AMBER Archive (2003)

Subject: Re: AMBER: memory SC45

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Oct 20 2003 - 22:17:25 CDT

Mu -
Are you talking pmemd here, or sander 6, or sander 7? How many atoms? How
many cpu's? How many processors sharing memory? How much physical memory
total? You can run a 90906 atom problem in about 79 MB on a single
processor, and since the pairlist is divided when running in parallel,
memory requirements growth will be less than linear in processor count.
Thus, about 25 processes would run in 2 GB on a shared memory machine (rough
estimate). That is half the memoryuse listed. It is possible, but
unlikely, for weird things to happen with mpi buffering. Without knowing
more about your problem size and memory configuration, it is not possible to
determine if it is reasonable for you to be running out of memory.
Regards - Bob
----- Original Message -----
From: "Mu Yuguang (Dr)" <YGMu_at_ntu.edu.sg>
To: <amber_at_scripps.edu>
Sent: Monday, October 20, 2003 10:39 PM
Subject: AMBER: memory SC45

> Dear all,
> Thank you very much for your help.
>
> Now I have been successful in
>
> prun -
>
> But when I ask for more memory, in case my program treats with more
> atoms,
>
> The program failed in allocate memory .
>
> I check my limit , it wrote as :
>
>
> cputime unlimited
>
> filesize unlimited
>
> datasize 4194304 kbytes
>
> stacksize 3465214 kbytes
>
> coredumpsize 0 kbytes
>
> memoryuse 4089768 kbytes
>
> vmemoryuse 4194304 kbytes
>
> descriptors 4096
>
> Could I ask for the system administrator for setting the memoryuse and
> vmemoryuse to be unlimited ?
>
>
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