[gmx-users] Minimal PCI Bandwidth for Gromacs and Infiniband?

[Simon Kit Sang Chu]

Hi everyone,

Our group is also interested in purchasing cloud GPU cluster. Amazon only
supplies GPU cluster connected by 10Gb/s bandwidth. I notice this post but
there is no reply by far. It would be nice if someone give any clue.

Regards,
Simon

2018-03-06 1:31 GMT+08:00 Daniel Bauer <bauer at cbs.tu-darmstadt.de>:

> Hello,
>
> In our group, we have multiple identical Ryzen 1700x / Nvidia GeForce
> 1080 GTX computing nodes and think about interconnecting them via
> InfiniBands.
>
> Does anyone have Information on what Bandwidth is required by GROMACS
> for communication via InfiniBand (MPI + trajectory writing) and how it
> scales with the number of nodes?
>
> The mainboards we are currently using can only run one PCIe slot with 16
> lanes. When using both PICe slots (GPU+InfiniBand), they will run in
> dual x8 mode (thus bandwidth for both GPU and InfiniBand will be reduced
> to 8 GB/s instead of 16 GB/s). Now we wonder if the reduced bandwidth
> will hurt GROMACS performance due to bottlenecks in GPU/CPU
> communication and/or communication via InfiniBand. If this is the case,
> we might have to upgrade to new mainboards with dual x16 support.
>
>
> Best regards,
>
> Daniel
>
> --
> Daniel Bauer, M.Sc.
>
> TU Darmstadt
> Computational Biology & Simulation
> Schnittspahnstr. 2
> 64287 Darmstadt
> bauer at cbs.tu-darmstadt.de
>
> Don't trust atoms, they make up everything.
>
>
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