AMBER Archive (2004)

Subject: Re: AMBER: recompiling amber8

From: Robert Duke (
Date: Mon Aug 02 2004 - 20:12:52 CDT

Carsten -
Most probably, your mpich installation was done with a different compiler
than ifc7, and thus the naming conventions for the mpi library subroutines
are not correct. I would first check how the mpi libraries under
$MPICH_HOME/lib were built. I would not worry a lot about the MKL stuff;
everything will work fine without it, but be a bit slower (for pmemd, MKL
actually does not help much at all, but I think it does help some for
sander - I have not figured out how to get them without paying a bundle, so
I tend to not worry about it). This is all very much off the top of my
Regards - Bob

----- Original Message -----
From: "Carsten Detering" <>
To: <>
Sent: Monday, August 02, 2004 8:57 PM
Subject: AMBER: recompiling amber8

> Dear all,
> 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:
> 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_'
> mexit.o: In function `mexit_':
> mexit.o(.text+0x26): undefined reference to `mpi_abort_'
> mexit.o(.text+0x44): undefined reference to `mpi_finalize_'
> new_time.o: In function `timer_barrier_':
> new_time.o(.text+0xa): undefined reference to `mpi_barrier_'
> new_time.o: In function `profile_time_':
> new_time.o(.text+0x1d4): undefined reference to `mpi_send_'
> new_time.o(.text+0x3a9): undefined reference to `mpi_recv_'
> make[1]: *** [sander] Error 1
> make[1]: Leaving directory `/usr/local/amber8/src/sander'
> make: *** [parallel] Error 2
> I did the following
> source /opt/intel/compiler70/ia32/bin/ifcvars.csh
> set AMBERHOME /usr/local/amber8
> set MPICH_HOME /usr/local/mpich
> make clean
> ./configure -mpich ifc7
> make parallel
> It might be that I simlpy overlooked something, but at the moment I
> wouldn't know what.
> 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.
> The MKL is recommended for optimal performance.
> The configuration file, config.h, was successfully created.
> The only answer I found was by Bob Duke to source my ifcvars.csh script.
> Thanks for help on this.
> Carsten
> PS my system is a dual Zeon running redhat 8
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