<div dir="ltr">The hash function is there, and is used for communicator splitting, but does not (yet) implement gmx_hostname_num in release-5-0.<div><br></div><div>Mark</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Thu, May 29, 2014 at 7:02 PM, Szilárd Páll <span dir="ltr"><<a href="mailto:pall.szilard@gmail.com" target="_blank">pall.szilard@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="">On Thu, May 29, 2014 at 6:56 PM, Mark Abraham <<a href="mailto:mark.j.abraham@gmail.com">mark.j.abraham@gmail.com</a>> wrote:<br>
><br>
> On May 29, 2014 4:53 PM, "Vedran Miletić" <<a href="mailto:rivanvx@gmail.com">rivanvx@gmail.com</a>> wrote:<br>
>><br>
>> 2014-05-29 16:36 GMT+02:00 Anders Gabrielsson <<a href="mailto:andgab@kth.se">andgab@kth.se</a>>:<br>
>> > You'll probably have to supply -npernode/-ppn too so that your mpirun<br>
>> > doesn't put all MPI ranks on the same host.<br>
>> ><br>
>> > /Anders<br>
>> ><br>
>> > On 29 May 2014, at 13:17, Vedran Miletić <<a href="mailto:rivanvx@gmail.com">rivanvx@gmail.com</a>> wrote:<br>
>> ><br>
>> > Fatal error:<br>
>> > Incorrect launch configuration: mismatching number of PP MPI processes<br>
>> > and GPUs per node.<br>
>> > mdrun_mpi was started with 5 PP MPI processes per node, but you provided<br>
>> > 1<br>
>> > GPU.<br>
>><br>
>> Hi Anders,<br>
>><br>
>> thanks for your response. Weirdly enough, mpirun actually doesn't run<br>
>> processes all on one node, it distributes them as equally as possible,<br>
>> going around your hostfile in a round-robin fashion. (I verified this<br>
>> by running hostname.)<br>
><br>
> What were the hostnames? There is some logic that tries to reconstruct the<br>
> nodes from hostnames as supplied by MPI, but GROMACS assumes the form<br>
><br>
> yourmachinename043<br>
><br>
> with the digits varying across nodes. So far, this has worked, since<br>
> sysadmins are orderly types... IIRC we use a hash in GROMACS 5, or at least<br>
> we talked about it!<br>
<br>
</div>There is hostname hashing implementation (a gmx_hostname_num()) which<br>
I don't remember anymore what was it implemented for, but neither 4.6<br>
nor (the current) 5.0 uses this is for splitting the MPI_comm_world<br>
into groups of ranks per node.<br>
<div class="HOEnZb"><div class="h5"><br>
> Mark<br>
><br>
>> However, it seems that for some reason Gromacs assumes mpirun does run<br>
>> 5 processes on a single node. Regardless, i tried<br>
>><br>
>> mpirun -np 5 -npernode 1 -hostfile ... mdrun_mpi -v -deffnm ... -gpu_id 0<br>
>><br>
>> but it produces the same error. Anything else I could try?<br>
>><br>
>> Regards,<br>
>> Vedran<br>
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</div></blockquote></div><br></div>