AMBER Archive (2003)

Subject: RE: AMBER: memory SC45

From: Mu Yuguang (Dr) (YGMu_at_ntu.edu.sg)
Date: Mon Oct 20 2003 - 22:46:50 CDT

Thanks Bill,Bob
My system is 57999 atoms with PME uing PMEMD. The system is Compac Tru64
SC45.

FATAL global dynamic memory setup allocation error!

I try a smaller system, 331 atoms, it works
With memory used printed in mdout file:

| Dynamic Memory, Types Used:
| Reals 95863
| Integers 6957

| Nonbonded Pairs Initial Allocation: 3472

Alos I try

unlimit memoryuse
no effects

What is the Dynamic Memory, how it scales with the number of atoms,
Here 331 atoms ~ 100K
How about 57999 atoms ?

-----Original Message-----
From: Robert Duke [mailto:rduke_at_email.unc.edu]
Sent: Tuesday, October 21, 2003 11:17 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: memory SC45

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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