[gmx-users] gmx-users: Running jobs using loadleveler

[Nkwe Monama]

Dear users,

I have never used gromacs. I'm trying to submit a gromacs job using loadleveler. Below is the script I'm using:

**************************************************************************
# @ shell = /usr/bin/bash
# @ output = $(Executable).$(jobid).out
# @ error = $(Executable).$(jobid).err
# @ wall_clock_limit = 24:00:00
# @ class=cspeed
# @ node = 2
# @ node_usage = shared
# @ job_type = MPICH
# @ notification = error
# @ resources = ConsumableCpus(1)
# @ tasks_per_node = 2
# @ environment = GOTO_NUM_THREADS=1; OMP_NUM_THREADS=1; VIADEV_CLUSTER_SIZE=AUTO; VIADEV_DEFAULT_RETRY_COUNT=15; VIADEV_DEFAULT_TIME_OUT=22; VIADEV_NUM_RDMA_BUFFER=4; VIADEV_ADAPTIVE_RDMA_LIMIT=2; VIADEV_SQ_SIZE_MAX=64; VIADEV_DEFAULT_MAX_SG_LIST=1; VIADEV_MAX_INLINE_SIZE=80; VIADEV_SRQ_SIZE=2048; VIADEV_VBUF_TOTAL_SIZE=2048; VIADEV_VBUF_POOL_SIZE=512; VIADEV_VBUF_SECONDARY_POOL_SIZE=128; VIADEV_ENABLE_AFFINITY=0; DISABLE_RDMA_ALLTOALL=1; DISABLE_RDMA_ALLGATHER=1; DISABLE_RDMA_BARRIER=1
# @ queue
./CHPC/home/chpc/Test/oscar/gromacs-4.0.5/bin/GMXRC.bash
echo "++++++++++"
echo "host files is:"
echo " "
cat $LOADL_HOSTFILE
cp $LOADL_HOSTFILE $LOADL_STEP_OUT.hostfile
echo " "
echo "++++++++++"
/CHPC/usr/local/mvapich/bin/mpirun \
#-np $LOADL_TOTAL_TASKS \
#-hostfile $LOADL_HOSTFILE \
#grompp
/CHPC/home/chpc/Test/oscar/gromacs-4.0.5/bin \
mdrun -np 2 -s eq.tpr -o eq.trr -c eq_out.gro -v -g $LOADL_JOB_NAME.log

************************************************************************************

I'm getting the following error: 

/CHPC/home/chpc/Test/oscar/gromacs-4.0.5/bin/mdrun: error while loading shared libraries: libmv.so.1: cannot open shared object file: No such file or directory.

Regards,
Nkwe

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