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Arcca Software

Software list

As part of the SRIF-3 procurement a variety of software was procured to assist users developing applications on Raven. In addition, in consultation with the researchers, a number of commercial applications are available and can be found under the /software directory. 

This page contains information on the latest software releases installed on the system and a brief summary of the application. These fall under 4 main categories:

1. Compilers

2. Math Libraries

3. Software Development Tools - application debuggers and profilers

4. Research Applications/Packages.

 

1. Compilers

Compiler Location
Intelmodule load intel
Portland Groupmodule load compiler/portland/12.5
GNU compilersmodule load compiler/gnu-4.6.2

 

2. Math Libraries

Library Location
FFTW/FFTW3module load fftw/3.3-avx
mpimodule load mpi/intel-4.1.0
GSLmodule load gsl/1.15
HDF5module load hdf5/1.8.12
netCDFmodule load netcdf/4.3.1

 

3. Software Development Tools

Application Brief Description

 

Allinea OPT

 

OPT profiles the performance of parallel and scalar applications, allowing users to find the bottlenecks in programme performance quickly and easily
Allinea DDTDDT helps developers fix bugs in code (serial and parallel) - with a powerful and easy to use GUI.
Intel VTunePerformance analysis tool which assists with code optimization. The GUI enables various kinds of code profiling including time based profile, event based profile etc.
Intel Trace AnalyzerProvides information to help understand and optimise application performance by quickly locating performance bottlenecks with MPI communication.
ipmIPM is a portable profiling infrastructure for parallel codes. It provides a low-overhead performance profile of the performance aspects and resource utilization in a parallel program.
tauTAU is a program and performance analysis tool framework being developed for the DOE Office of Science, ASC initiatives at LLNL, the ZeptoOS project at ANL, and the Los Alamos National Laboratory.

 

4.Research Applications / Packages

Application Brief Description
BlastNCBI Blast - finds regions of similarity between biological sequences.
MolproMolpro is a complete system of ab-initio programs for molecular electronic structure calculations.
siestasiesta performs electronic structure calculations and ab-initio molecular dynamic simulations
gromacsGromacs is a versatile package to perform molecular dynamics.
nwchemNWChem provides a quantum mechanical description of the electronic wavefunction / density.
VASPVASP is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set.
AbaqusApache's Hadoop Implementation. This open source Java installation relies on LSF and Lustre
wrfThe Weather Research & Forecasting Model.
bowtie2Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes, and contains a number of enhancements compared to its predecessor, bowtie.
plinkPLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.

For a more complete list of applications please refer to the ARCCA software catalogue (PDF).