[gmx-users] Gromacs performance on virtual servers

[Mark Abraham]

On Fri, Jul 25, 2014 at 1:51 AM, Szilárd Páll <pall.szilard at gmail.com>
wrote:

> Hi
>
> In general, virtualization will always have an overhead, but if done
> well, the performance should be close to that of bare metal. However,
> for GROMACS the ideal scenario is exclusive host access (including
> hypervisor) and thread affinities which will both depend on the
> hypervisor configuration. Hence, if you can, you should try to get
> access to virtual hosts that fully utilize a compute node and do not
> share it with others.


Definitely.


> On Fri, Jul 25, 2014 at 12:31 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> > Hi,
> >
> > 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.
>
> Two remarks:
>
> * With a slow network the only parallelization you can potentially
> make use of is multi-sim, unless your environment is so could-y that
> some nodes can have tens to hundreds of ms latency which can kill even
> you multi-sim performance (depending on how fast each simulation is
> and how often do they sync).
>

I would not encourage multi-sim on such a setup, unless you actually want
replica exchange. The multi-sim implementation unnecessarily syncs
simulations every min(nstlist,nstcalcenergy,nstreplex) step, so that might
be ~tens of times per second. Unnecessary multi-sim is good for pretending
you are doing a big parallel calculation to get access to a large chunk of
a machine, but this is not really the case here.

* I've seen several claims that *good* 10/40G Ethernet can get close
> to IB even in latency, even for MD, and even for GROMACS, e.g:
> http://goo.gl/JrNxKf, http://goo.gl/t0z15f


Interesting, thanks.

Mark


>
>
> Cheers,
> --
> Szilárd
>
> > Mark
> >
> >
> > 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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