Re: [AMBER] Specify amount of memory

From: David A Case <david.case.rutgers.edu>
Date: Sun, 15 Oct 2017 13:28:45 -0400

On Sun, Oct 15, 2017, David Sez wrote:

> Hello. I am using A16/AT17. I run sander using a queue system, but my
> colleagues complain because it allocates more memory than the amount
> actually used. I have read the User's Manual, but I did not find a way to
> specify an upper bound for the allocated memory. Is there a way to do that
> in Amber?

What is the amount allocated? What is the amount used? How are these numbers
arrived at? Are you asking for a specific amount of memory in your submission
script?

As Bill said, for most large memory items, sander will only allocate what it
needs. Are you using non-standard options (pbsa, for example)? And, how
many atoms in your system? For "ordinary" sytems (say 50,000 atoms), sander
should use less than 1 Gb of memory for standard MD.

....dac


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Received on Sun Oct 15 2017 - 10:30:02 PDT
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