AMBER Archive (2008)

Subject: Re: AMBER: memory limitation of Amber 9

From: David A. Case (
Date: Tue Apr 01 2008 - 00:50:41 CDT

On Mon, Mar 31, 2008, wrote:

> We have a problem with running Amber 9 with OpenMPI using multiple
> threads, on our system with the following configuration:
> CPU: 2 x Intel Xeon Quad Core 2.66 GHz
> OS: Redhat 4 Update 4 (X86_64)
> MPI: OpenMPI 1.2.4
> COMPILERS: Intel C++, Fortran (version 10.1.008) and MKL 9.1.023
> SCHEDULER: Sun Grid Engine 6u4
> Sander and pmemd are compiled using intel compilers both for serial and
> parallel configurations and for x86_64. The command "make test" returns no
> error. However, when a parallel simulation is submitted through openmpi
> (smp configuration - all threads running on the same machine), amount of
> total virtual memory is limited to 1 GB no matter how many threads are
> used (as seen from the "top" command). Hence, the speed of the simulation
> is too slow. What would be the possible cause of this memory limitation?

Nothing that I can think of. Amber doesn't use much memory, but the aggregate
should be above 1 Gbyte if you have enough threads (you don't say how many you
used.) And it's not clear, based on so little information, whether the memory
has anything to do with performance here or not.


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