VPAC Systems Blog

After too long a break on the blog, here’s a quick update on software packages that have arrived at VPAC over the past few months, and some information on how to access them.

A sample of the new and updated packages are:

• Gaussian 03 with Linda (Tango)
• Gaussian 03 SMP, single node only (Edda)
• Amber 10 (Tango)
• MATLAB Distributed Computing Server (Tango)
• GAMESS-US (Tango)
• MrBayes (Tango, already on Edda)
• Dock v6 (Tango and Edda)
• Schrodinger (Tango)
• MOPAC 2007 (Tango)
• AMD Core Maths Libraries - ACML (Tango)
• Wine 1.0 and 1.1.1 (Tango)

We are introducing controls to licensed commercial software to ensure that users are aware of their rights and obligations when using such packages. To get access to such a package just login to the VPAC website at www.vpac.org with your cluster user name and password and click the “Add Software” button.

We have now installed Abaqus 6.7-1 on Wexstan, this software will also be made available on the new large cluster, Tango, when it is commissioned.

Both the MPI and non-MPI versions of MrBayes 3.1.2 have now been installed on Edda as 64-bit programs.

To access the standard (non-MPI) version of MrBayes put the following into your PBS script before calling “mb [arguments]“:

module load mrbayes/3.1.2

To access the MPI version of MrBayes put the following into your PBS script before calling “mpiexec mb [arguments]“:

module load mrbayes/3.1.2-mpi

MrBayes is a program for the Bayesian estimation of phylogeny.

XmdS, the eXtensible multi-dimensional Simulator has now been installed on Brecca, Wexstan and Edda.

XMDS is a code generator that integrates equations. You write them down in human readable form in an XML file, and it goes away and writes and compiles a C++ program that integrates those equations as fast as it can possibly be done in your architecture.

You can access the package by doing module load xmds and then xmds to build your xmds based executable.

GANSO (Global And Non-Smooth Optimization) is a library of optimization solvers, developed at the University of Ballarat by CIAO researchers, and is now available on the VPAC system.

GANSO utilises a number of novel optimization algorithms to tackle the most difficult of nonlinear programming problems, in which the objective function is non-differentiable and has multiple extrema. It also allows for combining these algorithms in different ways (e.g., to combine local and global search).

GANSO provides both a class and a procedural interface to all algorithms, and can be linked to programs written in C/C++, FORTRAN. It can also be called from other packages. The library, including files and examples of use, can be found in the directory /usr/local/ganso/ on the VPAC machines.

The GANSO user manual, Matlab and Maple toolboxes, as well as demo versions of GANSO, allowing the solving of problems with up to 100 variables, can also be downloaded from the website http://www.ganso.com.au/.

CIAO researchers would be interested in hearing feedback on the use of the GANSO library in practical applications. You are invited to provide suggestions and comments, and to report issues via email to j.ugon at ballarat.edu.au.

The open source render system Blender is now installed on Edda (version 2.43) and Wexstan (version 2.42a from Fedora Extras).

Note that the version on Edda is currently the 32-bit binary package, we hope to get a native 64-bit package going eventually.