AMBER: recompiling amber8

From: Carsten Detering <>
Date: Mon, 02 Aug 2004 17:57:19 -0700

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.


PS my system is a dual Zeon running redhat 8

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Received on Tue Aug 03 2004 - 02:53:00 PDT
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