AMBER Archive (2005)

Subject: Re: AMBER: amber 8 installation

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri Jan 21 2005 - 12:03:42 CST


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_at_scripps.edu>
To: <amber_at_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
>
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