[Beowulf] Amber 8 Execution problem

Sangamesh B forum.san at gmail.com
Wed Dec 19 00:05:26 PST 2007

Hi All,

I installed AMBER8 on Opteron Dual core, dual processor, Rocks cluster with
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 found
this lib's availability at /usr/lib64/. But the makefile of
amber8/src/leap/src/leap/ has /usr/lib -lXt .. . I changed it to /usr/lib64

After this I built both serial and parallel AMBER executables successfully.

But when I execute with the following:

mpirun -np 4  /usr/bin/numactl -c0-1 $AMBERHOME/amber8/exe/sander ...input
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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