[gmx-users] mdrun crashing on Power4/P690+

[Campbell Millar]

Hi Fiona,

I'm not sure about under Aix5.2 but certainly under Aix4.* we also 
found that we needed to specify -qmaxstack and -qmaxdata as well, 
otherwise the code would segfault at apparently random positions. I 
never did managed to pin down exactly when and why it was happening. 
But the memory handling under aix does seem a little problematic.

Hope this helps,

Campbell


On 15 Jun 2004, at 18:19, Fiona Reid wrote:

> Dear Gromacs Users,
>
> I have also experienced problems running Gromacs 3.2.1 on an
> IBM P690+ with 1.7 GHz POWER4 processors.
>
> The following options were used to compile the code.
>
> Build 1:
>
> OS: AIX 5.2
> Fortran Compiler: XL Fortran for AIX version 8.1.1
> C compiler: C for AIX Compiler, Version 6
>
> LDFLAGS=-L/usr/local/packages/fftw/lib
> CPPFLAGS=-I/usr/local/packages/fftw/include
> CC=xlc_r -q64
> F77=xlf_r -q64
> CFLAGS=-O3 -qarch=pwr4 -qtune=pwr4
> FFLAGS=-O3 -qarch=pwr4 -qtune=pwr4
> OBJECT_MODE=64
> MPICC=mpcc_r -q64
>
> Build 2: As above but with (Following the suggestion of Campbell Millar
> http://www.gromacs.org/pipermail/gmx-users/2004-June/010800.html )
>
> -O2 and -qmaxmem=-1
>
> I have attempted to run both the 'demo' script from the
> tutor/gmxdemo and the water demo from tutor/water. In
> each case the demos ran successfully with Gromacs 3.1.4.
>
> The 'demo' script crashes at the first call of mdrun with
> the error message:
>
> <snip>
> Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+03
>    Number of steps    =          100
> Segmentation fault (core dumped)
> mdrun finished
>
> The water demo crashes as follows:
>
> Reading file topol.tpr, VERSION 3.2.1 (single precision)
> starting mdrun 'Pure Water'
> 10000 steps,     20.0 ps.
>
> Wrote pdb files with previous and current coordinates
>
> Back Off! I just backed up step0.pdb to ./#step0.pdb.1#
> Wrote pdb files with previous and current coordinates
> Warning: Only triclinic boxes with the first vector parallel to the 
> x-axis
> and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={        NaNQ,         NaNQ,         NaNQ}
>             Box[    1]={        NaNQ,         NaNQ,         NaNQ}
>             Box[    2]={        NaNQ,         NaNQ,         NaNQ}
>          Can not fix pbc.
>
> Back Off! I just backed up step1.pdb to ./#step1.pdb.1#
> Wrote pdb files with previous and current coordinates
> Warning: Only triclinic boxes with the first vector parallel to the 
> x-axis
> and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={        NaNQ,         NaNQ,         NaNQ}
>             Box[    1]={        NaNQ,         NaNQ,         NaNQ}
>             Box[    2]={        NaNQ,         NaNQ,         NaNQ}
>          Can not fix pbc.
>
> Can anyone help?
>
> Thanks in advance,
>
> Fiona Reid
>
>
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__________________________
Dr Campbell Millar,
University of Glasgow,
Device Modelling Group,
Oakfield Avenue,
Glasgow G12 8LT
tel: +44 141 330 4792  fax: +44 141 330 4907

"Diplomacy is the art of saying 'nice doggy', till you can find a rock"
Larry Niven.
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