[Beowulf] RE: Amber 8 Execution problem

Gabb, Henry henry.gabb at intel.com
Wed Dec 19 12:23:30 PST 2007

Hi Sangamesh,
It sounds like the executable can't find some shared objects. The
$MKL_HOME/tools/environment directory contains initialization scripts to
automatically update the $MKL_ROOT, $LD_LIBRARY_PATH, etc. Since you're
running on Opteron, you should use the mklvarsem64t.{sh|csh}. Likewise,
you should be using the libraries in $MKL_HOME/lib/em64t rather than the
IA-32 (lib/32) or Itanium (lib/64) libraries.

Best regards,

Henry Gabb
Intel Cluster Software and Technologies

Message: 1
Date: Wed, 19 Dec 2007 13:35:26 +0530
From: "Sangamesh B" <forum.san at gmail.com>
Subject: [Beowulf] Amber 8 Execution problem
To: "Beowulf ML" <beowulf at beowulf.org>
	<cb60cbc40712190005o59692763v192444db31001012 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi All,

I installed AMBER8 on Opteron Dual core, dual processor, Rocks cluster
the following options/libraries:

Compiler: Intel 9 Fortran and C++ compilers.
Blas Library: MKL8
MPI: MPICH2 compiled with Intel compiler.

During make serial, I got an error for xterm library(libXt.so). Then
this lib's availability at /usr/lib64/. But the makefile of
amber8/src/leap/src/leap/ has /usr/lib -lXt .. . I changed it to

After this I built both serial and parallel AMBER executables

But when I execute with the following:

mpirun -np 4  /usr/bin/numactl -c0-1 $AMBERHOME/amber8/exe/sander
file parameters

Note: Numactl is used to bind the processes to particular processors for
better performance.

its giving:

symbol lookup error:       undefined symbol: __intel_cpu_indicator

I guessed, this might relate to MKL library.

During 'make' it was taking MKL lib*.so files from $MKL_HOME/lib/32 (in
config.h file).

Changed $MKL_HOME/lib/32 to $MKL_HOME/lib/64 since the arch is AMD64
opteron. But it is giving incompatible -libvml.so file.

I'm not getting why this error is coming.

Any help for this will be appreciated.

Thanks & Regards,

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