Re: Using multi-processor for model_free -- September 30, 2016

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.846@xxxxxxxxxxx>
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 <edward@xxxxxxxxxxxxx>
wrote:

On 29 September 2016 at 00:23, Mahdi, Sam <sam.mahdi.846@xxxxxxxxxxx>
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

Re: Using multi-processor for model_free

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