[AMBER] OpenMP programs

From: Marc Moreau <jebnor.gmail.com>
Date: Thu, 8 Jul 2010 11:46:21 -0600

Hello all,

I'm installing Amber 11 and AmberTools 1.4 on our systems using
gcc-4.1.2. I'm wondering which tools utilize the OPENMP directives.
 I have grep'd for OPENMP in the source code, but it looks like the
majority (once compiled) are libraries that are linked in. As far as
I can tell, only 'nab' and 'sander' utilize openmp. Did I miss any?

A couple further questions.
1 - Do these programs honour the OMP_NUM_THREADS environment variable?
 Must this be set by way of static variable before compilation?
2 - Does MPI and OPENMP play nice together? That is, do the algorithms
understand running MPI between compute nodes and openmp within nodes?
For example: run 32 threads, across 4 nodes. So, 8 openmp threads per
node with MPI communication across the 4 nodes.
3 - To compile with openmp I need to add the '-openmp' directive to
./configure. Does it qualify as 'parallel' in Amber? I would consider
it parallel, but how do the configuration and compilation see it?

Pointers to docs accepted at par. :)

-- Marc

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Received on Thu Jul 08 2010 - 11:00:03 PDT
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