On Wed, Sep 22, 2010 at 5:02 AM, colvin wrote:
> Dear all,
>
> I am running MD on a system consisting 112550 atoms using pmemd on a
> quad-core workstation and it tooks about 17 hrs to complete 500ps.
>
> Then, i run the same system on 2 quad-core connected with Gigabit
> ethernet, and it took about 13 hrs.
>
> Is this normal? or there are some configurations that can be made for
> better performance?
So, just to make it clear: your system is running **faster** on the 2
quad-core/ Gigabit ethernet system than in the 1 quad-core
workstation, right?
There are a number of competing factors here, and interconnect is just
one of them. Personally, I don't see anything wrong in your numbers
(others may correct me): It seems that your system is large enough
that you are gaining more by spreading it to 8 processors (2
quad-cores) than what you loose due to the slow interconnect. If you
really want to test the effect of the slow interconnect, you have to
restrict the second calculation to use only 2 processes per node for a
total of 4 processes, as the first calculation.
Cheers,
Gustavo.
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Received on Wed Sep 22 2010 - 06:30:05 PDT
