AMBER Archive (2009)

Subject: RE: [AMBER] AMBER for dual core processor?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu May 07 2009 - 10:26:09 CDT

Hi Annie,

> Do you have any sucessful case to install AMBER8 to dual core
> processors?

AMBER (all versions since 4.0) use MPI for parallel execution so it doesn't
matter what the topology of the underlying hardware is (except for
performance). Hence AMBER8 will work fine on dual core. I used it for many
years. Note we are now on AMBER 10 so I don't think anyone can guarantee
that AMBER 8 will work properly on all modern architectures and compilers.
For example I very much doubt it has been tested with Intel compilers >v7 or
so. Maybe some people still use it. There are also compiler bugs etc that
have been worked around in later versions of the code. And of course AMBER 8
came out before all the x86_64 madness started so there could be issues
there as well.

If you build the serial version of the code it will run on one core of a
dual core machine. You can then run two completely independent single
processor runs at the same time. If you build the parallel version (against
a correctly setup MPI installation) then you can run with -np 2 and use both
cores at the same time. (Note, if you use MKL you should set the environment
variable OMP_NUM_THREADS=1 to avoid thrashing due to additional MKL threads
being spawned).

All the best
Ross

/\
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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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