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Unsupported Software

Package listed on this page are NOT included on the Officially Supported Sharcnet software page.

User-Installed Packages

This table provides manual build and installation instructions for various packages provided by sharcnet researchers and staff. We encourage all researchers to add build instructions for newer versions or add new pages altogether so this information can be used by other SHARCNET users. To do so click the package name to edit any information. To add a package simply add a new row in the table in alphabetical location. Please follow the prototype example https://www.sharcnet.ca/help/index.php/LRS noting that instructions for each new version should be separated by a horizontal line with the version, authors name, email and date clearly indicated, as well the most recent version should appear nearest to the top on each page. Older version contents should not be deleted or altered without consent of the owner.

Package name Research Area
AMICA Code for AMICA: Adaptive Mixture ICA with shared components
ARPACK fortran eigenvalue solver
ASE DFT (DACAPO) computational chemistry package, ticket-9255
BIDMach BIDMach is an interactive environment designed to make it extremely easy to build and use machine learning models.
BIO-SAMTOOLS Perl interface to libbam library
Bowtie2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
Caffe Caffe is a deep learning framework developed with cleanliness, readability, and speed in mind.
CaMa-Flood The CaMa-Flood (Catchment-based Macro-scale Floodplain) model is designed to simulate the hydrodynamics in continental-scale rivers.
cuDNN The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
Cufflinks Assembles aligned RNA-Seq reads into transcripts, estimates abundances, tests differential expression and regulation transcriptome-wide
cutadapt Cutadapt removes adapter sequences from high-throughput sequencing data
Cryptominisat An advanced SAT Solver
Dice Semistochastic heat bath configuration interaction (SHCI) algorithm for ab initio Hamiltonian of a quantum chemical system
DIGITS The NVIDIA Deep Learning GPU Training System (DIGITS) puts the power of deep learning in the hands of data scientists and researchers.
EMBOSS EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
Enzo Cosmological structure formation code
ffmpeg See ticket 24851[1]
FSL Comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data
GAMESS_US Gamess computational chemistry package, ticket-12007
Geneious Commercial DNA alignment,assembly and analysis software
GlimmerHMM Gene finder based on a Generalized Hidden Markov Model (GHMM)
Grass Geographical information system (GIS)
GEOS Geometry Engine, Open Source
Google Test Google's C++ test framework
HDF5 Library for the HDF5 data format
HOOMD-blue general-purpose particle simulation toolkit
ISAACS Interactive structure analysis of amorphous and crystalline systems
idba Iterative De Bruijn graph short read Assembler
ITK Insight Segmentation and Registration Toolkit
JULIA High-level, high-performance dynamic programming language for technical computing
KmerGenie Estimates the best k-mer length for genome de novo assembly.
LinBox C++ template library for symbolic linear algebra
LRS Convert polyhedron between H and V representation in parallel using plus
MAFFT Multiple (amino acid or nucleotide) sequence alignment
MEEP Finite-difference time-domain simulations from MIT
MEME Parallel implementation of MEME
Mesa3D OpenGL implementation with off-screen rendering support via osmesa
MPICH2 Message passing library
MODE Lumerical EME Solver
Ogre3D 3D rendering engine
OpenMM Library providing tools for modern molecular modeling simulation. It can be easily hooked into any code, and has a strong emphasis on hardware acceleration
ORCA Computational Chemistry
PDP++ neural network simulation
PopAlu No description on web site. See https://github.com/aimeida/PopAlu .
popins Population-scale detection of novel sequence insertions. URL: https://github.com/bkehr/popins
PHYLIP Inference Package
Rmpi software for statistical computing
ROOT Data analysis framework
samtools Tools (written in C using htslib) for manipulating next-generation sequencing data. URL: http://samtools.sourceforge.net/ Git: https://github.com/samtools/samtools
SeqAn SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.
SIMPSON general simulation program for solid-state NMR
Singular Computer algebra system for polynomial computations
SPAI SParse Approximate Inverse Preconditioner
Sunrise Astronomical simulation analysis tool
Tensorflow TensorFlow is an Open Source Software Library for Machine Intelligence.
Theano Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
TopHat TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons
Torch Torch is a scientific computing framework with wide support for machine learning algorithms.
Transposome Transposome is a toolkit for annotation of transposable element families from unassembled sequence reads.
Trilinos Object-oriented software framework for the solution of large-scale, complex problems
Deal.II Solution of partial differential equations using adaptive finite elements
TRINITY Trinity RNA-Seq de novo transcriptome assembly
UCSC Kent Utilities The "UCSC Kent Utilities" is a source code collection of genomics and related utilities developed by Jim Kent, from the UCSC Genome Bioinformatics Site.
UMFPACK Set of routines for solving unsymmetric sparse linear systems
VASP The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.
Wise2/Genewise The Wise2 form compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
WIEN2k DFT simulation package
Wise2/Genewise The Wise2 form compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
WRF Weather Research and Forecasting Model
YAML-CPP A YAML parser and emitter for C++
yambo Associated with Espresso, Many-Body calculations in solid state and molecular physics
pymol A molecular visualization system. www.pymol.org

Undocumented Modules

This table provides a listing of untested modules that are installed on various sharcnet clusters but have no official sharcnet software page or documentation yet:


Module name URL Systems Installed On
arprec http://crd-legacy.lbl.gov/~dhbailey/mpdist/ all centos6 systems (except vdi-centos6)
glpk http://ftp.gnu.org/gnu/glpk all centos6 systems (include vdi-centos6)
mpfun2015-fort/v06 http://www.davidhbailey.com/dhbsoftware/ all centos6 systems (except vdi-centos6)
mpfun2015-mpfr/v01 http://www.davidhbailey.com/dhbsoftware/ all centos6 systems (except vdi-centos6)

Retired Packages

From time to time software packages appearing on the Supported Software page become obsolete and are removed. Their corresponding wiki pages remain accessible in the table below for a period of at least six months for reference purposes before being removed.


Package Name Notes Date Retired Obsolete
SCALAPACK use MKL or ACML instead Jan 01, 2014 no
HYPERMESH superceded by ANSYS Jan 01, 2014 no
LAPACK use MKL or ACML instead Jan 01, 2014 no
BLAS use MKL or ACML instead Jan 01, 2014 yes
PERLMODULES use ACTIVEPERL instead Jan 01, 2014 no
NAG use GSL, ACML or MKL Jan 01, 2014 no
GPC no replacement Jan 01, 2014 no
IBM_XL no replacement Jan 01, 2014 no
HARMINV insufficient use June 26, 2014 no
FPC replaced by fpc from epel Jul 4, 2014 no
ACTIVEPERL use cpan instead Jul 8, 2014 no
PHYLIP locally supported Jul 8, 2014 no
YORICK insufficient use Jul 8, 2014 no
JASPER replaced by jasper from centos Jul 8, 2014 no
CLN replaced by cln from centos Jul 9, 2014 no
DeMON insufficient use Jul 23, 2014 no
NXCLIENT replaced by vnc Aug 11, 2014 no
RMPI move to user installed area Nov 4, 2014 no
PETSC maintained as module Feb 10, 2015 yes