[gmx-developers] MC integrator
David van der Spoel
spoel at xray.bmc.uu.se
Thu Aug 6 08:16:04 CEST 2009
Mark Abraham wrote:
> David van der Spoel wrote:
>> Erik Marklund wrote:
>>> Swell! It's been missing from gromacs for a long time in my oppinion.
>>> Regarding parallelism, MC is highly parallelizable in "step-space",
>>> and computing different MC steps on different processors will most
>>> likely be faster than distributing particles or domains, since
>>> virtually nothing needs to be communicated. Therefore, a
>>> step-decomposition option is a good idea. Plus, it would be very easy
>>> to implement.
>> This is not necessarily true if we move to many (tens of thousands of
>> processors) which soon will be feasible with gmx 4.1 once it is
>> finished. Hence I would prefer if the code did not "interfere" with
>> the parallellisation, but rather just uses the existing logic. Maybe I
>> misunderstand it, but you do a trial move and then recompute the
>> energy, right?
> Reworking the multi-simulation feature that already exists would be the
> best of all worlds. In REMD you have a bunch of the same system in
> different states, which sometimes move, but in straight MC you can have
> many copies of the same system computing different trial moves. The
> catch is that when you accept a move, you probably have to throw away
> any work on the old state and communicate the successful move to all
> systems. Does that suggest constructing low-probability moves to
> minimise wastage? Dunno.
Multisim sits on top of the normal parallellisation, so you still need
to adapt to DD. But what could be simpler than handling the trial moves
sequentially? Nevertheless, once a DD implementation works that does the
trial moves sequentially, the Multisim solution that you are suggesting
would be simple to implement, and it would lead to slightly higher
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David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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