Re: AMBER: Amber9 parallel installation error (with openMPI)

From: Wei Zhang <>
Date: Mon, 29 Oct 2007 16:16:45 -0500

Hi Joe,

Which compiler are you using? if you are using intel compiler, maybe you
need recompile
openmpi using intel compiler too. The reason is intel compiler will add
an additional "_" to
the end of function name.

try to run nm on your MPI library, grep for "mpi_bcast", does the
function name has a
tailing "_"? If not, you probably need recompile OpenMPI with the
compiler you are using.



Joe Nolan wrote:

> Dear Amber community,
> I have been attempting to install a parallel version of Amber9 with
> OpenMPI. I have edited my config.h file as follows:
> >>FPPFLAGS= -I/usr/local/include -P -DMPI-xassembler-with-cpp
> -Dsecond=ambsecond $(AMBERBUILDFLAGS)
> >>FC=/usr/local/bin/mpif90
> This is in response to a previous error by which the "mpif-common.h"
> can not be found. "/usr/local" is synonymous with $MPI_HOME on this
> machine.
> The tail end of the error is as follows:
> >>_force.f:(.text+0x19d3): undefined reference to `mpi_bcast_'
> >>_force.f:(.text+0x1a03): undefined reference to `mpi_bcast_'
> >>force.o:_force.f:(.text+0x1a32): more undefined references to
> `mpi_bcast_' follow
> >>force.o: In function `force_':
> >>_force.f:(.text+0x226a): undefined reference to `mpi_allgather_'
> >>_force.f:(.text+0x22aa): undefined reference to `mpi_allgather_'
> >>collect2: ld returned 1 exit status
> >>make[1]: *** [sander.MPI] Error 1
> >>make[1]: Leaving directory `/usr/local/amber9/src/sander'
> >>make: *** [parallel] Error 2
> Any and all input is always greatly appreciated!
> -Joe Nolan
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Received on Wed Oct 31 2007 - 06:07:38 PDT
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