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We are interested in benchmarking the serial, MPI, cuda and cuda.MPI versions of pmemd.

First we get some CPU based data.

# serial run of pmemd
nohup $AMBERHOME/bin/pmemd -O -i mdin -o mdout -p prmtop \
-c inpcrd -r restrt -x mdcrd </dev/null &

# parallel run, note that you will need create the machinefile
# if -np=4 it would would contain 4 lines with the string 'localhost'...does not work, use hostname
mpirun --machinefile=nodefile -np 4 $AMBERHOME/bin/pmemd.MPI \
-O -i mdin -o mdout -p prmtop \
-c inpcrd -r restrt -x mdcrd </dev/null &

The following script should be in your path … located in ~/bin

You need to allocate one or more GPUs for your cuda runs.

node2$ gpu-info
====================================================
Device  Model           Temperature     Utilization
====================================================
0       Tesla K20       27 C             0 %
1       Tesla K20       28 C             0 %
2       Tesla K20       27 C             0 %
3       Tesla K20       30 C             0 %
====================================================

Next we need to expose these GPUs to pmemd …

# expose one
export CUDA_VISIBLE_DEVICES="0"

# serial run of pmemd.cuda
nohup $AMBERHOME/bin/pmemd.cuda -O -i mdin -o mdout -p prmtop \
-c inpcrd -r restrt -x mdcrd </dev/null &

# parallel run, note that you will need create the machinefile
# if -np=4 it would could contain 4 lines with the string 'localhost'
mpirun --machinefile=nodefile -np 4 $AMBERHOME/bin/pmemd.cuda.MPI \
-O -i mdin -o mdout -p prmtop \
-c inpcrd -r restrt -x mdcrd </dev/null &

You may want to try to run your pmemd problem across multiple GPUs if problem set is large enough.

# expose multiple (for serial or parallel runs)
export CUDA_VISIBLE_DEVICES="0,2"

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