[gmx-users] Running gmx-4.6.x over multiple homogeneous nodes with GPU acceleration

Szilárd Páll szilard.pall at cbr.su.se
Tue Jun 4 18:30:14 CEST 2013

mdrun is not blind, just the current design does report the hardware
of all compute nodes used. Whatever CPU/GPU hardware mdrun reports in
the log/std output is *only* what rank 0, i.e. the first MPI process,
detects. If you have a heterogeneous hardware configuration, in most
cases you should be able to run just fine, but you'll still get only
the hardware the first rank sits on reported.

Hence, if you want to run on 5 of the nodes you mention, you just do:
mpirun -np 10 mdrun_mpi [-gpu_id 01]

You may want to try both -ntomp 8 and -ntomp 16 (using HyperThreading
does not always help).

Also note that if you use GPU sharing among ranks (in order to use <8
threads/rank), (for some technical reasons) disabling dynamic load
balancing may help - especially if you have a homogenous simulation
system (and hardware setup).


On Tue, Jun 4, 2013 at 3:31 PM, João Henriques
<joao.henriques.32353 at gmail.com> wrote:
> Dear all,
> Since gmx-4.6 came out, I've been particularly interested in taking
> advantage of the native GPU acceleration for my simulations. Luckily, I
> have access to a cluster with the following specs PER NODE:
> 2 E5-2650 (2.0 Ghz, 8-core)
> 2 Nvidia K20
> I've become quite familiar with the "heterogenous parallelization" and
> "multiple MPI ranks per GPU" schemes on a SINGLE NODE. Everything works
> fine, no problems at all.
> Currently, I'm working with a nasty system comprising 608159 tip3p water
> molecules and it would really help to accelerate things up a bit.
> Therefore, I would really like to try to parallelize my system over
> multiple nodes and keep the GPU acceleration.
> I've tried many different command combinations, but mdrun seems to be blind
> towards the GPUs existing on other nodes. It always finds GPUs #0 and #1 on
> the first node and tries to fit everything into these, completely
> disregarding the existence of the other GPUs on the remaining requested
> nodes.
> Once again, note that all nodes have exactly the same specs.
> Literature on the official gmx website is not, well... you know... in-depth
> and I would really appreciate if someone could shed some light into this
> subject.
> Thank you,
> Best regards,
> --
> João Henriques
> --
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