Dear amber users,
Iam trying to run equilibration step in GPU but its showing the
cudaMalloc error. Here iam attaching my Pbs script. please any help can be
appreciated.
#!/bin/bash
#PBS -l nodes=1:ppn=16:GPU
#PBS -l walltime=07:00:00:00
#PBS -q GPUq
#PBS -e err_""$PBS_JOBID
#PBS -o out_""$PBS_JOBID
#PBS -r n
#PBS -V
#PBS -M bo14resch11004.iith.ac.in
export I_MPI_JOB_CONTEXT=$PBS_JOBID
export OMP_NUM_THREADS=2
echo PBS JOB id is $PBS_JOBID
echo PBS_NODEFILE is $PBS_NODEFILE
echo PBS_QUEUE is $PBS_QUEUE
NPROCS=`wc -l < $PBS_NODEFILE`
echo NPROCS is $NPROCS
NRINGS=`cat $PBS_NODEFILE |sort|uniq|wc -l`
echo NRINGS is $NRINGS
NGPUS=`expr $NRINGS \* 2`
echo NGPUS is $NGPUS
cd $PBS_O_WORKDIR
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib64
setenv AMBERHOME /home/external/iith/yajjugal/programs/amber_gpu/amber12
cd $PBS_O_WORKDIR
mpirun -machinefile $PBS_NODEFILE -np 16
/home/external/iith/yajjugal/programs/amber_gpu/amber12/bin/pmemd.cuda -O
-i step1.inp -o step1.out -r step1.rst -p ../input/pr
mtop -c ../input/prmcrd -ref ../input/prmcrd
mpirun -machinefile $PBS_NODEFILE -np 16
/home/external/iith/yajjugal/programs/amber_gpu/amber12/bin/pmemd.cuda -O
-i step2.inp -o step2.out -r step2.rst -p ../input/pr
mtop -c step1.rst -ref step1.rst
Regards
yoogi
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Received on Tue Dec 08 2015 - 22:00:03 PST
