On Fri, Jul 25, 2014 at 1:51 AM, Szilárd Páll <pall.szil...@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.abra...@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 <elto...@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 > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.