Annoying older Mailman bug with certain MIME types.

Multipurpose Internet Mail Extensions (MIME) is an Internet standard that extends the format of e-mail to support various extended formats. However with older versions of Mailman there is a serious bug which affects the archives.

MIME allows the following:

  • Text in character sets other than ASCII
  • Non-text attachments
  • Message bodies with multiple parts
  • Header information in non-ASCII character sets
  • etc.,

Installing Velvet 0.7.31 on a 64-bit AMD Opteron Cluster running CentOS 5 Linux

From their website; "Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom."

Installing Desmond-2.0.4-0 on a 64-bit AMD Opteron Cluster running CentOS 5 Linux

Developed by D.E. Shaw Research, Desmond performs high-speed molecular dynamics simulations of biological systems using parallel algorithms and numerical techniques. The README.txt explains the horror that will prevail...

Installing NAMD 2.7b1 with CUDA on a 64-bit AMD Opteron Cluster running CentOS 5 Linux

NAMD is a parallel molecular dynamics code for large biomolecular systems. Version 2.7b1 has some advantages over 2.6 and an extensive user's guide. CUDA (Compute Unified Device Architecture) is a parallel computing architecture developed by NVIDIA providing a computing engine in NVIDIA graphics processing units or GPUs. It should make NAMD awesome, if it works.

Dreadmwidth/Livejournal Collaboration for ARCS

Dreadmwidth/Livejournal Collaboration for ARCS v0.1, May 11, 2009

1. What is this?

A proposal to use the free and open source technologies used by Livejournal ( and further developed by Dreamwidth ( to create an effective social collaboration and journaling site for Australian researchers.

2. Background

The Access Grid FAQ v0.2

The Access Grid FAQ v0.2, May 11, 2009


1.0 Administrivia
1.1 Where can I find an up-to-date copy of this FAQ?
1.2 Who wrote this FAQ?

2.0 About Access Grid
2.1 What is The Access Grid?
2.2 Where is it used and by how many people?

3.0 Setting Up Hardware and Software
3.1 What software is required?
3.2 What hardware is required?

4.0 Basic Operations
4.1 How do I manage the Venue Client?
4.2 How do I join A Venue?
4.3 How do I enable sound?
4.4 How do I enable video?
4.5 What is multicast/unicast? How do I change between multicast and unicast?

Underworld on a 64 bit Opteron Fedora Core 5 Cluster

Underworld is a "3D-parallel geodynamic modelling framework capable of deriving viscous / viscoplastic thermal, chemical and thermochemical models consistent with tectonic processes, such as mantle convection and lithospheric deformation over long time scales.... Underworld utilises a Lagrangian particle-in-cell finite element scheme (the prototype of which is the Ellipsis code), and is visualised using gLucifer."

Firewall Configuration for the Access Grid

Also available at the Access Grid website.

Purpose of the Document

The Access Grid is a software suite that provides video, audio and file collaboration, built on well-known streaming audio (Robust Audio Tool, or RAT) and Vic (Video Conferencing tool). This document seeks to help network administrators implement Access Grid with respect to local security policies and firewalls.

OpenMPI-PGI on a 64 bit Opteron Fedora Core 5 Cluster

This is the procedure for compiling OpenMPI with Portland group versions of C, C++ and Fortran. Part of the continuing adventure of installing Underworld on Wexstan.

First, collect the necessary modules: module load pgi/7.2, Download and extract (tar xvf openmpi-1.3.2.tar.gz) openmpi in the appropriate place (/usr/local/src/OPENMPI).

Bad superblock recovery

What do you do when you receive a "bad superblock" error on a USB or other Flash drive? Well, firstly you kick yourself for not backing up important data on said drive for the past nine days; you're old enough to know better than that. Secondly, you kick yourself for using that piece of rubbish called the FAT32 filesystem which was default for Windows 95, but is what every USB drive ships with because it's the last file format released by Microsoft that actually communicates with other operating systems, despite the fact that it's as buggy as hell and is prone to disaster.


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