AMBER Archive (2009)

Subject: Re: [AMBER] how many processors for parallel test

From: David A. Case (
Date: Thu Jan 08 2009 - 06:08:06 CST

On Thu, Jan 08, 2009, michael wrote:

> Morning folks. I'm new to Amber and have been tasked with installing
> Amber10 on a local machine. The installation appears to have succeeded
> and I wished to try the provided tests. However, if I use 4 processors
> as suggested in the documentation then for the
> cd tgtmd/change_target.ntr && ./Run.tgtmd
> test I get an error:
> Must have more residues than processors!
> If I reduce the number of processors to 2 I then get errors such as
> cd ti_mass/pent_LES_PIMD && ./Run.pentadiene
> This test not set up for parallel
> cannot run in parallel with #residues < #pes
> make[1]: Leaving directory
> `/software/horace/applications/amber/amber10/test'
> cd PIMD/full_cmd_water/equilib && ./Run.full_cmd
> This test case requires a least 4 mpi threads.
> The number of mpi threads must also be a multiple of 4 and not more
> than 32.
> Not running test, exiting.....

The above are not errors. Some of the test cases have limitations on
the number of processors that can be used, as the messages indicate. So
the test suite just skips these tests.

> Finally, I also see the error
> ** Error ** : could not determine NUMPROCS in
> '/software/horace/applications/amber/amber10/test/ncsu/premd'

We would need to know what your DO_PARALLEL variable is set to: see
$AMBEHROME/test/ncsu/ NUMPROCS is extracted from this
variable by a script that may not cover all possibilities; or your
environment variable might be wrong...


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