AMBER Archive (2009)

Subject: Re: [AMBER] Compilation and usage of NAB in parallel ?

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Jan 29 2009 - 07:22:08 CST

On Wed, Jan 28, 2009, Marek Mal? wrote:
>
> I need urgently parallel version of NAB to use it for huge system (15000
> atoms) analysis.
>
> I found just a little about this topic in AmberTools manual pages 115-116.
>
> Our platform is "SGI AltixXE 310" with "Intel Xeon Quad-core 5365"
> processors.

With this platform, I think you should give the "-openmp" flag to get a
parallel NAB.

> But it just loaded 8 serial jobs in one time nothing more.

Since you compiled NAB in a serial fashion, this result makes sense.

>
> The main problem is probably that I was not able to compile NAB in
> parallel way.
> I tried -mpi flag but using this option was absolutely useless it even
> didn't add
> the proper flags into config.h.

You give few details here. The "-mpi" flag in NAB assumes that you have
a correctly configured "mpicc" in you PATH.

> -openmp successfully propagated into config.h in this two lines:
> -L$(MKL_HOME)/lib/em64t -lguide -lpthread -openmp
> OCFLAGS=-wd117,177,266,880,1011 -O2 -DBINTRAJ -openmp -DOPENMP
> $(AMBERBUILDFLAGS)

Now you should set OMP_NUM_THREADS and see what happens.

Don't confuse openmp with MPI: they are distinct and not compatible with
each other. If you use the -openmpi flag, don't use mpiexec (etc.)

>
> If "-intelmpi way" (IntelMPI) is really unpossible could anyone who has
> some experience with parallel compilation/run of NAB with -openmp (under
> OpenMPI)

This is an example of the last point: openmp has nothing to do with
openMPI...

Admittedly, this is hard stuff, and not for the faint of heart. I've
never run a truly parallel normal mode calculations (via Scalapak). If
you have an altix, you may well have the Intel MKL libraries. If so,
try using them, since I think(?) they automagically will parallelize
some of the linear algebra.

...good luck...dac

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