Re: [AMBER-Developers] incompatible processor requirements in parallel tests

From: Jason Swails <>
Date: Thu, 18 Feb 2010 16:29:55 -0500

On Thu, Feb 18, 2010 at 4:13 PM, Ross Walker <> wrote:
> Hi All,
> Just to throw a spanner in the works here, you cannot assume that the number
> of threads can be specified on the mpirun / mpiexec command line. Often it
> is an environment variable or a setting set by the queuing system that the
> user cannot override. For example IBM Power systems use :

I know this to be true for a large number of queuing systems in HPC
environments. For example, with mpich2/derivatives, you can pass
mpdboot a machinefile (i think), and mpiexec needs no processor count
associated with it. In this case, $AMBER_NTHREADS would be unused.
To this end, the new 4proc, 8proc, and 32proc test rules would still
serve their purpose.

However, if I'm understanding numprocs.awk correctly (I don't know awk
that well, but I'm familiar with some C-type syntax, and it looks like
a very simple script), it will grab the number of processors from the
argument following -np or -n (perhaps -c should be tossed in there as
well), so wouldn't this, also, be useless in the situations described

However, if any of the tests are being done interactively, I'd imagine
that -np or -n (or something of the like) would have to be specified
(because how else would the MPI know how many threads to start?). The
main reason I can think of for not implementing this would be that the
gains would not be worth the effort required to implement the change.

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER-Developers mailing list
Received on Thu Feb 18 2010 - 14:00:03 PST
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