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All the BlueFern systems (Power 755, BlueGene L and P, Visualisation cluster) have a core of common software and packages. However because of the different types of architectures, operating systems and user requirements, there are some differences in the software/applications available on each system.

Executables for commonly used software can usually be found under your default login environment.

This is not an exhaustive list and is not meant to be entirely up-to-date, but it is rather an indication of the type of software and environment that users may find on each system.

Requesting software installation

Some packages may have been installed for testing or at the request of a limited number of researchers and they may not be listed here. Alternatively some packages may not have already been installed for various reasons. Either way, please email us at  bluefern@canterbury.ac.nz to ask if a package is available or can be installed.

Computational Resources

Category

Software

BlueGene P

foster.canterbury.ac.nz

Power 7 AIX

kerr.canterbury.ac.nz

Power 7 Linux

beatrice.canterbury.ac.nz

Visualisation cluster

viz0.canterbury.ac.nz

Operating System

all systems run a variant of UNIX

SuSE Linux Enterprise server

Login node: SLES 10, 64 bits, PowerPC

Compute nodes: compute kernel, 32 bits, PowerPC

Advanced Interactive eXecutive

AIX, 64 bits, PowerPC

SuSE Linux Enterprise server

SLES 11, 64 bits, PowerPC

SuSE Linux Enterprise server

SLES 11, 64 bits, x86

Editors

nanoYYYY
emacsYYYY
vimYYYY
EclipseY

Y

Y

N
geditYYNY

File format libraries

HDF4NYNN
HDF5YYYY with ParaView
NetCDFYYYY with ParaView
AdiosNNNY (1.3.1 and 1.4.0)

Programming

Category

Software

BlueGene P

foster.canterbury.ac.nz

Power 7 AIX

kerr.canterbury.ac.nz

Power 7 Linux

beatrice.canterbury.ac.nz

Visualisation cluster

viz0.canterbury.ac.nz

Compilers

C

gcc/mpicc: GNU 4.1.2

xlc/mpixlc: IBM

 

xlc/mpcc: IBM

gcc: GNU 4.3.4

xlc/mpcc: IBM

gcc/mpicc: GNU 4.3.4

 

Fortran

gfortran/mpif90,mpif77: GNU 4.1.2

xlf90/mpixlf90,mpixlf77 xlf95/mpixlf95, xlf2003/mpixlf2003: IBM  

 

xlf90/mpxlf90, xlf95/mpxl95, xlf2003/mpxlf2003: IBM

gfortran: GNU 4.3.4

xlf90, xlf95, xlf2003, mpifort: IBM

gfortran/mpif90,mpif77: GNU 4.3.4

 

C++

g++/mpicxx: GNU 4.1.2

xlc++/mpixlcxx: IBM

 

xlc++/mpCC: IBM

g++: GNU 4.3.4

xlc++/mpCC: IBM

g++/mpicxx: GNU 4.3.4

 

Other languages

Pythonlogin node:Y compute nodes:NYY (see Python)Y
Javalogin node:Y compute nodes:NYYY
Perllogin node:Y compute nodes:NYYY
RNY (old)Y 

Utilities

makeY (GNU)Y Note: GNU make is available as gmake. make is IBM version of make. Y (GNU)Y (GNU)
CmakeYYYY

Debuggers

TotalViewYYYN
GNU debugger: gdbYNYY

IBM debugger:

xldb

YYYN

Version control

gitYYYY
subversion (svn)YNYY
mercurial (hg)NNYY
cvsYYYY

Scientific Software and Libraries

Category

Software

BlueGene P

foster.canterbury.ac.nz

Power 7 AIX

kerr.canterbury.ac.nz

Power 7 Linux

beatrice.canterbury.ac.nz

Visualisation cluster

viz0.canterbury.ac.nz

Numerical Libraries


 

 

 

 

 

 

LAPACK

linear algebra

Y (reference/GotoBlas/OpenBlas

are available)

Y (reference-3.3.1/xlf)

Y (ATLAS-3.8.4 - both gfortran and xlf interface available)

N

ScaLAPACK

scalable LAPACK

YNNN

BLAST/MpiBlast

Basic Local Alignment Search Tool

YYYY

ESSL

IBM Engineering and Scientific Software Library

YYYN
FFTW
Fast Fourier (FFT) implementation
YYYN

GSL

GNU scientific library

NY (1.15)Y (1.15)N

NumPy, Scipy, matplotlib

Scientific Computing with Python

NNY 

Image Libraries

libpng

For handling png images

YYYY

libjpeg

compression library and image conversion

Y YY

zlib

Data compression library

YYYY

Parallel Utility Library

ADLB (Asynchronous Dynamic Load Balancing), batcher

Library designed by Argonne National Laboratory to help rapidly build scalable parallel programs.

batcher is an MPI/ADLB parallel program that executes shell script commands in parallel using the leader/worker model

Ideal for Multiple serial jobs, e.g Parameter Sweeps

NNYN

General Purpose

Octave (serial and parallel)

Multi-physics high-level programming language compatible with MATLAB.
Parallel capabilities available with the  pMatlab and MatlabMPI libraries.

NNYN

Computational Fluid Dynamics



OpenFOAM

Toolkit for building CFD applications

Y YN
CFX CFD multiphysics applicationsNYNY (interactive visualisation only)

FLUENT

CFD multiphysics applications

NYNY (interactive visualisation only, please see Fluent on the Viz Cluster)

MODFLOW

3D FD Ground-water flow modelling

 Y N
GerrisNNY 
FDS (fire simulation) Y  

Chemistry/Biochemistry

Amber

Package for electronic structure and other properties

Y YN

BLAST+

Package to search nucleic acid or protein databases for sequences similar to one or more query sequences of any type.

NNYN

Gromacs

The ultimate molecular dynamics simulation package

Y (unreleased 4.5.6 version)Y (4.5.5)Y (4.6.5)N

NAMD

Molecular dynamics

YYYN

Gamess

Quantum chemistry

N (to be installed)N (can install on request)Y (2012R2)N

Rosetta

Protein design and analysis

N YN
Quantum Espresso  Y (single node only) 

Bioinformatics

MrBayes

Bayesian Inference of Phylogeny

NYYN
phymlNNYN

BLAST+

Package to search nucleic acid or protein databases for sequences similar to one or more query sequences of any type.

NNYN
FSL (Neuro biology, brain image processing)  YY

Meteorology

WRF

Weather Research and Forcasting Model

YYYN
 pism (parallel ice sheet modelling)Y   

Network Simulation

Omnet++NYYN

Scientific Data Visualisation

 




VTK

Libraries for visualisation of multi-dimensional data

Y YY

PyVTK

Tools for manipulating VTK files in Python

NNYN

ParaView

GUI application for visualising many types of multi-dimensional large datasets

NNNY

Rasmol

Molecular graphics visualisation

 YYN

Smokeview (smv5)

Viewer for simulations produced by FDS (Fire Dynamics Simulator)

NNNY

Visit

GUI application for visualising many types of multi-dimensional large datasets

NNNY

Ensight

GUI application for Post-processing and Visualisation for Scientific data (can process model size >100 million cells)

NNNY

VMD

Visual Molecular Dynamics

NYYY

PyMOL

Molecular Visualisation

NNNY

ncview

netCDF file browser

NY (2.1.1)NY (2.1.2)

gnuplot

Command driven plotting program

NNYN

 

How to get started on the systems?

For more information specific to each of the BlueFern system please check out the following links:

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