[gmx-users] mdrun doesn't run in version 4.0 on sgi server

Carsten Kutzner ckutzne at gwdg.de
Mon Oct 27 09:23:15 CET 2008


Mark Abraham wrote:
> Lee Soin wrote:
>> By invoking "uname -a":
>> Linux sgi4700 #1 SMP Thu May 17 14:00:09 UTC
>> 2007 ia64 ia64 ia64 GNU/Linux
>> I don't know any other command to retrieve system information.
> Hmm, that looks like an SGI Altix 4700. IA64 kernels work on those
> machines. 
Well, not exactly. They work in combination with Gromacs version <= 3.3.x,
but at least I have never managed to get them working with this year's
CVS Gromacs or Gromacs 4.x - see also


The strange thing is that these inner loops have not changed since 3.3.x,
so the problem might be somewhere else. But actually the Fortran loops
have a quite decent performance on that machine compared to assembly: In
a single-CPU test I did with gmx 3.3 they were just about 10% slower.


> There have been issues over the years with GROMACS and various
> Intel compilers for these machines. Do try different compiler versions
> (I suggest icc 10 or higher) or gcc and see how fast things go.
> Mark
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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