[gmx-users] XT3 porting

[David van der Spoel]

Shawn T. Brown wrote:
> Hello, I am trying to port GROMACS 3.3.1 to the CRAY XT3, which is 
> essentially an Opteron machine with the PGI compilers.  I can get 
> everything to compile, but when I run mdrun, I am “randomly” getting 
> segmentation faults.  This seems to happen no matter what input file I 
> use.  It happens in init_forcerec (line 1001), in add_gbond, and in 
> solvent_check.  Some times it runs fine.  I am configuring with the 
> following command:
> 
>  
> 
> ./configure --with-fft=fftw3 --disable-nice --enable-mpi 
> --program-suffix="_xt3" --enable-float --with-external-blas 
> --with-external-lapack --disable-threads 
> --prefix=/usr/local/packages/gromacs-3.3.1
> 
>  
> 
> I am wondering if anyone else has seen these types of problems and knows 
> how to fix them.  I have tried compiling the code without optimization, 
> to no avail.
> 
>  
> 
> Thanks in advance,
> 
> Shawn
> 


Hi Shawn, last time I tested the PGI compiler gave at most equal 
performance as the gcc compilers. I presume you could try compiling with 
gcc.

 From your mail it is not clear whether the problems occurs in parallel 
or in sequential execution of mdrun. Anyway it is of course difficult to 
debug remotely, e.g. line 1001 is force.c does not look very suspect.


>  
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> Shawn T. Brown
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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