On 3/26/07, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> >> i.e for six residues and 3 nodes
> >>
> >> node 1 calculates
> >> res 1 [m1 m2 m3...]
> >> res 2 [[m1 m2 m3..]
> >>
> >> node 2 calculates
> >> res 3 [m1 m2 m3...]
> >> res 4 [[m1 m2 m3..]
> >>
> >> node 3 calculates
> >> res 5 [m1 m2 m3...]
> >> res 6 [[m1 m2 m3..]
> >>
> >> this obviously places some limitations of the design of the
> >> minimisation function as it might needs to have a set and tear down
> >> region that cope with this batched data....
> >
> > The minimise() main loop is the finest grain parallelisation you can
> > get without writing a specific parallelised optimisation algorithm.
> >
>
> actually what i was aiming for was as coarse grained and well load
> balanced a set of calculations as possible (i.e. minimum of
> communication overhead (i.e. bigger chunks of data with similar
> computations times going over the wire))
The coarse grained target of the looping over data pipes, which the
user must specifically ask for, will limit the number of active nodes
to the number of data pipes, which could be a specific list of
model-free models (assuming this is the only target). The next level
is the main loop over the minimisation instances. Finally, the finest
grain is from the parallelised grid search of grid searches (as
discussed in the thread starting at
https://mail.gna.org/public/relax-devel/2007-03/msg00088.html,
Message-id: <45FEAC46.8020307@xxxxxxxxxxxxxxx>). Can you see anything
else which could be targeted for parallelisation?
no see above if you combine the calculations from the various models
with those by spin etc you get the largest number of calculations that
need/can to be carried out together...
> just as another comment (or two)
>
> 1. why does do we send no arguments to the fucntions e.g.
> -#-num_frq [2]
> -#-frq [[750800000.0, 599.71900000000005]]
Sorry, again I don't understand the question. I'll try to answer it
anyway. The num_frq value is used to deconvolute the 'remap_table',
'frq', 'ri_labels', and 'relax_data'. This can vary for different
spin systems. The frequencies are essential for the calculation of
the spectral density values (and hence the chi-squared value).
what is the difference between
num_frq
and the number of numbers in
frq [[750800000.0, 599.71900000000005]]
> 2. how does the data return from minimisation work (specifically why is
> param_vector a instance vaiable of Model_free
> e.g. we have
>
> self.param_vector, self.func, iter, fc, gc, hc, self.warning = results
>
> ....
>
> # Disassemble the parameter vector.
> self.disassemble_param_vector(index=index, sim_index=sim_index)
>
>
>
> inside a tight loop. So even though self.param_vector is an instance
> variable it doesn't contain state for a Model_free object it just keeps
> being overwritten by the latest contents of the result
>
> so why not
>
> param_vector, self.func, iter, fc, gc, hc, self.warning = results
>
> ....
>
> # Disassemble the parameter vector.
> self.disassemble_param_vector(param_vector, index=index,
> sim_index=sim_index)
Yes, this is probably how this should be done. Grep for
'self.param_vector' in 'specific_fns/model_free.py' to see why there
has been an inertia for me to make this change. If necessary for the
MPI code, please try to minimise the number of changes to this setup
as possible.
I will
Sorry about the legacy code, but because of the nature
of the multi_processor branch you may need to work with it.
of course, I have made my bed and (be it nails or feathers) am having
a good go at lying in it!
Hopefully
I'll have all these legacy issues completely removed in the 1.3 line
once the data model redesign is complete. That being said, if you
need to, please feel free to make the above changes.
I don't need to change this ;-) it was more a question trying to
understand the way things are, ask the obvious question, and check
that I am not missing something deep...
Cheers,
Edward
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Re: how to parallelise model_free minimise