Also please note that pmemd does not support mpirun -np 1, because in the
pmemd code there is definitely additional overhead, and you will get a
faster single processor run from the uniprocessor code.
Regards - Bob
----- Original Message -----
From: "David A. Case" <case.scripps.edu>
To: <amber.scripps.edu>
Sent: Friday, January 21, 2005 12:55 PM
Subject: Re: AMBER: amber 8 installation
> On Fri, Jan 21, 2005, Stern, Julie wrote:
>
>> Is it okay to install the serial version of amber 8 in the
>> same directory as the parallel version?
>
> For sander, the serial and parallel versions have the same name, so if you
> want access to both, you might manually rename "sander" to "sander.serial"
> before making the parallel version.
>
> Similar comments apply to pmemd.
>
>> Is the serial
>> version the same as the parallel version with 1 node? If not,
>> is there a performance difference between serial and 1 node of
>> parallel?
>
> They are not the same, but the performance difference is usually tiny.
> But try some tests on your machine if you are concerned about this.
> Note that the parallel versions must be invoked using "mpiurn", even if
> you
> are running on only one processor.
>
> ...good luck...dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Jan 21 2005 - 18:53:00 PST
