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Gizmo
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...
NEW - 31 May 2018 - 14:34 by AdminUser
GridEngineJobSubmission
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...
r11 - 31 Oct 2019 - 15:57 by AdminUser
Hoomd
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...
r2 - 04 Feb 2020 - 14:40 by AdminUser
LAMMPS
LAMMPS LAMMPS is a classical molecular dynamics code, and an acronym for Large scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soli...
r3 - 04 Sep 2019 - 14:29 by AdminUser
LS-Dyna
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...
NEW - 26 Aug 2016 - 16:15 by AdminUser
Mathematica
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...
r2 - 05 Feb 2020 - 13:56 by AdminUser
MessagePassingInterface(MPI)
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,...
r6 - 18 Dec 2020 - 16:15 by AdminUser
OpenFOAM
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...
NEW - 23 Jul 2019 - 14:46 by AdminUser
ParallelProgrammingInPython
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...
r2 - 11 Aug 2020 - 22:37 by AdminUser
ParallelProgrammingInR
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...
r4 - 14 May 2021 - 17:17 by AdminUser
RunningParallelBatchJobs
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 ...
NEW - 18 Aug 2016 - 19:00 by AdminUser
SampleSGESubmitScripts
Sample SGE Submit Scripts * OpenMPI * Abaqus * Single Thread Job * R * GPU Main.AdminUser 17 May 2016
r4 - 14 Jun 2018 - 13:38 by AdminUser
UseSlurmOnShamu
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...
r9 - 23 Mar 2021 - 16:55 by AdminUser
UsingSingularity
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...
r5 - 26 Aug 2020 - 22:49 by AdminUser
Number of topics: 14
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