[gmx-developers] Gromacs with GPU
ake.sandgren at hpc2n.umu.se
Fri Sep 22 13:54:57 CEST 2017
Ok, then I'll have to write better instructions for our users.
On 09/22/2017 01:19 PM, Mark Abraham wrote:
> Currently the hwloc support doesn't do much except inspect the hardware
> and help produce the report in the log file. Obviously it should be used
> for helping with such placement tasks, and that's why we're adopting it,
> but nobody has prioritized specializing the task-assignment code yet.
> For the moment, such things are still up to the user.
> On Fri, Sep 22, 2017 at 1:10 PM Åke Sandgren <ake.sandgren at hpc2n.umu.se
> <mailto:ake.sandgren at hpc2n.umu.se>> wrote:
> I am seeing a possible performance enhancement (possibly) when running
> gromacs on nodes with multiple gpu cards.
> (And yes I know this is perhaps a mote point since current GPU cards
> don't have dual engines per card)
> dual socket 14-core broadwell cpus
> 2 K80 cards, one on each socket.
> Gromacs built with hwloc support.
> When running a dual node (56 core)
> gmx_mpi mdrun -npme 4 -s ion_channel_bench00.tpr -resetstep 20000 -o
> bench.trr -x bench.xtc -cpo bench.cpt -c bench.gro -e bench.edr -g
> bench.log -ntomp 7 -pin on -dlb yes
> job, (slurm + cgroups), gromacs doesn't fully take hwloc info into
> account. The job correctly gets allocated on cores, but looking at
> nvidia-smi and hwloc-ps i can see that the PP processes are using a
> suboptimal selection of GPU engines.
> The PP processes are placed one on each CPU socket (according to which
> process-ids are using the GPUs and the position of those pids according
> to hwloc-ps), but they both uses gpu engines from the same (first)
> K80 card.
> It would be better to have looked at the hwloc info and selected CUDA
> devices 0,2 (or 1,3) instead of 0,1.
> Any comments on that?
> Attached nvidia-smi + hwloc-ps output
> Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
> Internet: ake at hpc2n.umu.se <mailto:ake at hpc2n.umu.se> Phone: +46 90
> 7866134 <tel:090-786%2061%2034> Fax: +46 90-580 14 <tel:090-580%2014>
> Mobile: +46 70 7716134 <tel:070-771%2061%2034> WWW:
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Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
Internet: ake at hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14
Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
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