LAMMPS-Sapelo2: Difference between revisions
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=== Version === | === Version === | ||
23Jun2022 | |||
=== Author / Distributor === | === Author / Distributor === | ||
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For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page. | For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page. | ||
'''Version | '''Version 23Jun2022''' | ||
*Using the foss/ | *Using the foss/2022a toolchain | ||
This version was compiled with the foss/ | This version was compiled with the foss/2022a toolchain (GNU 1.3.0 compilers and OpenMPI 4.1.4) and it is installed in /apps/eb/LAMMPS/23Jun2022-foss-2022a-kokkos | ||
The binary is called lmp and it was compiled with the following packages: | The binary is called lmp and it was compiled with the following packages: | ||
Enabled packages: ASPHERE;ATC;AWPMD;BOCS;BODY;BPM;BROWNIAN;CG-DNA;CLASS2;COLLOID;COLVARS;COMPRESS;CORESHELL;DIELECTRIC;DIFFRACTION;DIPOLE;DPD-BASIC;DPD-MESO;DPD-REACT;DPD-SMOOTH;DRUDE;EFF;ELECTRODE;EXTRA-COMPUTE;EXTRA-DUMP;EXTRA-FIX;EXTRA-MOLECULE;EXTRA-PAIR;FEP;GRANULAR;H5MD;INTERLAYER;KIM;KOKKOS;KSPACE;LATBOLTZ;MACHDYN;MANIFOLD;MANYBODY;MC;MDI;MEAM;MGPT;MISC;ML-IAP;ML-PACE;ML-RANN;ML-SNAP;MOFFF;MOLECULE;MOLFILE;MPIIO;NETCDF;OPENMP;OPT;ORIENT;PERI;PHONON;PLUGIN;PLUMED;POEMS;PTM;PYTHON;QEQ;QTB;REACTION;REAXFF;REPLICA;RIGID;SCAFACOS;SHOCK;SMTBQ;SPH;SPIN;SRD;TALLY;UEF;VORONOI;VTK;YAFF | |||
To use this version of Lammps, first load the modules with | To use this version of Lammps, first load the modules with | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
ml LAMMPS/ | ml LAMMPS/23Jun2022-foss-2022a-kokkos | ||
</pre> | </pre> | ||
'''Example of shell scripts to run LAMMPS on the batch queue:''' | '''Example of shell scripts to run LAMMPS on the batch queue:''' | ||
'''To use version | '''To use version 23Jun2022 with the foss-2022a toolchain''' | ||
To run lmp version | To run lmp version 23Jun2022 as a parallel job, using e.g. 2 node2 and 16 cores per node (sub.sh) | ||
<pre class="gscript"> | <pre class="gscript"> | ||
#!/bin/bash | #!/bin/bash | ||
#SBATCH --job-name=lammpsjob # Job name | #SBATCH --job-name=lammpsjob # Job name | ||
#SBATCH --partition=batch # Partition (queue) name | #SBATCH --partition=batch # Partition (queue) name | ||
#SBATCH --nodes=2 # Number of nodes | |||
#SBATCH --nodes= | #SBATCH --ntasks=32 # Number of MPI ranks | ||
#SBATCH --ntasks= | #SBATCH --ntasks-per-node=16 # How many tasks on each node | ||
#SBATCH --ntasks-per-node=16 | |||
#SBATCH --cpus-per-task=1 # Number of cores per MPI rank | #SBATCH --cpus-per-task=1 # Number of cores per MPI rank | ||
#SBATCH --mem-per-cpu=600mb # Memory per processor | #SBATCH --mem-per-cpu=600mb # Memory per processor | ||
| Line 100: | Line 65: | ||
#SBATCH --output=%x.%j.out # Standard output log | #SBATCH --output=%x.%j.out # Standard output log | ||
#SBATCH --error=%x.%j.err # Standard error log | #SBATCH --error=%x.%j.err # Standard error log | ||
cd $SLURM_SUBMIT_DIR | cd $SLURM_SUBMIT_DIR | ||
ml LAMMPS/ | ml LAMMPS/23Jun2022-foss-2022a-kokkos | ||
srun lmp -in file.in > file.out | |||
</pre> | </pre> | ||
Note: Here file.in and file.out are only sample filenames for the input parameters and the output file. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the email address need to be modified appropriately as well. | Note: Here file.in and file.out are only sample filenames for the input parameters and the output file. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the email address need to be modified appropriately as well. | ||
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Latest revision as of 11:29, 7 September 2023
Category
Chemistry
Program On
Sapelo2
Version
23Jun2022
Author / Distributor
Please see http://lammps.sandia.gov/authors.html
Description
From http://lammps.sandia.gov/ : "LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.
LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. "
Running Program
Also refer to Running Jobs on Sapelo2.
For more information on Environment Modules on Sapelo2 please see the Lmod page.
Version 23Jun2022
- Using the foss/2022a toolchain
This version was compiled with the foss/2022a toolchain (GNU 1.3.0 compilers and OpenMPI 4.1.4) and it is installed in /apps/eb/LAMMPS/23Jun2022-foss-2022a-kokkos
The binary is called lmp and it was compiled with the following packages:
Enabled packages: ASPHERE;ATC;AWPMD;BOCS;BODY;BPM;BROWNIAN;CG-DNA;CLASS2;COLLOID;COLVARS;COMPRESS;CORESHELL;DIELECTRIC;DIFFRACTION;DIPOLE;DPD-BASIC;DPD-MESO;DPD-REACT;DPD-SMOOTH;DRUDE;EFF;ELECTRODE;EXTRA-COMPUTE;EXTRA-DUMP;EXTRA-FIX;EXTRA-MOLECULE;EXTRA-PAIR;FEP;GRANULAR;H5MD;INTERLAYER;KIM;KOKKOS;KSPACE;LATBOLTZ;MACHDYN;MANIFOLD;MANYBODY;MC;MDI;MEAM;MGPT;MISC;ML-IAP;ML-PACE;ML-RANN;ML-SNAP;MOFFF;MOLECULE;MOLFILE;MPIIO;NETCDF;OPENMP;OPT;ORIENT;PERI;PHONON;PLUGIN;PLUMED;POEMS;PTM;PYTHON;QEQ;QTB;REACTION;REAXFF;REPLICA;RIGID;SCAFACOS;SHOCK;SMTBQ;SPH;SPIN;SRD;TALLY;UEF;VORONOI;VTK;YAFF
To use this version of Lammps, first load the modules with
ml LAMMPS/23Jun2022-foss-2022a-kokkos
Example of shell scripts to run LAMMPS on the batch queue:
To use version 23Jun2022 with the foss-2022a toolchain
To run lmp version 23Jun2022 as a parallel job, using e.g. 2 node2 and 16 cores per node (sub.sh)
#!/bin/bash #SBATCH --job-name=lammpsjob # Job name #SBATCH --partition=batch # Partition (queue) name #SBATCH --nodes=2 # Number of nodes #SBATCH --ntasks=32 # Number of MPI ranks #SBATCH --ntasks-per-node=16 # How many tasks on each node #SBATCH --cpus-per-task=1 # Number of cores per MPI rank #SBATCH --mem-per-cpu=600mb # Memory per processor #SBATCH --time=02:00:00 # Time limit hrs:min:sec #SBATCH --output=%x.%j.out # Standard output log #SBATCH --error=%x.%j.err # Standard error log cd $SLURM_SUBMIT_DIR ml LAMMPS/23Jun2022-foss-2022a-kokkos srun lmp -in file.in > file.out
Note: Here file.in and file.out are only sample filenames for the input parameters and the output file. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the email address need to be modified appropriately as well.
Documentation
Please see links from http://lammps.sandia.gov/
A user manual is available at http://lammps.sandia.gov/doc/Manual.html
Installation
Source code downloaded from https://www.lammps.org/download.html
System
64-bit Linux