[gmx-developers] Two problems about Gromcas-4.5 new features

Sander Pronk pronk at cbr.su.se
Tue Aug 31 08:31:24 CEST 2010

On Aug 31, 2010, at 04:50 , xuji wrote:

> Hi all:
> It is a very good news that Gromacs-4.5 is coming soon!
> I have two problems not very clearly.
> First, Gromacs-4.5 can use GPU to accelerate simulations. But in 
> the "Limitations", it's said that "Multiple GPU cards are not supported".
> So can't I accelerate the simulations with parallel mdrun? 
GPUs are inherently parallel so a single GPU-accelerated mdrun is 'parallel' by its very nature. This restriction reflects a restriction in GPU hardware: multiple GPU cards don't share memory, so supporting them would require an entirely new set of algorithms beyond what has already been done to support single GPUs.
> Second, in Gromacs-4.5 new features, it's said:
> "Running on multi-core nodes now automatically uses thread-based parallelization".
> If there're two nodes with 8 CPU cores each, and I use all of the CPU cores, 
> is there 8 threads other than 8 MPI processes in one node? 
> If true, do the 8 threads in one node share with one large memory? 
> And what is the parallelization scheme inner the node and inter the nodes?

Right now, threads and inter-node MPI communication are mutually exclusive: either you run a single node parallel run (with 8 threads in your case), or you run on multiple nodes with MPI. In that case, you specify the total number of cores as the number of MPI processes.

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