The February 2014 SUG HPC Tech Talk focused on using the NVIDIA GPUs for computational chemistry. Slides are attached.
Here are the queues available on Oakley. Please note that you will be routed to the appropriate queue based on your walltime and job size request.
|Name||Nodes available||max walltime||max job size||notes|
Available minus reservations
The MATLAB Parallel Computing Toolbox and Distributed Computing Server are designed to allow users to create and launch parallel MATLAB jobs on a cluster of compute nodes. It also allows users to remotely connect to OSC resources, whether to run parallel jobs in MATLAB or to use toolboxes for which users own their own licenses. This guide will explain the basics of how to configure your Parallel Computing Toolbox for OSC systems.
The following versions of the MATLAB Parallel Computing Toolbox are supported at OSC:
TURBOMOLE is an ab initio computational chemistry program that implements various quantum chemistry algorithms. It is developed at the group of Prof. Reinhart Ahlrichs at the University of Karlsruhe.
GLPK (GNU Linear Programming Kit) is a set of open source LP (linear programming) and MIP (mixed integer problem) routines written in ANSI C, which can be called from within C programs.
Availability & Restrictions
GLPK is available to all OSC users without restriction.
The following versions are available on OSC systems:
Principal Investigators of OSC projects are responsible for updating their authorized user list, their outside funding sources, and their publications and presentations that acknowledge OSC. All of these tasks can be accomplished through the ARMSTRONG portal (https://armstrong.osc.edu). PIs are also responsible for monitoring their project's Resource Unit balance and for submitting a proposal to the Allocations Committee of the Statewide Users Group before the balance goes negative.
CFX is a computational fluid dynamics (CFD) program for modeling fluid flow and heat transfer in a variety of applications.
Quantum ESPRESSO is a program package for ab-initio molecular dynamics (MD) simulations and electronic structure calculations. It is based on density-functional theory, plane waves, and pseudopotentials.
SSHing directly to a compute node at OSC - even if that node has been assigned to you in a current batch job - and starting VNC is an "unsafe" thing to do. When your batch job ends (and the node is assigned to other users), stray processes will be left behind and negatively impact other users. However, it is possible to use VNC on compute nodes safely.
STAR-CCM+ provides the world’s most comprehensive engineering physics simulation inside a single integrated package. Much more than a CFD code, STAR‑CCM+ provides an engineering process for solving problems involving flow (of fluids and solids), heat transfer and stress. STAR‑CCM+ is unrivalled in its ability to tackle problems involving multi‑physics and complex geometries. Support is provided by CD-adapco.