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

Mark Abraham Mark.Abraham at anu.edu.au
Mon Oct 27 14:02:07 CET 2008

Carsten Kutzner wrote:
> Hi,
> 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.

Ah, oops. I was thinking of the Altix 3700 series, which predates 
Montecito. My bad.

> 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
> http://www.gromacs.org/pipermail/gmx-developers/2008-February/002405.html
> 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.

Good to know. Lee should definitely compare performance when using 
configure with and without --enable-fortran (and using 
--disable-cpu-optimization to avoid needing to set the environment 


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