[gmx-users] help to solve this problem

[valiente]

Dear gromacs users:
I'm trying to run a MD simulation using gromacs 4.6.5 in a cluster but 
when I submit my job using the following script:

/bin/bash
#Name of your job
#PBS -N PlmII+Inhibitor_free
#number of nodes you are using
#PBS -l nodes=8
#time
#PBS -l walltime=48:00:00
#which queue you are submitting to
#PBS -q  qwork at mp2


# go to our working directory
cd $PBS_O_WORKDIR

# add module
module rm mvapich2_intel64/1.6_ofed
module add openmpi_intel64/1.4.3_ofed
module rm gromacs64/4.5.4_ompi
module add gromacs64/4.6.5_ompi

# choose mpi-tasks per node *** there are 24 cores/node
export ppn=24

# set your executable file
myExe=`which mdrun_mpi`

# start the application
export RUN_NAME=PlmII+Inhibitor_free
export P4_GLOBMEMSIZE=200000000
#export OPTIONS=" -cpi PlmII+Inhibitor_free.cpt -dlb yes"
#export  OPTIONS=" -cpi prot_md.cpt -dlb yes"

#actual command line
mpiexec -n $[PBS_NUM_NODES*ppn] -npernode $ppn $myExe -deffnm $RUN_NAME 
$OPTIONS

echo "Job finished at: `date`"

#########################################################

I have the following error:

cp2456:22501] *** Process received signal ***
[cp2456:22501] Signal: Segmentation fault (11)
[cp2456:22501] Signal code:  (128)
[cp2456:22501] Failing at address: (nil)
[cp2456:22501] [ 0] /lib64/libpthread.so.0() [0x3638c0f710]
[cp2456:22501] [ 1] 
/opt/gromacs64/4.6.5/bin/../lib/libmd_mpi.so.8(nbnxn_kernel_simd_4xn_tab_comb_lb_energrp+0x4183) 
[0x2b88117267c3]
[cp2456:22501] [ 2] 
/opt/gromacs64/4.6.5/bin/../lib/libmd_mpi.so.8(nbnxn_kernel_simd_4xn+0x4b1) 
[0x2b88117a4951]
[cp2456:22501] [ 3] 
/opt/intel/composerxe-2011.5.220/compiler/lib/intel64/libiomp5.so(__kmp_invoke_microtask+0x93) 
[0x2b88149e6b83]
[cp2456:22501] *** End of error message ***
--------------------------------------------------------------------------
mpiexec noticed that process rank 0 with PID 22501 on node cp2456 exited 
on signal 11 (Segmentation fault).


with kind regards,
Pedro

-- 
**********************************************************
Dr. Pedro Alberto Valiente Flores
Profesor e Investigador Auxiliar
Jefe Laboratorio de Bioinformática y Dinámica Biomolecular
Centro de Estudios de Proteínas
Facultad de Biología
Universidad de La Habana
Email:valiente at fbio.uh.cu
Fax:+5378321321 Tel: +5378324830
**********************************************************