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Parallel Programming Presentation to Linux Users of Victoria

Parallel programming is the implementation of simultaneous computation typically applied through either tasks or data. In this introduction the need, core concepts, potential problems, and implementations will be described and illustrated with multiple examples in R, Python, C, and Fortran.

Presentation to Linux Users of Victoria, November 2015

Open Source Vocational Engineering with High Performance Computing

High performance computing is a necessity for scientific research and increasingly so; however initial steps are also being made in vocational engineering at RMIT. Applying the andragogical principles in the education sector with free and open source content encourages educational connectivism which improves learning and relevance.

Presentation to the Open Source Developers Conference, Hobart, October 2015

Julia cluster install with MPI packages

Julia is a high-level, high-performance dynamic language for technical computing. With a "just in time" compiler, it is very fast, especially compared to languages like MATLAB, Octave, R etc. However it is relatively new and a cluster installation and package deployment has a few quirks.

Download the source from github. By default you will be building the latest unstable version of Julia from the git checkout. However, we want to run 0.4.0 (or rather, 0.4rc4) which is the last stable release.


# cd /usr/local/src/JULIA

Storage Limitations on Android Devices

Many Android devices come with storage configurations that are surprising to end-users. A product that is advertised as having 32 gigabytes of memory may in fact turn out to have much less available in terms of installing applications.

Parallel and MPI Octave

There are some excellent packages for GNU Octave, the free and open-source numerical computation language that is "highly compatible" with the proprietary and closed-source MATLAB (tm).

Some Interesting R Library Quirks

A researcher uses an HPC system to analyse DNA methylation data. However when they try to install some related libraries, the installation fails.

MrBayes HPC Installation

Mr. Bayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.

Download, extract. Note that the developers have produced a tarbomb which will require a separate directory created before download. This has been raised as a bug.

Note that more recent versions of MrBayes make much better use of autoconfiguration tools.


cd /usr/local/src/MRBAYES
mkdir mrbayes-3.2.5
cd mrbayes-3.2.5

General Atomic and Molecular Electronic Structure System HPC Installation

GAMESS (General Atomic and Molecular Electronic Structure System (GAMESS)) is a general ab initio quantum chemistry package. You will need to agree to the license prior to download, which will provide a link to gamess-current.tar.gz

Download and extract, load the environment variables for atlas and gcc.


cd /usr/local/src/
tar gamess-current.tar.gz
cd gamess
module load atlas/3.10.2
module load gcc/4.9.1

JAGS (Just Another Gibbs Sampler) Installation

JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS.


cd /usr/local/src/JAGS
wget http://downloads.sourceforge.net/project/mcmc-jags/JAGS/3.x/Source/JAGS-...
tar xvf JAGS-3.4.0.tar.gz
mv JAGS-3.4.0 jags-3.4.0
cd jags-3.4.0
../config
make
make check
make install
make installcheck

The config script takes the following form


#!/bin/bash
install=$(basename $(pwd) | sed 's%-%/%')

MuTect Installation

MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

For complete details, please see the publication in Nature Biotechnology:

Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnology (2013).doi:10.1038/nbt.2514

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