Hi Edward, I also wanted to add, for running a multi-processor platform problem. I installed openmpi from the fedora package list, not from the site itself. I installed both openmpi, mpi4py, and the openmpi devel. I did not modify anything. I can also successfully open relax using mpirun in a single processor mode (as in I can load the module, and do mpirun relax and it'll work). Do I actually have to do some modifications to openmpi for relax? The other computer I was able to successfully run multi-processor on, already had openmpi installed and set up, so I only downloaded mpi4py on that computer. So I don't know what their setting or configuration was.
Sincerely, Sam On Fri, Sep 30, 2016 at 8:22 AM, Mahdi, Sam <sam.mahdi....@my.csun.edu> wrote: > Hi Edward, > > I have uploaded a bug with the pdb file, the relax data, and the script as > well. I can upload the original pdb file I recieved from HADDOCK (without > changing the HN to H). I will attempt to re-run my data again then on both > computer. Most of the data was the same, but there were some data in from > one computer, that was virtually non-existent in the other. Also to the > relax -x error, I believe that was on the relax 2.5 version. I am > re-running it on the 4.0.2. version. > > Sincerely, > Sam > > On Fri, Sep 30, 2016 at 12:04 AM, Edward d'Auvergne <edw...@nmr-relax.com> > wrote: > >> On 29 September 2016 at 00:23, Mahdi, Sam <sam.mahdi....@my.csun.edu> >> wrote: >> > Hi Troels, >> > Update on both proteins: So for protein 1, I can upload all the spins (H >> > and N), but then I recieve an error. This is the error I recieved for >> > protein 2 as well. These are both dimer pdb files. Meaning they have 2 >> sets >> > (set A) and set (B) (e.g. >> > http://www.rcsb.org/pdb/explore/explore.do?structureId=1DJ8 this pdb >> > protein has 4 sets, A,B,C, and D ours only have A and B). For both these >> > proteins I recieve this error >> > File "/home/crowlab/relax-4.0.2/multi/processor.py", line 494, in run >> > self.callback.init_master(self) >> > File "/home/crowlab/relax-4.0.2/multi/__init__.py", line 318, in >> > default_init_master >> > self.master.run() >> > File "/home/crowlab/relax-4.0.2/relax.py", line 199, in run >> > self.interpreter.run(self.script_file) >> > File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 279, in >> run >> > return run_script(intro=self.__intro_string, local=locals(), >> > script_file=script_file, show_script=self.__show_script, >> > raise_relax_error=self.__raise_relax_error) >> > File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 585, in >> > run_script >> > return console.interact(intro, local, script_file, >> > show_script=show_script, raise_relax_error=raise_relax_error) >> > File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 484, in >> > interact_script >> > exec_script(script_file, local) >> > File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 363, in >> > exec_script >> > runpy.run_module(module, globals) >> > File "/usr/lib64/python2.7/runpy.py", line 180, in run_module >> > fname, loader, pkg_name) >> > File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code >> > exec code in run_globals >> > File "/home/crowlab/relax-4.0.2/RGS4_modelfree_sample_script.py", >> line >> > 31, in <module> >> > >> > dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,di >> ff_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 "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py", >> > line 246, in __init__ >> > self.execute() >> > File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py", >> > line 600, in execute >> > self.multi_model(local_tm=True) >> > File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py", >> > line 888, in multi_model >> > self.interpreter.minimise.grid_search(inc=self.grid_inc) >> > File "/home/crowlab/relax-4.0.2/prompt/uf_objects.py", line 225, in >> > __call__ >> > self._backend(*new_args, **uf_kargs) >> > File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 172, >> in >> > grid_search >> > model_lower, model_upper, model_inc = grid_setup(lower, upper, inc, >> > verbosity=verbosity, skip_preset=skip_preset) >> > File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 341, >> in >> > grid_setup >> > elif values[i] in [None, {}, []]: >> > IndexError: index out of bounds >> > >> > Which from my understanding basically means, the co-ordinates of the >> spins >> > are out of the acceptable range for relax. I've checked all the >> > co-ordinates for both, nothing is extreme or outlandish (all within a >> range >> > of -20 to 20). >> > Is relax unable to process pdb files that are dimers (with 2 sets A and >> > B).? Furthermore, is it unable to process trimers and tetramers? >> >> Hi, >> >> For the model-free analysis in relax, as well as all other analyses, >> we have designed the program to try to catch all user input errors and >> to produce a specific RelaxError prior to minimisation explaining >> exactly what went wrong. An IndexError here simply shows that not all >> erroneous data input has been caught. Let me go back to your PDB >> file. You should not edit this file unless you know exactly what you >> are doing, but relax will handle all PDB files. There is no need to >> rename protons. You just specify the correct proton name in the input >> script. I may have missed it as there is a lot of correspondence I >> have to catch up on, but did you upload your script and a truncated >> set of data to the relax bug or support trackers? Do you have a >> mini-data set (1 or 2 residues) and script that triggers this error? >> If we can reproduce the IndexError, then finding the error would be >> easy. >> >> 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
