For the parallelisation of the Monte Carlo simulations, I would target the minimise() function again. I'll get to the grid search in a second post. The grid computing code that I wrote targeted the file 'generic_fns/minimise.py'. You can see this code executed in the minimise() method of the Minimise class and in the two threading classes at the end of the module. This could be a good place to target the parallelisation because that minimise() function is where the looping over the MC sims occurs. If this is the target, then there is the question of whether the main loop of the model-free minimise() function should also be parallelised. Obviously the slave nodes can't act as a parent node sending out calculations to other nodes. Therefore if the generic minimise() function is targeted, the specific minimise() function would need to operate in single processor mode. Unfortunately there will need to be a lot of data transmitted - essentially one entire data pipe in the relax data storage object will need to be pickled and transmitted to all nodes. That is unless the specific simulation data is pulled out each time and treated as normal non-simulation data.
Alternatively, the looping over simulations could be brought into the specific model-free code. This will require greater changes to the original relax code base. In this option, again it should be decided if individual optimisation instances should be parallelised together with the simulations. My opinion is that communication overhead would be significantly decreased by parallelising only the simulation loop. The reason for this is that for an individual optimisation, the simulation parameter vector starts very close to the minimum and hence optimisation is orders of magnitude quicker for that problem (and there is no grid search). So in this case, I would guess that the speed limitation of the parallelisation of simulations + optimisations will be almost all due to inter-node communications. Cheers, Edward On 3/30/07, Gary S. Thompson <[EMAIL PROTECTED]> wrote:
Do you have any thoughts on the question of how to parallelise grid searches and monte carlo runs and where to dig into the code base? regards gary note I have already realise one wrinkle about paralleliseing the montecarlo runs. We need to have consistent (!) use of random numbers on the various processors. Therefore am going to create a command in processor that will create and resturn a block of random numbers (I guess we also need to think about what distributions we need as well) regards gary -- ------------------------------------------------------------------- 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: [EMAIL PROTECTED] Fax +44-113-2331407 -------------------------------------------------------------------
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