[gmx-users] Re: Compiling Gromacs 3.2.1 on IBM p690+ Power4

Sekwan Oh ohsk75 at stanford.edu
Fri Jul 30 21:16:44 CEST 2004


First of all, thanks for the kind tips which is of great help.

I followed Fiona's advice in installing Gromacs on IBM power4 machine and 
the 'configuration part' went smoothly.
However, I faced several problems when doing 'make install' such as 

>  "/usr/include/macros.h", line 30.10: 1506-236 (W) Macro name abs has 
> been redefined.
>  "/usr/include/macros.h", line 30.10: 1506-358 (I) "abs" is defined on 
> line 372 of /usr/include/stdlib.h.
> "/usr/include/Xm/Xm.h", line 42.10: 1506-296 (S) #include file 
> <X11/extensions/Print.h> not found.
> "/usr/include/Xm/Xm.h", line 750.5: 1506-046 (S) Syntax error.

,which Pim reported this and showed his solutions about a month ago @:


Therefore, I followed Pim's advice from the link above and installation 
was completed without any fatal errors other than bunch of repeated 
messages as follows:

> "innerf.f", 1500-036 (I) The NOSTRICT option (default at OPT(3)) has the 
> potential to alter the semantics of a program.  Please refer to 
> documentation on the STRICT/NOSTRICT option for more information.

Anyways I have all the executables and tried serial version of mdrun which 
turns out to be ok.

I am wondering if anyone working on IBM power4 machine have these kinds of 
problems or it went all smoothly when following Fiona's tips.

I'm truly thankful to you all for sharing the information on IBM machine.



p.s. Has anyone tried parallel simulation with 'mpiexec' ?

Quoting Pim Schravendijk <schraven at mpip-mainz.mpg.de>:

> Thanks to Fiona for her tips.
> Just one additional note: --disable-float will result in a double 
> precision compilation, the name is a bit confusing I guess.
> I managed to install it now on a 1.7 Ghz Power4 machine. The benchmark
> result for d.villin is quite dissappointing: 5997 ps/day on one node,
> this
> is more or less half the result of a single node simulation on a 2 ghz
> powermac (11220 ps/day)! Is this the result of the altivec loops on the
> mac? Is there no performance-boosting alternative for the power4? Then
> the
> power4s are quite a bad buy for gromacs users I guess, 
> performance/pricewise.
> Greetings, Pim
> --
> Pim Schravendijk - PhD Student
> Max Planck Institute for Polymer Research
> http://www.mpip-mainz.mpg.de/~schraven/
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