Advanced Computing Research Centre

Software - BlueCrystal Phase 2

Application Development

The following languages have been installed on Phase 2.

GCC-4.3.3

Location: /usr/local/languages/gnu/gcc-4.3.3
Module name: languages/gcc-4.3.3

Java JDK 1.6.0_13

Location: /usr/local/languages/jdk1.6.0_13
Module name: languages/java-jdk-1.6.13

R-2.8.1

Location: /usr/local/languages/R-2.8.1
Module name: languages/R-2.8.1

Additional Packages:
BioConductor
snpMatrix

Updated R-2.9.1

Location: /usr/local/languages/R-2.8.1
Module name: languages/R-2.8.1

Additional Packages: BioConductor
snpMatrix
rjags
R2jags
coda
R2WinBugs
Rmpi_0.5-8

Weka-3-6-0

Location: /usr/local/languages/weka-3-6-0
Module name: languages/weka

Python 2.6.1

Location: /usr/local/languages/python-2.6.1/
Module name: languages/python-2.6.1

Applications

The following applications have been installed on Phase 2.

Abaqus 6.8

Module name: /apps/abaqus-6.8

Ansys 11.0

Module name: /apps/ansys11

Sample script available

Eigensoft2

Module name: apps/eigensoft-2

fbat-202C

Module name: apps/fbat-202c

Genehunter

Module name: apps/genehunter

The following citation must be included:
L. Kruglyak, M.J. Daly, M.P. Reeve-Daly, and E.S. Lander. "Parametric and Nonparametric Linkage Analysis: A Unified Multipoint Approach". American Journal of Human Genetics 58:1347-1363 (June 1996).

L. Kruglyak and E.S. Lander. "Faster Multipoint Linkage Analysis Using Fourier Transforms". Journal of Computational Biology 5:1-7 (1998).

Gromacs (Serial)

Module name: apps/gromacs-serial

Gromacs (MPICH2)

Module name: apps/gromacs-mpi

gtool v0.5.0

Module name: apps/gtool

Haploview

Module name: apps/haploview

Impute

Module name: apps/impute

LS-Dyna Standard

Module name: apps/ls-dyna

Mach

Module name: apps/mach

Matlab

Module name: apps/matlab-R2010a or apps/matlab-R2011a

Meep serial

Module name: meep-serial

Meep-1.1.1 MPI

Module name: meep-mpi

Mendel-900

Module name: apps/mendel-900

Moses

Module name: apps/moses

NAMD

Module name: namd

Sample script available

NAMD with fftw

Module name: apps/namd-fftw

Openbugs

Module name: apps/openbugs

ParaView

Module name: apps/paraview

Online Documentation

plink-1.05

Module name: apps/plink-1.05

Root 5.22

Module name: apps/root

snptest v1.1.5

Module name: apps/snptest

Solar

Module name: apps/solar

SPM8

Module name: apps/spm8

Structure 2.3.1 (with Graphical Front End)

Module name: apps/structure-gui

Structure 2.3.1 (without Front End)

Module name: apps/structure

Debugging and Optimisation

Tau 2.19.2

Tau Compiled with Intel Compiler and MPI support

Module name: profile/tau-2.19.2-intel-mpi

Tau Compiled with Intel Compiler and OpenMP support

Module name: profile/tau-2.19.2-intel-openmp

Tau Compiled with Portland Group Compiler and MPI support

Module name: profile/tau-2.19.2-pgi-mpi

Tau Compiled with Portland Group Compiler and OpenMP support

Module name: profile/tau-2.19.2-pgi-openmp

ViTE

Module name: apps/vite

GPGPUs

Nvidia provide a list of applications which have been accelerated using the CUDA parallel computing architecture of NVIDIA Tesla GPUs - http://www.nvidia.co.uk/object/cuda_app_tesla_uk.html.

Libraries

GNU Builds

Intel Builds

PGI Builds