[gmx-users] Gromacs performance on virtual servers

[Szilárd Páll]

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.
>
> 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

*inter-node parallelizaion

> 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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