[gmx-users] Problems running in paralell on IBM SP

[Erik Lindahl]

"David L. Bostick" wrote:

> Hi Erik,
>
> Thanks for the response on the IBM.  Let me be more specific.  The SP I use
> has 32 bit mpi.  I did the following because I kept getting errors
> pertaining to "large files":
>
> setenv CC xlc
> setenv CFLAGS "-O3 -bmaxdata:2147483648 -I/gpfs/dbostick/fftw/include"
> setenv CPPFLAGS -I/gpfs/dbostick/fftw/include
> setenv F77 mpxlf
> setenv FFLAGS "-O3 -bmaxdata:2147483648 -I/gpfs/dbostick/fftw/include"
> setenv LDFLAGS  "-L/gpfs/dbostick/fftw/lib -L/usr/local/lib
>         -bmaxdata:2147483648"
>
> Then I ran configure like,
>
> ./configure --enable-mpi --prefix=/gpfs/dbostick/gmx-3.1
> --disable-largefile --program-suffix="_mpi"
>
> Then make mdrun, make install-mdrun.
>
> The fftw libraries were installed using the same variables.
>
> The non-mpi stuff seems to have compiled fine.  A few notes however:
>
> I have a test system that worked in my version of gmx-2.0 that is basically
> a 4-helix alamethicin bundle in a hydrated POPC bilayer.
>
> 1) The tutorial of 216 spc waters in a box works with the mpi gmx-3.1 I
> compiled as above.
>
> 2) The test POPC/alamethecin system does not work.  The log files are
> started, but standard error gives,
>
> ERROR: 0031-250  task 5: Segmentation fault
> ERROR: 0031-250  task 6: Segmentation fault
> ERROR: 0031-250  task 4: Segmentation fault

Hi David,

I think I just might have found something; in the latest version of the GNU
config.guess (that comes with gromacs 3.1) my IBM system is now detected as

powerpc-ibm-aix4.3.3.0

instead of

rs6000-ibm-aix4.3.3.0

This could interfere with the detection script for optimization flags... What
kind of system does the configure script say you have, and what compiler flags
does it use?

Cheers,

Erik