RE: AMBER: MPI for sander8

From: Ross Walker <>
Date: Tue, 22 Feb 2005 09:54:37 -0800

Dear Frank,

> I'm trying to compile the parallel version of sander8 on a Linux
> cluster. The MPI library on the node seems to have second trailing
> underscore:
> nm /usr/local/mpi/lib/libmpich.a | grep mpi_init
> 00000000 W mpi_init__
> 00000000 T pmpi_init__
> 00000000 W mpi_initialized__
> 00000000 T pmpi_initialized__
> However the package compiled with either ifort or ifc (the
> Intel Fortran
> compilers version 8 or 7) only has one trailing underscore, which
> results in linking error. I was wondering if there's any way to
> reconcile this discrepancy without recompiling the MPI.

This is a common problem when the mpi libraries were compiled with a
different compiler to the program you want to run. Typically on Linux
machines people compile the mpi libraries with GCC and g77. Hence you cannot
link against ifort F90. Aome compilers support flags such as
-Mnosecondunderscore but my advice would be to download the latest version
of either mpich or lam and compile it yourself (statically if you can) using
the same compiler as you are using to compiler sander.
Make sure you enable fortran 90 support when compiling the mpi libraries.
Adjust your paths so that the version you have compiled in your home
directory is used in place of the version installed in /usr/local. This way
you will have much more control on how things are compiled and fewer

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Tue Feb 22 2005 - 18:53:00 PST
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