[gmx-users] Gromacs performance on virtual servers

[Szilárd Páll]

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.

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'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


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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