Thanks for both replies. The simulation does run fine in serial. I checked
em1.out. It says "CUDA (GPU): Minimization is NOT supported in parallel on
GPUs. " The message is pretty clear. I then tested the parallel calculation
with a production run. The command is
mpirun --machinefile=nodefile -np 2 pmemd.cuda.MPI -O -i prod.in -o
prod.out -c md3.rst -p complex_wat.prm -r prod.rst -x prod.crd -ref md3.rst
&
In the nodefile, I put
localhost:2
(My machine has 4GPU and 24 CPU)
This time, the error message is "cudaMemcpyToSymbol: SetSim copy to cSim
failed all CUDA-capable devices are busy or unavailable". But I do have 2
idle GPUs in the machine. Any idea?
Thanks.
Victor
On Wed, Aug 7, 2013 at 1:50 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Wed, Aug 07, 2013, Victor Ma wrote:
> >
> > I have amber12 and openmpi installed and configured on a 4GPU machine.
> I'd
> > like to run multi-GPU amber simulation. Here is the command I used:
> > mpirun --machinefile=nodefile -np 2 pmemd.cuda.MPI -O -i em1.in -o
> em1.out
> > -c complex_wat.inpcrd -p complex_wat.prm -r em1.rst -ref
> complex_wat.inpcrd
> > &
> >
> > And the error messageI got is,
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >
> > Does that mean my openmpi is not properly configured?
>
> Could be anything. First, run the test suite to see if you have a generic
> problem (e.g. with openmpi configuration).
>
> Second, look at the output files, especially em1.out. Most likely, there
> is
> an error message there. The MPI_Abort message just informs you that the
> process failed. You have to look at the acutal outputs to find out why.
>
> ...dac
>
>
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Received on Wed Aug 07 2013 - 13:00:03 PDT
