Fwd: [gmx-users] mdrun on several clusternodes using PME gromacs 3.3.1

[Joern Lenz]

thank you lars and sorry guys, 
i forgot to let you know about another outputfile concerning the problem
discussed above:
lars: i submitted my jobs with an mdrun_mpi command to our cluster with:
"qsub run_the_simulation.sh" and in the sh script the command is 

grompp -np $NODES -n $1_ion -f pr_mdrun01 -c $1_b4pr_mdrun01 -r 
$1_b4pr_mdrun01 -p $1 -o $1_pr_mdrun01 2>&1 > output.grompp_pr_mdrun01

/opt/mpich/ch-p4/bin/mpirun -machinefile ~/machines.lst -np $NODES 
-v /.../${CONFIGGUESS}/bin/mdrun_mpi -np $NODES -s $1_pr_mdrun01.tpr -o 
$1_pr_mdrun01 -c $1_pr_mdrun01 -v -e $1_pr_mdrun01 2>&1 > 
output.mdrun_pr_mdrun01

where $NODES is 16 and CONFIGGUESS guesses the architecture of the system (32 
or 64 bit)

i dont know if nohup and/or & will change anything about the problem.

SOME FURTHER INFORMATION OF THE PROBLEM:

running /../i686-pc-linux-gnu/bin/mdrun_mpi on 2 LINUX ch_p4 processors
Created /../PI13506
/home/blah
p0_13586: (5921.985420) net_recv failed for fd = 6
p0_13586:  p4_error: net_recv read, errno = : 104


perhaps this gives you further information.
i tried nearly everything and also discussed the problem with our
system-administrators... no ideas to solve ...
the thing only works if I run it local, but this is very time-consuming

please help me with suggestions or i will die unhappy
thank you so much
joern