[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P

[arrow50311]

Hi,

Gromacs 4.0.7 is different story, and I did not test it with the same system
though.

The job script is as follows

#@ job_name = job4.6
#@ comment = "Hello World Job"
#@ error = $(job_name).$(jobid).err
#@ output = $(job_name).$(jobid).out
#@ environment = COPY_ALL
#@ wall_clock_limit = 10:00:00
#@ notification = error
#@ job_type = bluegene
#@ class = compute
#@ bg_size = 128 
# #@ bg_connection = torus 
#@ queue
dir=/home/user/test
GROM=4.6
DDIR=/bgpscratch/user/test.$GROM
mkdir -p $DDIR
cd $DDIR
MDRUN=/opt/apps/gromacs/$GROM/bin/mdrun_mpi

ln -s $dir/run.tpr run.tpr

/bgsys/drivers/ppcfloor/bin/mpirun -cwd $DDIR -mode VN -np 512 -exe $MDRUN
-args "-s run.tpr -pd"


With domain decomposition, it will be killed by signal 6, with particle
decomposition, it will be killed by signal 11. I have no idea why it is like
that.

Do you have any suggestions?

Thank you,





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