also didn't get the problem for mpirun when I used a subset of my data, suggesting that the problem is with my input. I found an anomaly in my 500 MHz noe data that appears to be the culprit. Here is what that file looks like for the subset that did cause a crash: # Parameter description: The NOE. # mol_name res_num res_name spin_num spin_name value error None 5 MET None None None None DesG 7 THR 15 N 0.718432367479729 0.0326572234546261 DesG 8 TYR 29 N 0.65401446462264 0.033499533240881 DesG 5 MET -1 N -0.420574006604573 0.037900692900274 This happened because of how I loaded my spins. The pdb file I used is missing the N-terminus, so I adding the MET using residue.create(res_num=5, res_name='MET'), which I later realized should be residue.create(res_num=5, res_name='MET',mol_name='DesG'). So now it's working for me. I have created bug report #21001 with relevant files attached in case you want to track down the "bug" to prevent future user error. On Fri, Aug 2, 2013 at 8:12 AM, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:Hi Jack, Welcome to the relax mailing lists! Wow, it's rare to see bugs in the model-free part of relax nowadays! Though this problem has been seen before by Martin Ballaschk, see the thread at: http://thread.gmane.org/gmane.science.nmr.relax.user/1291 The thread continues at: http://thread.gmane.org/gmane.science.nmr.relax.user/1312 Unfortunately you will see that no solution was found in the end, apart from a problem with the input relaxation data. But you will see that the problem is identical to what you see. Would you be able to perform the checks I mention in my response at: http://thread.gmane.org/gmane.science.nmr.relax.user/1291/focus=1292 If you can create a mini data set of 1 or 2 residues, as mentioned in that link, which reproduce the bug, I will then be able to add that to the relax test suite and eliminate the bug within a very short time. Files can be attached directly to your bug report (http://gna.org/bugs/?21001). With a good truncated data set and script, it usually takes me about 5-10 min to eliminate the bug. If I can replicate it, I can quickly eliminate it. Cheers, Edward On 1 August 2013 22:30, Jack Skinner <skinnerj@xxxxxxxxxxxx> wrote:I am having a problem with the dauvergne_protocol.py script crashing when I set DIFF_MODEL = 'sphere' All other models run fine except for 'final', which complains about the missing 'sphere' results. I am running this script with 8 processors using mpirun mpirun -np 8 relax --multi='mpi4py' -n 7 --tee rnd2.log relax_rnd2.py The error message starts: relax> grid_search(lower=None, upper=None, inc=11, constraints=True, verbosity=1) Over-fit spin deselection: No spins have been deselected. Only diffusion tensor parameters will be used. Parallelised diffusion tensor grid search. Traceback (most recent call last): File "/export/home/skinnerj/mypackages/relax-2.2.5/multi/processor.py", line 479, in run ...many lines that might not be helpful... then: Capturing_exception: File "/export/home/skinnerj/mypackages/relax-2.2.5/multi/processor.py", line 522, in run command.run(self, completed) File "/export/home/skinnerj/mypackages/relax-2.2.5/specific_fns/model_free/multi_processor_commands.py", line 129, in run results = self.optimise() File "/export/home/skinnerj/mypackages/relax-2.2.5/specific_fns/model_free/multi_processor_commands.py", line 175, in optimise results = grid_point_array(func=self.mf.func, args=(), points=self.opt_params.subdivision, verbosity=self.opt_params.verbosity) File "/export/home/skinnerj/mypackages/relax-2.2.5/minfx/grid.py", line 264, in grid_point_array n = len(points[0]) Nested Exception from sub processor Rank: 1 Name: kff4-pid14220 Exception type: IndexError Message: index out of bounds Any suggestions will be appreciated. Thanks! John "Jack" Skinner, Ph. D. | Postdoctoral Fellow | University of Chicago Lab: 773.834.0658 | GCIS Room W107E, 929 E. 57th St. Chicago, IL 60637 _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@xxxxxxx 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-- John "Jack" Skinner, Ph. D. | Postdoctoral Fellow | University of Chicago Lab: 773.834.0658 | GCIS Room W107E, 929 E. 57th St. Chicago, IL 60637