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Updating Lammps instructions #1

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Updating Lammps instructions #1

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14d65fc
Modify SLURM script for LAMMPS job configuration
BeckDun Mar 10, 2026
95835b9
Modify SLURM script for improved resource allocation
BeckDun Mar 10, 2026
e36d66e
Enhance LAMMPS input file with mass and settings
BeckDun Mar 10, 2026
c30d156
Add mass definition and update thermo settings
BeckDun Mar 10, 2026
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12 changes: 11 additions & 1 deletion lammps/multi-node/in.lj
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Original file line number Diff line number Diff line change
@@ -1,11 +1,21 @@
units lj
atom_style atomic

lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box

mass 1 1.0

pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5

velocity all create 1.44 87287

neighbor 0.3 bin
neigh_modify delay 0 every 1

fix 1 all nve
run 10

thermo 100
21 changes: 16 additions & 5 deletions lammps/multi-node/slurm-test.sh
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Original file line number Diff line number Diff line change
@@ -1,12 +1,23 @@
#!/bin/bash
#SBATCH --job-name=test-lammps
#SBATCH --output=output.txt
#SBATCH --error=error.txt
#SBATCH --time=00:05:00
#SBATCH --mem=2G
#SBATCH --partition=debug
#SBATCH --nodes=2
#SBATCH --ntasks=64
#SBATCH --cpus-per-task=1
#SBATCH --nodes=2
#SBATCH --mem=248G

module purge
module load openmpi/4.1.7-3ilj
module load fftw
module load lammps
/usr/bin/time -v srun -n 64 lmp -in in.lj

# Expose OpenMP thread count explicitly
export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
export LD_LIBRARY_PATH=${FFTW_LIB}:${LD_LIBRARY_PATH}

echo "MPI ranks: $SLURM_NTASKS"
echo "CPUs per task: $SLURM_CPUS_PER_TASK"
echo "OMP threads: $OMP_NUM_THREADS"

srun lmp -in in.lj
12 changes: 11 additions & 1 deletion lammps/single-node/in.lj
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Original file line number Diff line number Diff line change
@@ -1,11 +1,21 @@
units lj
atom_style atomic

lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box

mass 1 1.0

pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5

velocity all create 1.44 87287

neighbor 0.3 bin
neigh_modify delay 0 every 1

fix 1 all nve
run 10

thermo 100
21 changes: 16 additions & 5 deletions lammps/single-node/slurm-test.sh
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Original file line number Diff line number Diff line change
@@ -1,12 +1,23 @@
#!/bin/bash
#SBATCH --job-name=test-lammps
#SBATCH --output=output.txt
#SBATCH --error=error.txt
#SBATCH --time=00:05:00
#SBATCH --mem=2G
#SBATCH --partition=debug
#SBATCH --nodes=1
#SBATCH --ntasks=64
#SBATCH --cpus-per-task=1
#SBATCH --nodes=1
#SBATCH --mem=248G

module purge
module load openmpi/4.1.7-3ilj
module load fftw
module load lammps
/usr/bin/time -v srun -n 64 lmp -in in.lj

# Expose OpenMP thread count explicitly
export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
export LD_LIBRARY_PATH=${FFTW_LIB}:${LD_LIBRARY_PATH}

echo "MPI ranks: $SLURM_NTASKS"
echo "CPUs per task: $SLURM_CPUS_PER_TASK"
echo "OMP threads: $OMP_NUM_THREADS"

srun lmp -in in.lj