[gmx-developers] Running Gromacs on GPUs on multiple machines
pall.szilard at gmail.com
Thu May 29 19:02:28 CEST 2014
On Thu, May 29, 2014 at 6:56 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> On May 29, 2014 4:53 PM, "Vedran Miletić" <rivanvx at gmail.com> wrote:
>> 2014-05-29 16:36 GMT+02:00 Anders Gabrielsson <andgab at kth.se>:
>> > You'll probably have to supply -npernode/-ppn too so that your mpirun
>> > doesn't put all MPI ranks on the same host.
>> > /Anders
>> > On 29 May 2014, at 13:17, Vedran Miletić <rivanvx at gmail.com> wrote:
>> > Fatal error:
>> > Incorrect launch configuration: mismatching number of PP MPI processes
>> > and GPUs per node.
>> > mdrun_mpi was started with 5 PP MPI processes per node, but you provided
>> > 1
>> > GPU.
>> Hi Anders,
>> thanks for your response. Weirdly enough, mpirun actually doesn't run
>> processes all on one node, it distributes them as equally as possible,
>> going around your hostfile in a round-robin fashion. (I verified this
>> by running hostname.)
> What were the hostnames? There is some logic that tries to reconstruct the
> nodes from hostnames as supplied by MPI, but GROMACS assumes the form
> with the digits varying across nodes. So far, this has worked, since
> sysadmins are orderly types... IIRC we use a hash in GROMACS 5, or at least
> we talked about it!
There is hostname hashing implementation (a gmx_hostname_num()) which
I don't remember anymore what was it implemented for, but neither 4.6
nor (the current) 5.0 uses this is for splitting the MPI_comm_world
into groups of ranks per node.
>> However, it seems that for some reason Gromacs assumes mpirun does run
>> 5 processes on a single node. Regardless, i tried
>> mpirun -np 5 -npernode 1 -hostfile ... mdrun_mpi -v -deffnm ... -gpu_id 0
>> but it produces the same error. Anything else I could try?
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