Software Available on the NSCC System
Last updated Nov 21, 2019
ARM Allinea Forge & Performance Reports
Available version: 19.1.4
Description: Allinea Forge is the complete toolsuite for software development – with everything needed to debug, profile, optimize, edit and build C, C++ and Fortran applications on Linux for high performance – from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA.
Documentation: https://developer.arm.com/products/software-development-tools/hpc/arm-forge/videos
Usage: module load arm/forge arm/reports
AmberTools
Available version: 15update6
Description: AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. The sander program is now a part of AmberTools.
Documentation: http://ambermd.org/#AmberTools
Example job script: /app/amber/example/
Notes: This is the Opensource package, not the commercial Amber molecular dynamics package.
Aspera command line client
Available version: 3.5.4.102989
Description: Aspera is high-speed file transfer software.
Documentation: http://asperasoft.com/
Usage: module load aspera
Autoconf
Available version: 2.69
Description: Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages.
Documentation: http://www.gnu.org/software/autoconf/autoconf.html
Usage: module load autoconf
Bcl2fastq
Available version: 2.20.0
Description: Demultiplex data and convert BCL files to FASTQ file formats for downstream analysis.
Documentation: http://support.illumina.com/downloads/bcl2fastq-conversion-software-v217.html
Usage: module load bio
Bedtools
Available version: 2.25
Description: A swiss-army knife of tools for a wide-range of genomics analysis tasks.
Documentation: http://bedtools.readthedocs.org
Usage: module load bio
Bowtie & Bowtie2
Available version: 1.1.2 & 2.29
Description: Bowtie is an ultrafast, memory-efficient short read aligner.
Documentation: http://bowtie-bio.sourceforge.net
Usage: module load bio
BWA
Available version: 0.7.13
Description: BWA is a software package for mapping low-divergent sequences against a large reference genome.
Documentation: http://bio-bwa.sourceforge.net/
Usage: module load bio ; man bwa
CMake
Available version: 3.5.0-rc3
Description: CMake is an open-source, cross-platform family of tools designed to build, test and package software.
Documentation: http://cmake.org
Usage: module load cmake
CPMD
Available version: 3.15.3
Description: CPMD is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.
Documentation: http://www.cpmd.org
Usage: module load cpmd
Example job script: /app/cpmd/example
Licensing: Users must have individually agreed to the CPMD licensing agreement. To use the software on NSCC please register on the CPMD website and then submit a helpdesk request to be given access to the application.
Cufflinks
Available version: 2.2.2
Description: Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
Documentation: http://cole-trapnell-lab.github.io/cufflinks/
Usage: module load bio
Gromacs
Available version: 5.1.2, 2016 & 2018
Description: GROMACS is a versatile package to perform molecular dynamics.
Documentation: http://www.groamcs.org/
Usage: module load gromacs
Notes: Preprocessing commands (gmx …) have been built in serial, mdrun_mpi has been compiled separately with MPI & OpenMP (with and without CUDA support). Built with GCC 4.9.3, CUDA 7.5 and Intel MPI.
Example job script: /app/gromacs/example
Build procedure: /app/build-procedures/gromacs
gnuplot
Available version: 5.0.3
Description: gnuplot is a portable command-line driven graphing utility.
Documentation: http://www.gnuplot.info/
Usage: module load gnuplot
Hmmer
Available version: 3.0
Description: HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
Documentation: http://hmmer.org/
Intel Composer XE
Available version: 2016.1.056, 2017.0.098, 2018.0.128, 2019.0.0.117
Description: Optimizing compilers for Fortran, C and C++ supported by Intel
Documentation: C/C++ Compiler Guide, Fortran User Guide, Quick Reference Guide for Optimization Flags
Intel MPI
Available version: 5.1.2
Description: Implementation of the MPI standard supported by Intel
Documentation: Developer Reference Manual
Julia
Available version: 0.4.5
Description: Julia is a high-level, high-performance dynamic programming language for technical computing.
Documentation: http://julialang.org/
Usage: module load julia
MEEP
Available version: 1.3
Description:MEEP is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems.
Documentation: http://ab-initio.mit.edu/wiki/index.php/Meep
Usage: module load meep
Example job scipt: /app/meep/example
MPIBlast
Available version: 1.6.0
Description: mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST.
Documentation: http://mpiblast.org/
NAG Fortran Compiler & NAG libraries
Available version: NAG Fortran Compiler Release 6.1. Library versions: FLL6I25DCL, FLL6A24DFL, FLL6A23DHL, FLL6A24D9L, CLLUX25DCL, CLL6I25DCL, CLL6A23DGL, FSL6A23DFL, FSL6I24DCL and FSL6I24DDL.
Description:A large collection of robust, documented, tested and maintained numerical algorithms.
Documentation: http://www.nag.co.uk/content/software-documentation
NCBI Blast
Available version: 2.3.0+
Description: The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
Documentation: http://blast.ncbi.nlm.nih.gov/Blast.cgi
NCL (NCAR Command Language)
Available version: 6.3.0
Description: NCL is an interpreted language designed specifically for scientific data analysis and visualization.
Documentation: https://www.ncl.ucar.edu/
Usage: module load ncl
NWChem
Available version: 6.6
Description: NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.
Documentation: http://www.nwchem-sw.org
Example job script: /app/nwchem/example
Build procedure: /app/build-procedures/nwchem
Notes: Built with Intel compilers, Intel MPI, MKL and using InfiniBand build of ARMCI.
OpenFOAM
Available version: 3.0+, 4.0 & 5.0
OpenFOAM is free, open source software for computational fluid dynamics (CFD).
Documentation: http://www.openfoam.org/
Usage information: module help openfoam/3.0+
Notes: Built with Intel compilers and OpenMPI
Parallel
Available version: 20160222
Description: GNU parallel is a command-line driven utility for GNU/Linux or other Unix-like operating systems which allows the user to execute shell scripts in parallel.
Documentation: http://gnu.org/software/parallel/
Usage: module load parallel
Python
Available version: 2.7.12 & 3.5
Description: Python is a widely used high-level, general-purpose, interpreted, dynamic programming language.
Documentation: http://www.python.org
Usage: module load python
Quantum Espresso
Available version: 5.3.0
Description: Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
Documentation: http://www.quantum-espresso.org/
Example job script: /app/quantum-espresso/example
Build procedure: /app/build-procedures/quantum-espresso
Notes: Initial installation only contains Plane-Wave and Car-Parinello modules, rest of modules to be installed at a later date.
R
Available version: 3.3.1
Description: R is a free software environment for statistical computing and graphics.
Documentation: https://www.r-project.org/
Usage: module load R
Samtools
Available version: 1.3
Description: Samtools is a suite of programs for interacting with high-throughput sequencing data.
Documentation: http://www.htslib.org/
Usage: module load bio
Tophat
Available version: 2.1.1
Description: TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions.
Documentation: http://ccb.jhu.edu/software/tophat/
Usage: module load bio
WRF
Available version: 3.8
Description: The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting needs.
Documentation: http://www.wrf-model.org/index.php
Usage: module load wrf
Build instructions: /app/build-procedures/wrf
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