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

[Mark Abraham]

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