AMBER Archive (2009)

Subject: Re: [AMBER] Number of processor in pmemd

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon May 04 2009 - 12:28:11 CDT

Processor count for parallel pmemd can be 2 to any value greater than 2 with
no penalty, and on decent hardware pmemd will drive all cpu's at 100%. Are
you perhaps using a slow interconnect like ethernet? That will cause
processor underutilization. Also, if you are writing the pmemd output files
to a slow disk, especially something like an nfs-shared disk, that can stall
the whole multiprocessor job and result in processor underutilization.
Other than that, the only other likely reasons for problems have to do with
machine and mpi configuration issues.
Regards - Bob Duke
----- Original Message -----
From: "Hemant Kumar" <hemant_at_physics.iisc.ernet.in>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Monday, May 04, 2009 1:17 PM
Subject: [AMBER] Number of processor in pmemd

> Hi,
> I am using pmemd on 12 processor,but only 30% of processor is being used
> while running the program. Is it because of number of processor not being
> some integer power of 2 or something else.
>
> With regrads,
> Hemant Kumar
> Graduate Student
> CCMT,Department of Physics
> IISC,Bangalore
>
>
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