AMBER Archive (2004)

Subject: Re: AMBER: recompiling amber8

From: David A. Case (case_at_scripps.edu)
Date: Mon Aug 02 2004 - 20:18:25 CDT

On Mon, Aug 02, 2004, Carsten Detering wrote:
>
> after fixing a bug in pbsa (#4 in amber8) I needed to recompile amber,
> which worked ok for the serial version. For parallel however, the
> compilation interrupted with an error:

First: the fix to pbsa has nothing to do with problems you may have compiling
sander. The two codes are unrelated, and sander does not use any of the
files in $AMBERHOME/src/pbsa.

>
> ew_dipole_recip.o: In function `do_pmesh_dipole_kspace_':
> ew_dipole_recip.o(.text+0x5c8): undefined reference to `mpi_barrier_'
> ew_dipole_recip.o(.text+0x74e): undefined reference to `mpi_barrier_'
> ew_dipole_recip.o(.text+0xa64): undefined reference to `mpi_barrier_'

You should check your $LOADLIB variable in config.h: is it actually pointing
to the correct place to find the mpich libraries? Have you previously
compiled a parallel sander?

There are detailed instructions for setting up mpich here:

    http://amber.scripps.edu/cluster_info/index.html

> set AMBERHOME /usr/local/amber8
> set MPICH_HOME /usr/local/mpich

I suspect that each of the above should use "setenv" rather than "set". It
may be that AMBERHOME and MPICH_HOME are not really in your environment, so
that the Makefile may not see them.

>
> Also, I am missing the MKL libraries. When I configure, I get
>
> # ./configure -mpich ifc7
> AMBERHOME is set to /usr/local/amber8
> Setting up Amber configuration file for architecture: ifc7
> Using parallel communications library: mpich
> MPICH_HOME is set to /usr/local/mpich
> The MKL_HOME environment variable is not defined.

Again, you need to "setenv" (not just "set") MKL_HOME to point to the
location of the MKL libraries on your machine. This is typically (but not
always) in a place like /opt/intel/mkl61.

...good luck...dac

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