[gmx-users] Gromacs and perhaps infiniband problem

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Thu Dec 30 18:53:11 CET 2004

Hi  all,

i want to run mdrun on our new cluster with infinitband (some with dual xeon 
with 3,2ghz and emt64), so i compiled gromacs with gcc-64 and mpi-gcc with 
infiniband support, also with mpi support.

So i want to submit it with qsub

#PBS -l nodes=2\:ppn=2
#PBS -q iband

/opt/mpich-1.2.6-ib-gcc64/bin/mpirun /home/cluster64/bco/bco117/mdrun_ib  -s 
topol -o t -c t -e t -np 4

Than "qsub -N test ./submit

but this didn^t work

in my log file 


     -deffnm string         Set the default filename for all file options
         -np    int      4  Number of nodes, must be the same as used for

Back Off! I just backed up md.log to ./#md.log.1#
Reading file topol.tpr, VERSION 3.2.1 (single precision)
Fatal error: run input file topol.tpr was made for 4 nodes,
             while mdrun_ib expected it to be for 1 nodes


So this is curious for me, cause some lines before mdrun say it is running 
with 4 nodes (=4cpu = 2 "real nodes") but if it starts it say something from 
one cpu.

greetings and happy new year,


 Florian Haberl                            Universitaet Erlangen/
 Computer-Chemie-Centrum    Nuernberg
                                                      Naegelsbachstr. 25
                                                      D-91052 Erlangen
  Mailto: florian.haberl AT chemie.uni-erlangen.de

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