[gmx-users] No DD grid found
aff at eq.uc.pt
Mon Mar 28 16:39:11 CEST 2011
Really appreciate the fast and very clear reply. Now I know how to
overcome this issue.
On 28-03-2011 13:25, Mark Abraham wrote:
> On 28/03/2011 10:37 PM, André Ferreira wrote:
>> Dear all,
>> I am having some problems with some molecules that I am currently
>> simulating. I got simulation box that is constituted by 100 oligomer
>> molecules (190 atoms each), in a cubic box with 7 nm side (50K).
>> Since the molecule is quite long I am using a rcoulomb of 2.8 nm and
>> rvdw of 3.4 nm.
> That does not seem like a good reason to choose massive values for
> cutoffs. What about the parameters used in your system makes you think
> you need to treat interactions accurately out to these distances?
> Proteins have physical dimensions larger than that, and nobody uses
> cutoffs greater than about 1.2nm for all-atom models.
>> When I try to perform the simulation mdrun can't find DD grid for
>> more than 48 cores, which is a huge handicap. This is the first time
>> that I am working with longer molecules, and I never had this problem.
> In order to obtain good parallel scaling, the DD implementation
> requires that the interaction partners of all atoms reside on a cell
> located on the same node or a cell located on an adjacent node. Thus,
> there is a minimum cell size. The size of your cutoffs creates a
> minimum cell size that is inconsistent with this principle when
> applied to your system.
> Fundamentally, a given parallelization algorithm is useful only for a
> certain range of problem sizes. Trivially, you won't get useful
> speedup for 100 atoms on 1000 processors without a seriously
> specialized algorithm. The same algorithm would be terrible for 1000
> atoms on 10 processors. If you had around 100 times the number of
> atoms, then 48-core DD would probably be fine. So you need to change a
> feature of your model physics, use fewer processors, or make your
> system bigger.
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