AMBER Archive (2009)

Subject: Re: [AMBER] Error in PMEMD run

From: Marek Malý (maly_at_sci.ujep.cz)
Date: Fri May 08 2009 - 12:57:36 CDT

Hi Gustavo,

thanks for your suggestion but we have only 14 nodes in our cluster (each
node = 2 x Xeon Quad-core 5365 (3,00 GHz) = 8 single CPUs per node
connected with "Cisco InfiniBand").

If I allocate 8 nodes and I use just 2 CPUs per node for one my job it
means that 8x6 single CPUs = 48 will be wasted. In this
case I am sure that my colleagues will kill me :)) Moreover I do not
assume that 8/2CPU combination will have significantly better
performance that 2/8CPU at least in case of PMEMD.

But anyway, thank you for your opinion/experience !

  Best,

    Marek

Dne Fri, 08 May 2009 19:28:35 +0200 Gustavo Seabra
<gustavo.seabra_at_gmail.com> napsal/-a:

>> the best performance I have obtained in case of using combination of 4
>> nodes
>> and 4 CPUs (from 8) per node.
>
> I don't know exactly what you have in your system, but I gather you
> are using 8core-nodes, and from it you got the best performance by
> leaving 4 cores idle. Is that correct?
>
> In this case, I would suggest that you go a bit further, and also test
> using only 1 or 2 cores per node, i.e., leaving the remaining 6-7
> cores idle. So, for 16 MPI processes, try allocating 16 or 8 nodes.
> (I didn't see this case in your tests)
>
> AFAIK, The 8-core nodes are arranged in 2 4-core sockets, and the
> communication between core, that was already bad within the 4-cores in
> the same socket, gets even worse when you need to get information
> between two sockets. Depending on your system, if you send 2 processes
> to the same node, it may put all in the same socket or automatically
> split it one for each socket. You may also be able to tell it to make
> sure that this gets split in to 1 process per socket. (Look into the
> mpirun flags.) From the tests we've run on those kind of machines, we
> do get the best performance by leaving ALL BUT ONE core idle in each
> socket.
>
> Gustavo.
>
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