From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Oct 17 2017 - 09:25:13 CDT
Please copy the mailing list on reply.
You are using the network-based (TCP) version, which ignores the InfiniBand
network, and the ++local flag, which launches all tasks on the local node
(hence the name of the flag).
Please read the user's guide and notes.txt carefully, and you'll be able to
fix these problems.
On Tue, Oct 17, 2017 at 8:10 AM, Rik Chakraborty <
rik.chakraborty01_at_gmail.com> wrote:
> Thank you, Giacomo for your suggestions.
>
> We used the following specifications,
>
> NAMD build: *NAMD 2.10 for Linux-x86_64-TCP*
>
> How we are launching (for 2 CPU nodes) the simulation:
> */data/namd/charmrun +p48 ++local /data/namd/namd2 /home/path/trial.inp >
> /home/path/trial.out *
>
> On Mon, Oct 16, 2017 at 10:46 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com
> > wrote:
>
>> Can you double-check that you are actually launching tasks in all
>> requested nodes? The fact that the time increases slightly leads to think
>> that you may be oversubscribing the first node. Meaning, you are dividing
>> up the work among the same CPU cores, but using more tasks for each core--001a113fc4b28f5af9055bbee67b--
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