[gmx-users] Gromacs performance on virtual servers

Mark Abraham mark.j.abraham at gmail.com
Fri Jul 25 00:31:40 CEST 2014


Except for huge simulation systems, GROMACS performance past a single node
is dominated by network latency, so unless you can extract a promise that
any multi-node runs will have Infiniband-quality latency (because the nodes
are physically in the same room, and on Infiniband) you can forget about
doing multi-node MD on such a system.


On Thu, Jul 24, 2014 at 10:54 PM, Elton Carvalho <eltonfc at if.usp.br> wrote:

> Dear Gromacs Users,
> My former university is focusing on cloud computing instead of
> physical servers, so research groups are now expected to buy virtual
> servers from the university coloud instead of buying their own
> clusters.
> The current setup employs Xeon E7- 2870 servers and there is an
> university-wide virtual cluster with 50 virtual servers each with 10
> CPUs.
> Does anyone here have information on gromacs performance on this kind
> of infrastructure? Should I expect big issues?
> One thing that comes to mind is that the CPUs may not necessarily be
> in the same physical server, rack, or even datacenter (their plan is
> to decentralize the colocation), so network latency may be higher than
> the traditional setup, which may affect scaling. Does this argument
> make sense or am I missing something on cloud management 101?
> Cheers.
> --
> Elton Carvalho
> Departamento de Física
> Universidade Federal do Paraná
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