LAMMPS¶
LAMMPS is a molecular dynamics application for large-scale atomic/molecular parallel simulations of solid-state materials, soft matter and mesoscopic systems.
LAMMPS is available as a module on Apocrita.
Versions¶
Regular and GPU accelerated versions have been installed on Apocrita.
Load the GPU accelerated module which matches the GPU type
As the lmp_gpu binary was compiled against a specific GPU card type,
ensure a compatible gpu type is requested and the matching module loaded
otherwise you will see a CUDA error when running your code. See the
example jobs below for further information.
Parallel support
Non-GPU versions of LAMMPS will only run on parallel nodes
using the parallel environment.
Usage¶
To run the required version, load one of the following modules:
- For LAMMPS (non-GPU), load
lammps/<version> - For GPU accelerated LAMMPS versions, load
lammps-gpu/<version>
To run the default installed version of LAMMPS, simply load the lammps
module:
$ module load lammps
$ mpirun -np ${NSLOTS} lmp_intel_cpu_intelmpi --help
Usage example: lmp_intel_cpu_intelmpi -var t 300 -echo screen -in in.alloy
...
For full usage documentation, pass the --help option.
Example jobs¶
Parallel job¶
Here is an example job running on 48 cores across 2 sdv nodes with MPI:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe parallel 48
#$ -l infiniband=sdv-i
#$ -l h_rt=240:0:0
module load lammps
mpirun -np ${NSLOTS} lmp_intel_cpu_intelmpi \
-in in.reax.rdx \
-log output.log
GPU jobs¶
Here is an example job running on 1 GPU on the SBG (Volta) nodes:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 8
#$ -l h_rt=240:0:0
#$ -l h_vmem=11G
#$ -l gpu=1
#$ -l gpu_type=volta
# Load the GPU-accelerated version which has been compiled
# for the Volta GPU type (installed in sbg1-3)
module load lammps-gpu/<version>-volta
mpirun -np ${NSLOTS} lmp_gpu \
-sf gpu \
-pk gpu 1 \
-in in.lc \
-log in.lc.log
Here is an example job running on 2 GPUs on the SBG (Volta) nodes:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 16
#$ -l h_rt=240:0:0
#$ -l h_vmem=11G
#$ -l gpu=2
#$ -l gpu_type=volta
# Load the GPU-accelerated version which has been compiled
# for the Volta GPU type (installed in sbg1-3)
module load lammps-gpu/<version>-volta
mpirun -np ${NSLOTS} lmp_gpu \
-sf gpu \
-pk gpu 2 \
-in in.lc \
-log in.lc.log