AMBER Archive (2009)

Subject: Re: [AMBER] Error installing Amber

From: David A. Case (
Date: Mon Feb 16 2009 - 08:21:41 CST

On Mon, Feb 16, 2009, David Pati?o wrote:

> We're trying to install Amber 10 and AmberTools in an SGI Altix450 machine.
> In a SUSE Enterprise Server 10.
> Everything was OK before the "make serial" command so we've just done:
> AMBERHOME=/opt/amber10
> export AMBERHOME
> cd $AMBERHOME/src
> ./configure_at -mpi -altix icc
> make -f Makefile_at
> cd /opt/amber10/test/
> make -f Makefile_at
> patch -p0 -N -r patch-rejects < bugfix.all
> cd $AMBERHOME/src
> ./configure_amber ifort
> make serial
> And now a lot of time before comes an error telling that everything is not
> referenced
> .
> .
> .
> .
> .
> _ncsu-pmd-hooks.f:(.text+0xb12): referencia a `mpi_bcast_' sin definir

This is quite odd: when you configured amber you did not specify a
parallel option, and your command (apparently) was "make serial". So it
is hard to see why the code would be looking for mpi commands.

You can also look at the commands that are being executed and see if
there are any "-DMPI" flags.

Try this: cd to $AMBERHOME/src and execute "make clean" before typing
"make serial". Also, examine your config_amber.h file to see if there
is any reference to MPI. If there is, remove the config_amber.h file
and re-run configure.


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