This tutorial aims to provide a 5 minute introduction to RADICAL-Pilot and its ability to execute multiple concurrent simulations on TITAN. Here we use GROMACS -- a commonly used MD kernel as an example, but also provide an example for a simple "executable" /bin/date.

export LD_PRELOAD=/lib64/librt.so.1

export RADICAL_PILOT_DBURL=mongodb://144.76.72.175/alessio

Please note that this database url is available for small tests. Use your own database for large experimental campaigns

module load python

module load python_setuptools

module load python_virtualenv

module load python_pip

git clone https://github.com/radical-cybertools/radical.pilot branch: devel

git clone https://github.com/radical-cybertools/radical.utils branch: devel

git clone https://github.com/radical-cybertools/saga-python branch: devel

virtualenv <name>

source <name>/bin/activate

pip install radical-utils/ saga-python/ radical-pilot/

The example consider a single thread gromacs simulation as a CU. The number of CUs and the number of cores can be set by the user. If the user does not set the parameters, the script runs 128 CUs on 128 cores by default.

git clone https://github.com/ATLAS-Titan/misc/

cd misc/fireworks

Try to reach the executable at:

/lustre/atlas/scratch/aleang9/csc108/gromacs/bin/gmx_mpi

If the executable is not accessible then change the path at line 5 in CUDef.py

Note that an Open-MPI version of gromacs must be used. Cray-MPI is not orte compatible. Thus, the module available on TITAN cannot be used

To compile your own Open-MPI gromacs follow this link

Note that by switching the comment between lines 95 and 96, it is also possible to run /bin/date

Execute gromacs simulation

DO NOT comment this line line

Comment this line line

Execute /bin/date

Comment this line line

DO NOT comment this line line

python example.py <# gromacs simulations> <# cores of the pilot>

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