The content of this page is how to use on OCTOPUS. For VCC users, please click here.
 

LAMMPS is a classical molecular dynamics code and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. OCTOPUS users can use LAMMPS freely on OCTOPUS by the batch job.
Please note that the execution file you specify in the job script changes when GPU is used or not used.

    †LAMMPS is undergoing trial service. Although support on "basic use" as described on this page is possible, technical support such as program tuning cannot be applied, so please understand.

 

How to use (no-GPU)

LAMMPS is permitted to use only for processing by the batch job.
Below is an explanation for using GROMACS and an example of a job script.
 
* Please refer to the LAMMPS Documentation in official site about LAMMPS.
 

Making a job script

The following example is a job script to execute LAMMPS(22 Aug, 2018) in 48 processes (using 2 nodes, 24 processes per node).

 

For various input files of LAMMPS, please visit official site.
Please see here for basic instructions on job script.

 
 

Installation status

The installation directory of LAMMPS is:

/octfs/apl/LAMMPS
/octfs/apl/LAMMPS/

 

The installed packages are:

ASPHERE,BODY,CLASS2,COLLOID,COMPRESS,CORESHELL,DIPOLE,
GRANULAR,KSPACE,MANYBODY,MC,MEAM,MISC,MOLECULE,MPIIO,
OPT,PERI,POEMS,PYTHON,QEQ,REAX,REPLICA,RIGID,SHOCK,SNAP,SPIN,
SRD,VORONOI,,USER-ATC,USER-AWPMD,USER-BOCS,USER-CGDNA,USER-CGSDK,
USER-COLVARS,USER-DIFFRACTION,USER-DPD,USER-DRUDE,USER-EFF,
USER-FEP,USER-INTEL,USER-LB,USER-MANIFOLD,USER-MEAMC,USER-MESO,
USER-MGPT,USER-MISC,USER-MOFFF,USER-NETCDF,USER-OMP,USER-PHONON,
USER-QTB,USER-REAXC,USER-SMTBQ,USER-SPH,USER-TALLY,USER-UEF,

 
 

Submitting a job script

Input the created job script by "qsub" command.

% qsub lammps.sh

When the execution is completed, the calculation result is output to the result file.
 
 

How to use with GPU

In OCTOPUS, LAMMPS can also be used with GPU. The version of CUDA is 9.0.
Below is an explanation for using GROMACS with GPU and an example of a job script.
 

Maiking a job script

The following example is a job script to execute LAMMPS(22 Aug, 2018) in 48 processes with GPU (using 2 nodes, 24 processes and 4 GPUs per node).

*The execution file and options to specify are different from those used for the CPU.
 
 

Installation status

The installation directory of LAMMPS for GPU is:

/octfs/apl/LAMMPS-GPU/

 

The installed packages are:

ASPHERE,BODY,CLASS2,COLLOID,COMPRESS,CORESHELL,DIPOLE,GPU,
GRANULAR,KSPACE,LATTE,MANYBODY,MC,MEAM,MISC,MOLECULE,MPIIO,
OPT,PERI,POEMS,PYTHON,QEQ,REAX,REPLICA,RIGID,SHOCK,SNAP,SPIN,
SRD,VORONOI,,USER-ATC,USER-AWPMD,USER-BOCS,USER-CGDNA,USER-CGSDK,
USER-COLVARS,USER-DIFFRACTION,USER-DPD,USER-DRUDE,USER-EFF,
USER-FEP,USER-INTEL,USER-LB,USER-MANIFOLD,USER-MEAMC,USER-MESO,
USER-MGPT,USER-MISC,USER-MOFFF,USER-NETCDF,USER-OMP,USER-PHONON,
USER-QTB,USER-REAXC,USER-SMTBQ,USER-SPH,USER-TALLY,USER-UEF,

 

Submitting a job script

Input the created job script by "qsub" command.

% qsub lammps_gpu.sh

When the execution is completed, the calculation result is output to the result file.