On 3/29/07, gary thompson <garyt.and.sarahb@xxxxxxxxx> wrote:
On 3/29/07, Gary S. Thompson <garyt@xxxxxxxxxxxxxxx> wrote:
> Edward d'Auvergne wrote:
[snip]
> > One
> > question I have is will there be a separate model-free minimise()
> > function for normal and MPI operation?
>
>
> no the non mpi version just calls the uniprocessor processor
> multi.uni_processor. The current uniprocessor implimentation is non
> optimal by space on single processor machines but will have the same
> overhead by time as any other implimentations (barring the use of
> command cacheing which may save to object creation overhead)
>
> > Another point is that I can't
> > run the code in the branch without having MPI up and running.
> >
> >
> you should be able to run relax without a --multi command line and
> without an mpirun and the uniprocessor implimentations should run.
> However, currently when I run it I get The dependency 'mpi4py' has not
> been installed is that the problem you have?? I will investigate the problem
>
>
correction I have just gone home and run the command on the same
machine remotely and get no messages about dependencies!. if this is
the error you get please tell me.
Ah revelation (realtime messaging and debugging!) in uni_processor I
am using multi.mpi4py_processor.Result_command which will load the
mpi4py_processor module which will result in load of mpi4py (lines 14
onwards in mpi4py_processor). This is just an oversight due to me
being lazy and winging it while testing corrections on the way ;-)
I had to work a bit harder than expected on this but 3248 should cure it
;-)
Also two other comments
1. This code is only compatible with python 2.4 currently. calling it
on 2.3.3 results in the crash
Traceback (most recent call last):
File "../relax", line 588, in ?
multi_processor.run()
File
"/usr/jessy/garyt/projects/relax_branch/branch_multi1/multi/uni_processor.py",
line 43, in run
self.relax_instance.run()
File "../relax", line 175, in run
self.interpreter.run()
File
"/usr/jessy/garyt/projects/relax_branch/branch_multi1/prompt/interpreter.py",
line 216, in run
run_script(intro=self.relax.intro_string, local=self.local,
script_file=self.relax.script_file, quit=1)
File
"/usr/jessy/garyt/projects/relax_branch/branch_multi1/prompt/interpreter.py",
line 392, in run_script
console.interact(intro, local, script_file, quit)
File
"/usr/jessy/garyt/projects/relax_branch/branch_multi1/prompt/interpreter.py",
line 343, in interact_script
execfile(script_file, local)
File "test_small.py", line 52, in ?
grid_search(name, inc=11)
File
"/usr/jessy/garyt/projects/relax_branch/branch_multi1/prompt/minimisation.py",
line 144, in grid_search
self.relax.generic.minimise.grid_search(run=run, lower=lower,
upper=upper, inc=inc, constraints=constraints, print_flag=print_flag)
File
"/usr/jessy/garyt/projects/relax_branch/branch_multi1/generic_fns/minimise.py",
line 96, in grid_search
grid_search(run=run, lower=lower, upper=upper, inc=inc,
constraints=constraints, print_flag=print_flag)
File
"/usr/jessy/garyt/projects/relax_branch/branch_multi1/specific_fns/model_free.py",
line 1520, in grid_search
self.minimise(run=run, min_algor='grid', constraints=constraints,
print_flag=print_flag, sim_index=sim_index)
File
"/usr/jessy/garyt/projects/relax_branch/branch_multi1/specific_fns/model_free.py",
line 2408, in minimise
mu0=self.relax.data.mu0, num_params=num_params, vectors=xh_unit_vectors)
File
"/usr/jessy/garyt/projects/relax_branch/branch_multi1/multi/commands.py",
line 84, in set_mf
self.mf_map.update(**kwargs)
TypeError: update() takes no keyword arguments
clearly update won't take dictionaries on 2.3.3
2. I ran the uniprocessor and the mpi4py versions on my machine and
was suprised to find that if you directed stdout to a file they had
almost identical ruintimes. so it appears that most of the
interprocess communication overhead is from returning stdout
3. note most of the text output is scrambled!
e.g.
Fitting to residue: 27 ALA
~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 11 (constraints may decrease this size).
Fitting to residue: 28 GLY
~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 11 (constraints may decrease this size).
Fitting to residue: 29 LYS
~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 11 (constraints may decrease this size).
Fitting to residue: 30 ASP
~~~~~~~~~~~~~~~~~~~~~~~~~~
Unconstrained grid search size: 11 (constraints may decrease this size).
followed by
Grid search
~~~~~~~~~~~
....
Grid search
~~~~~~~~~~~
.....
this is because the minimisation is carried out of order with the queuing
regards
gary
regards
gary
> >> obviously there is consdiderable code cleanup and documentation still
> >> to be done and also implimentation of processors for threading and
> >> ssh tunnels
> >
> >
> > The code is shaping up nicely. With a good clean up it should be
> > relatively easy to port to the 1.3 line later on.
>
> yep time to go from alpha to beta, glad you like it
>
> > 1It looks like a
> > great framework for the threading and grid computing via ssh tunnels.
> >
> indeed thats the intention and design goal ;-)
>
> > Cheers,
> >
> > Edward
> >
>
> regards
> gary
>
> > _______________________________________________
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> >
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> >
> > .
> >
>
>
> --
> -------------------------------------------------------------------
> Dr Gary Thompson
> Astbury Centre for Structural Molecular Biology,
> University of Leeds, Astbury Building,
> Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024
> email: garyt@xxxxxxxxxxxxxxx Fax +44-113-2331407
> -------------------------------------------------------------------
>
>
>
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Re: r3243 - in /branches/multi_processor: ./ multi/ prompt/ specific_fns/