Nkwe Monama wrote:
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
That leading period looks weird. Shouldn't there be a space after it?
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.
I'll assume this mdrun was configured with --enable-mpi. Regardless,
your system has linked to a shared library that was present at compile
time, but isn't present at run time. As such, it's not a GROMACS
problem. Talk to your system admins about how linking needs to work.
Mark
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