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Queues and Reservations

Here are the queues available on Glenn. 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

Serial

Available minus reservations

168 hours

1 node

HOWTO: Configure the MATLAB Parallel Computing Toolbox

Introduction

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.

Versions

The following versions of the MATLAB Parallel Computing Toolbox are supported at OSC:

CFX

ANSYS CFX (called CFX hereafter) is a computational fluid dynamics (CFD) program for modeling fluid flow and heat transfer in a variety of applications.

Availability and Restrictions

CFX is available on Oakley and Glenn Clusters. The versions currently available at OSC are:

HOWTO: Use VNC in a batch job

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+

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. CD-adapco usually releases new version of STAR-CCM+ every four months.

OpenACC

OpenACC is a standard for parallel programming on accelerators, such as Nvidia GPUs and Intel Phi. It consists primarily of a set of compiler directives for executing code on the accelerator, in C and Fortran. OpenACC is currently only supported by the PGI compilers installed on OSC systems.

VTK

Introduction

The Visualization ToolKit (VTK) is an open source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java and Python.

Version

 

RepeatMasker

"RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program." (http://www.repeatmasker.org/)

TreeBeST

"TreeBeST is an original tree builder for constrained neighbour-joining and tree merge, an efficient tool capable of duplication/loss/ortholog inference, and a versatile program facili- tating many tree-building routines, such as tree rooting, alignment filtering and tree plot- ting. TreeBeST stands for ‘(gene) Tree Building guided by Species Tree’. It is previously known as NJTREE as the first piece of codes of this project aimed to build a eighbour-joining tree.

TreeBeST is the core engine of TreeFam (Tree Families Database) project initiated by Richard Durbin. The basic idea of this project is to build a full tree constrained by a manually verified seed tree. The tree builder must know how to utilize the prior knowledge provided by human experts. This demand disqualifies any existing softwares. Given this fact, we devised a new algorithm to control the joining step of traditional neighbour-joining. This is origin the constrained neighbour-joining.

When trees are built, they are only meaningful to biologists. Computers generate trees, but they do not understand them. To understand gene trees, a computer must be equipped with some biological knowledges, the species tree. It will teach a computer how to discriminate a speciation from a duplication event and how to find orthologs, provided a correct gene tree.

Unfortunately, gene trees are not always correct. Since the advent of UPGMA algorithm in 1958, we have tried to find a ideal model for nearly half a century. But we failed. Evolution is so complex a thing. A model best fits in one lineage might mean a disaster in another. A unified model is far from being discovered. TreeBeST aims at improving the accuracy of tree building, but it does not try to set up a new model in a traditional way. Instead, it integrates two existing models with the help of species tree, finding the subtree that best fits the models and merging them together to build a new tree incorporating the advantages of the both. This is the tree algorithm." (treebest.pdf)

RECON

“Proper identification of repetitive sequences is an essential step in genome analysis. The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences. The underlying algorithm is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Specifically, our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. RECON should be useful for first-pass automatic classification of repeats in newly sequenced genomes.” (http://selab.janelia.org/recon.html)

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