[gmx-users] Re: [gmx-developers] installing the parallel version of Gromacs 3.3.1

Alexey Shvetsov alexxy at omrb.pnpi.spb.ru
Mon May 2 19:22:10 CEST 2011

Hi all!

There also another problem. You are using intel compilers on amd based 
machine. Intel compilers uses cpuid to identify processor and optimization and 
they doesnt include amd cpuids at all. So you will have bad performance on amd 
cpus. I'd recomend to use recent versions of gcc (gcc-4.5+) and math libs like 
atlas or gotoblas2 for blas and lapack. This combination will perform much 
better then icc

On 2 of May 2011 10:56:19 Justin A. Lemkul wrote:
> I am CC'ing this message to the general gmx-users list.  The gmx-developers
> list is for discussion about development.  Please send anything further via
> gmx-users.
> See comments below.
> West, Ana wrote:
> > Dear Gromacs Community,
> > 
> > I attempted to install the parallel version of Gromacs 3.3.1 on a
> > machine with the x86-64 architecture and 8 core AMD Opteron processors.
> > The operating system is openSusie 11.3. During my attempt I used the
> > following set of commands:
> > 
> > ./configure --prefix=/usr/local/packages/gromacs-3.3.1
> > --enable-mpi CC=icc CXX=icpc F77=ifort
> > make mdrun
> > make mdrun install
> > 
> > The version of the three compilers is 12.0.3. The installation seemed
> > unsuccessful. In the 'config.log' file the fatal error message reads as
> > :
> > 
> > "Fatal Error: This program was not built to run on the processor in your
> > system. The allowed processors are: Intel(R) Pentium(R) 4 and compatible
> > Intel processors with Intel(R) Streaming SIMD Extensions 3 (Intel(R)
> > SSE3) instruction support."
> > 
> > Could someone please provide me with some kind advice?
> Your hardware is too new to install the (archaic!) version of Gromacs you're
> trying to use.  I suspect you would have more success with a version of
> Gromacs that is not five years old.
> Either use a newer version of Gromacs, or find a slower machine.
> -Justin
> > Thank you,
> > Ana

Best Regards,
 Alexey 'Alexxy' Shvetsov
 Petersburg Nuclear Physics Institute, Russia
 Department of Molecular and Radiation Biophysics
 Gentoo Team Ru
 Gentoo Linux Dev
 mailto:alexxyum at gmail.com
 mailto:alexxy at gentoo.org
 mailto:alexxy at omrb.pnpi.spb.ru
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