Re: AMBER: parallel compilation

From: Francesco Pietra <>
Date: Mon, 23 Jul 2007 23:19:56 -0700 (PDT)


Unfortunately parallel compilation failed, while serial had been successful.
What I did (Amber9 Debian Linux amd64 etch):

openmpi-1.2.3 compiled with

./configure CC=/opt/intel/cce/9.1.042/bin/icc
CXX=/opt/intel/cce/9.1.042/bin/icpc F77=/opt/intel/fce/9.1.036/bin/ifort
FC=/opt/intel/fce/9.1.036/bin/ifort --with-libnuma=/usr/lib

ompi_info |grep libnuma

ompi_info |grep maffinity

reported OK

Then I set:

export MPI_HOME=/usr/local/openmpi-1.2.3


make clean

./configure -openmpi ifort_x86_64

make parallel


make[1]: [Sander_MPI] Error 1
make: *** [parallel] Error 2.

Then I did:

make clean

./configure -openmpi ifort_x86_64

make parallel >& errors.log

That log file is attached. Unfortunately, the very many errors of type
"undefined references to 'mpi_bcast'" are unclear to me.

Thanks for help.

francesco pietra

./configure -openmpi ifort_x86_64


Error, MPI_HOME must be set.

OK, for my installation and bash it should be

--- "David A. Case" <> wrote:

> On Mon, Jul 23, 2007, Francesco Pietra wrote:
> > I compiled OpenMPI with "ifort" and "icc".
> >
> > For the successful serial compilation of Amber9 I only set "ifort_x86_64"
> for
> > my platform in ./configure. Then, I noticed that also "gcc" was used for
> the
> > compilation.
> >
> > Should the equivalent (if any) for "icc" be set in ./configure for the
> parallel
> > compilation that I am ready to carry out? Or Sander and pmend and what else
> is
> > compiled parallel use only the fortran compiler?
> It's not clear if you tried what you have, and it failed, or if you have not
> yet tried anything. Don't be afraid to experiment!
> I don't *think* it makes any difference which C compiler is used.
> ...dac
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Received on Wed Jul 25 2007 - 06:07:28 PDT
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