Gizmo The simulation code GIZMO is a flexible, massively parallel, multi method multi physics code, with a wide range of different physics modules described in th...
Grid Engine Job Submission In order to use the Grid Engine commands you first need to load the "sge" module: abc123@login 0 0 abc123 $ module load sge You can su...
HOOMD blue is a general purpose particle simulation toolkit. It performs hard particle Monte Carlo simulations of a variety of shape classes, and molecular dynami...
LAMMPS LAMMPS is a classical molecular dynamics code, and an acronym for Large scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soli...
LS Dyna LS Dyna is a general purpose finite element program capable of simulating complex real world problems. It is used by the automobile, aerospace, constructi...
Sample submit script for non gui mode. You can copy/paste this script below to your Shamu directory, call it math.qsub. Submit the job on Shamu with qsub math.qsu...
MPI Basics MPI is standardized and portable standard which defines the syntax and semantics of library routines for users writing portable parallel programs in C,...
Sun Grid Engine submit file for OpenFOAM #!/bin/bash # #$ S /bin/bash #$ N name_of_job #$ pe openmpi 16 . /etc/profile.d/modules.sh # Load program modules modu...
Single Node Parallelization A program in Python programming language can utilize the power of the multiple CPU/Core on a computer to significantly improve the per...
R parallelization with mclapply mclapply is a parallelized version of lapply if provided mc.cores 1. For mc.cores == 1, it simply calls lapply​. By default, the m...
How to run Parallel Batch jobs On Shamu we have three (3) parallel Grid Engine environments but you only need to use one. First you need to load the "sge" module ...
Slurm (Simple Linux Utility for Resource Management) is a highly configurable workload manager and job scheduler for an HPC cluster. It is an open source software...
Singularity is available on Shamu for users to run container based applications. Users can access the software via the module system, as shown below: abc123@shamu...