LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It's an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. ( https://lammps.sandia.gov/index.html ) .

LAMMPS version 29Oct20, https://github.com/lammps/lammps/releases/tag/stable_29Oct2020 .

To prepare LAMMPS version 29Oct20 software login to tcr.cent.uw.edu.pl.

Then open interactive session on any computing node with :

srun -n16 -N1 --pty bash -l

When interactive session is started go through Quantum Espresso installation process described with bellow commands. It will take about 12 minutes.

#folder for source files
mkdir -p ~/downloads/lammps_29Oct20
#folder for compiled binares
mkdir -p ~/soft/lammps_29Oct20

cd ~/downloads/lammps_29Oct20
wget https://github.com/lammps/lammps/archive/stable_29Oct2020.tar.gz
tar xvzf stable_29Oct2020.tar.gz
cd lammps-stable_29Oct2020

module load mpi/openmpi-x86_64
module load compilers/gcc-9.3.0

mkdir build
cd build
cmake3 -D CMAKE_INSTALL_PREFIX=~/soft/lammps_29Oct20 -D LAMMPS_MACHINE=mpi ../cmake
make -j${SLURM_NTASKS}
make install

remember to end interactive session with exit command.

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If no errors occurred, compiled LAMMP binary is available in /home/users/${USER}/soft/lammps_29Oct20 .

Use LAMMPS 29Oct20. This description assumes that path to binaries is /home/users/${USER}/soft/lammps_29Oct20 . Use bellow lammps_29Oct20-test.sbatch file to run computation.

#!/bin/bash -l
#SBATCH --job-name="qe-test_N2_n32"
#SBATCH --nodes=2                   # number of computing_nodes
#SBATCH --ntasks=32                 # number of CPU's ( 16*computing_nodes )
#SBATCH --mem-per-cpu=2G
#SBATCH --partition=short
#SBATCH --constraint=intel
#SBATCH --exclusive
#SBATCH --time=2:00:00

WORKDIR="/home/users/${USER}/soft_tests/qe_run_`date +%s`_${RANDOM}/"
mkdir -p ${WORKDIR}
cd ${WORKDIR}

export BIN_DIR="/home/users/${USER}/soft/qe-6.5/bin"
export PATH=${BIN_DIR}:$PATH
export PSEUDO_DIR=${WORKDIR}
export TMP_DIR="/tmp"
   
#copy input files and pseudo files to ${WORKDIR} 
cp /home/users/${USER}/downloads/quantum_espresso_input_files/* ${WORKDIR}
  
module load mpi/openmpi-x86_64

T1=`date +%s`
  
mpirun -np ${SLURM_NTASKS} pw.x -npool ${SLURM_NNODES} -inp Ti2N.in > Ti2N.out
  
T2=`date +%s`
echo -e "stop ${T2}\t start ${T1}\t ${SLURM_NNODES}"

Bellow results show time of computation in function of used resources (computation scalability) for a specific computational task done with pw.x program.

Assigning a larger amount of computing nodes does not always lead to a (efficient) reduction in computing time (wall-time of the job). To find the most appropriate number of nodes for a specific type of job, it is essential to run one's own benchmarks. In general, parallel jobs should scale to at least 70% efficiency for the sake of other TCR users. One user using twice the resources to squeeze out 10% more performance may be keeping other users from working at all.

Bellow results should be consider as results of this specific computational task on this specific hardware (TCR cluster) and not overall benchmark for Quantum Espresso software suite.

*) values (min, avg, median, max, efficiency) do not include failed runs
*) efficiency as t1 / ( nodes * tn ) ( where t1 is min computation time at one node, tn is min computation time on N nodes )