Software Updates

Introduction

Starting with the September 2011 edition, a summary of software updates on WestGrid systems has been included in WestGrid newsletters.  Due to space limitations in the newsletters it has not always been possible to include a full list of updates.  The tables below give details of the updates for the periods shown, roughly categorized according to application area. Generally speaking it is only the most recent table that is likely to be of interest.

The tables below show only software changes.  For a more comprehensive view of software installed on WestGrid systems, please see the main software page.

Newsletters are archived at http://www.westgrid.ca/newsletters .

Updates for mid-February 2013 to present

Category Software package and version System Remarks
Bioinformatics


  BEAST 1.7.5 Bugaboo Bayesian MCMC analysis of molecular sequences.
       
Chemistry/Biochemistry


  PLUMED 1.3 plugin for CPMD 3.15.1 Bugaboo Added the PLUMED free energy calculation plugin to the existing CPMD molecular dynamics simulator.
  CPMD 3.15.3p1 Lattice/Parallel /global/software/cpmd/CPMD-3.15.3.p1_ifort_mpi_mkl_defaultfft/bin/cpmd.x
  GROMACS 4.6.1 Jasper Molecular dynamics.
module load application/gromacs/4.6.1
       
Files and data handling



       
Graphics


       
Mathematical Libraries      
       
Programming

 
 
Intel MPI 4.1.0.030 Grex

Minor update to the Intel MPI (Message Passing Interface) environment for parallel programs.

module load gcc/impi/4.1.0.030 or
module load intel/impi/4.1.0.030

       
Other      
  MEEP 1.2
Grex, Hermes/Nestor
Finite difference time-domain (FDTD) electromagnetic simulation package
module load meep/1.2
  MATLAB R2013a Jasper, Hungabee

General purpose numerical package
For U of A researchers only
module load uofa/matlab/R2013a

  MATLAB Distributed Computing Server  R2013a Orcinus Increased license for number of workers from 64 to 160.

Updates for mid-December 2012 to mid-February 2013

Category Software package and version System Remarks
Bioinformatics



BWA 0.6.2 Hungabee
Burrows-Wheeler Aligner - Aligns short nucleotide sequences to long reference sequences.
  ExaML 1.0.0 Bugaboo Fast parallel implementation of the RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.
 

Nemo 2.2.0

(serial version)

Hermes/Nestor

Stochastic simulation to study evolution of life history/phenotypic traits and population genetics

Initialize with module load nemo

 

SAMTools 0.1.18

Hungabee

 Utilities for manipulating SAM (Sequence Alignment/Map) format files.

  SOAPdenovo 2.04, pregraph_sparse 1.0.3 Breezy

De novo draft genome assembly from Illumina short-read data.

See /global/software/soapdenovo/r233/bin.

       
Chemistry/Biochemistry


  Chaste 3.1 Hungabee Cancer, Heart and Soft Tissue Environment - tissue and cell level electro-physiology, discrete and soft tissue modelling.
  DL_POLY 4.04 Jasper A suite of programs for molecular dynamics.
Initialize with module load application/dl_poly/4.04
  VASP 5.3.3 Lattice/Parallel

Ab initio quantum-mechanical molecular dynamics program.

Built with the Intel 12.0 compiler the MKL library with ScaLAPACK and FFTW3 interface (to the MKL FFT routines).

See /global/software/vasp/vasp533/bin . 

       
Files and data handling



  Climate Data Operators 1.5.9 Bugaboo Command-line tools to manipulate data associated with climate modelling and numerical weather prediction. See the  CDO home page
       
Graphics


       
Mathematical Libraries      
  FEniCS (DOLFIN 1.1.0) Hungabee FEniCS is a framework for the solution of differential equations by finite element methods.  DOLFIN is a key component of the FEniCS environment.
Initialize with module load application/dolfin/1.1.0 .
  JAGS 3.3.0 (Several) Just Another Gibbs Sampler - analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.
  Nektar++ 3.2.0 Hungabee  Framework for partial differential equation solvers based on finite-element methods. Initialize with module load application/nektar++/3.2.0.
  OpenBUGS 3.2.2 (Several) Bayesian inference Using Gibbs Sampling using Markov Chain Monte Carlo (MCMC) simulation.
  SCOTCH 6.0.0 Jasper Graph and mesh partitioning, sparse matrix ordering. Initialize with module load application/scotch/6.0.0.
       
 Programming

 
       
Other


       

Updates for mid-September to mid-December 2012

In addition to the specific updates shown below, there were minor updates to a large number of R packages on Breezy.  Also, R packages such as maptools, raster typically have many dependencies on other minor R packages, which are not shown separately.

Category Software package and version System Remarks
Bioinformatics



 
ALLPATHS-LG 43500
Hungabee
Sequence assembly package.
  Bioconductor core R packages Breezy

R-based tool suite for genomic analysis.

BiocGenerics 0.4.0, BioBase 2.18.0, IRanges 1.16.4, AnnotationDbi 1.20.2, RSQLite 0.11.2

  BWA 0.6.1 Hermes/Nestor Sequence alignment via Burrows-Wheeler transformation.
  ChIPpeakAnno (R Bioconductor package)
Bugaboo Analyze peaks in ChIP-seq or ChIP-chip experiments.
  FastQC 0.10.1 Hermes/Nestor Quality control tool for high throughput sequence data.
  HMMER 3.0 Hermes/Nestor Search a database for homologous protein sequences.
  IMa2 8.27.12
Bugaboo
Migration effects in population genetics.
  MUMmer 3.23
Hermes/Nestor
Ultra-fast alignment of large-scale DNA.
  PLINK 1.07
Hermes/Nestor
Analysis of genotype/phenotype data.
  QIIME 1.5.0

Quantitative Insights into Microbial Ecology - extensive software pipeline from sequence data to phylogenetic trees and subsequent analysis.
  Ray 1.7 Hermes/Nestor MPI-based genome assemblies for DNA sequencing.
  SAMtools 0.1.18 Hermes/Nestor Utilities for manipulating SAM (Sequence Alignment/Map)-format files.
  SurvComp (R package) Bugaboo Survival analysis.
  topGO 2.1.0 (R package)
Breezy, Bugaboo
Gene ontology analysis.
  TopHat 2.0.6 (Bugaboo), 2.0.4 (Hermes/Nestor)
Bugaboo, Hermes/Nestor Fast splice junction mapper for RNA-Seq reads.  Upgrade from version 1.3.3
  Trinity r2012-10-05 Hungabee De novo reconstruction of transcriptomes from RNA-seq data.
       
Chemistry/Biochemistry


  PSI3 3.4.0 Grex Quantum chemistry/electronic structure code whose strengths are in expensive electron correlation methods like Coupled Cluster, MP2-R12 etc.
  VASP 5.3.2 Grex Ab-initio quantum-mechanical molecular dynamics.
  Yambo 3.2.5 Hermes/Nestor Ab-initio tool for excited state calculations.
       
Files and data handling



  CDO 1.5.8 Breezy Climate Data Operators for handling NetCDF data.
  HDF 4 4.2.8 Breezy Hierarchical data format version 4 libraries.
  HDF 5 1.8.10 Breezy Hierarchical data format version 5 libraries.
  jEdit 4.5.1 Hermes/Nestor Programming text editor.
  NetCDF 4.2 (Fortran), 4.2.1.1 (C)
Breezy Network Common Data Form libraries.
  tecio 2009
Bugaboo Library for producing Tecplot file format .
  UDUNITS 2.1.22 Breezy C library for units of physical quantities and a unit-definition and value-conversion utility.
       
Graphics


  Circos 0.60 (Breezy), 0.62-1 (Bugaboo) Breezy, Bugaboo Bioinformatics visualization tool (with somewhat wider applicability).
  igraph 0.6-3 (R package) Breezy Network analysis and visualization.
  ncview 2.1.1 Jasper Visual browser for netCDF-format files.
 
Rgraphviz 2.2.1 (R package)
Breezy, Bugaboo
Graph visualization.
       
Mathematical Libraries      
  CERN Orcinus Special functions.
  deal.II 7.2.0 Bugaboo Library for partial differential equation solution with adaptive finite elements.
  FreeFem++ 3.20 Bugaboo Partial differential equation solver, typically applied for multiphysics non-linear systems.
  GEOS 3.3.6 Breezy Geometry calculation library.
  Ipopt Bugaboo Interior Point OPTimizer.
  JAGS 3.3.0 Checkers Bayesian modelling.  R interface, rjags also installed.
  MMG3D Bugaboo Anisotropic Tetrahedral Remesher/Moving Mesh Generation
  MUMPS 4.10.0 Bugaboo Parallel direct solver for sparse systems
  OpenBugs 3.2.2 Checkers Bayesian modelling.  R interface also installed.
  p4est 0.3.4 Bugaboo Adaptive mesh refinement using octrees
  SCOTCH 5.1.12 Bugaboo Graph and mesh partitioning, sparse matrix ordering.
  TetGen 1.4.3 Bugaboo Tetrahedral mesh generator and a 3D Delaunay triangulator.
  Trilinos 10.12.2 Bugaboo Object-oriented framework for linear algebra, meshing, preconditioners, solvers.
       
 Programming

 
  cmake 2.8.9 Jasper Software building utility.  Upgrade from version 2.6p4.
  GCC 4.6.3, 4.7.1 Grex To test earlier versions of Go language
  Open MPI 1.6.1 Grex Bug fix for MPI parallel programming libraries.
  R 2.15.1 (Breezy)
R 2.15.2 (Checkers)
Breezy, Checkers Language and environment for statistical computing and graphics.
  Szip 2.1
Breezy, Jasper Compression library.
  ZODB Jasper Database interface for storage of Python objects.
       
Other


  ABAQUS 6-12.1 Checkers Finite element modelling (approved U. of Alberta researchers only).
  GDAL 1.9.0 (Hermes/Nestor), 1.9.2 (Breezy) Checkers, Breezy Geospatial Data Abstraction Library.  Also installed rgdal R interface.
  HFSS 14.0 Hungabee ANSYS electromagnetic field simulation software (approved U. of Alberta researchers only).
  libLAS 1.7.0 Hermes/Nestor LiDAR data manipulation tool.
  LSA (R package) Breezy Latent semantic analysis.
  M_Map (MATLAB toolbox) Grex Mapping package for MATLAB (U. of Manitoba researchers only).
  maptools 0.8-20 (R package) Breezy Tools for reading and handling spatial objects.
  NLTK (Python module) Breezy Natural Language Toolkit.
   PROJ.4 Breezy
Cartographic projections library.
  raster (R package) Breezy Geographic data analysis and modeling.

 

Updates for mid-June to mid-September 2012

Category Software package and version System Remarks
Bioinformatics
ABySS 1.34
Bugaboo
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
 
ALLPATHS-LG 42069
Hungabee
Sequence assembly package.
  BEDTools 2.16.2 Bugaboo Utilities for comparing genomic features.
  Bowtie 2-2.0.0-beta7 Bugaboo, Hungabee Aligns short DNA sequences to large genomes.
  Coral 1.4 Breezy Error correction software for gene sequence analysis.
  Cufflinks 2.0.2 Bugaboo Assembles and analyzes transcripts from aligned RNA-Seq reads.
  MrBayes 3.2.1 Bugaboo Phylogenetic analysis
  SAMtools 0.1.18 Bugaboo Utilities for manipulating SAM (Sequence Alignment/Map)-format files.
  Trans-ABYSS 1.3.2 Bugaboo Software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.
  Trinity r2012-06-08 Hungabee De novo reconstruction of transcriptomes from RNA-seq data.
  wgs-assembler 7.0 Breezy Celera whole-genome shotgun sequence assembler and conversion utilities.
       
Chemistry/Biochemistry ABINIT 6.12.3
Bugaboo Electronic structure calculations.
 
Amber 12 Grex, Lattice/Parallel Molecular calculations, including molecular dynamics.
  APBS (Adaptive Poisson-Boltzmann Solver)
Grex Software for modelling biomolecular solvation.
 
NAMD 2.9 Bugaboo Molecular dynamics simulations of large biomolecular systems.
  NWCHem 6.1.1 Grex, Hungabee Large-scale molecular simulations.
  PDB2PQR 1.8
Grex
Prepare structures for continuum electrostatics calculations.
  SIESTA 3.1, tranSIESTA Orcinus Electronic structure and ab initio molecular dynamics
       
Graphics gnuplot 4.6p0
Bugaboo, Lattice/Parallel
General charting.
 
matplotlib 1.1.0
Lattice/Parallel
Charting for Python.
       
Programming Blitz++ 0.9 Bugaboo C++ template library for dense vectors and multi-dimensional arrays.
  Boost 1.51.0 Bugaboo Eclectic C++ utility library.
  Eigen 3.1.1 Bugaboo C++ template library supporting linear algebra.
  git 1.7.4.1 Bugaboo Version control system.
  GNU Data Language (GDL) Grex IDL substitute.
  HDF 5 1.8.9 Grex Hierarchical Data Format.
  Intel compilers 12.1.5.339 Grex C, C++ and Fortran compilers.
  Mercurial 2.3 Bugaboo Source code management software.
  NetCDF 4.1.3 Grex Network Common Data Format.
  netcdf4-python 1.0
Lattice/Parallel NetCDF 4 and HDF 5 support for Python.
  Octave 3.6.2 Grex, Bugaboo MATLAB-like programminga and visualization environment.
  R 2.15.1 Bugaboo Language and environment for statistical computing and graphics.
       
Other ABAQUS 6.12 Jasper Finite element modelling program.  (U of A researchers only).
  aria2c 1.15.1 Bugaboo File transfer utility.
  Midnight Commander Bugaboo, Hungabee, Jasper File manager and editor.
 
FileZilla 3.3.1 Grex File transfer client supporting ftpes.
  WRF-Chem 3.4 and WRF EMS 3.2.1.5.34.beta Bugaboo

Weather research and forecasting.

 

Updates for mid-April to mid-June 2012

Category Software package and version System Remarks
Bioinformatics
ABySS 1.3.2 Hungabee, Jasper De novo, parallel, paired-end sequence assembler.
 
ALLPATHS-LG 40691
Hungabee, Jasper
Sequence assembly package.
  BEAGLE (beagle-lib) 1.1.0 Lattice/Parallel A library to calculate phylogenetic likelihoods.
  BEAST Lattice/Parallel Bayesian evolutionary analysis sampling trees (BEAST) - evolutionary inference from molecular sequence.  Version on Parallel supports GPU acceleration through BEAGLE.
  hg 18 and hg 19 Bugaboo Human reference genomes.
  RSEM Bugaboo RNA-Seq gene transcript quantification (estimating gene and isoform expression levels) without a reference genome.
  Velvet 1.2.03 Hungabee Genomic sequence assembly from short-read data.
  Trans-ABYSS 1.3.2 Bugaboo Software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.
  Trinity r2012-05-18 Hungabee De novo reconstruction of transcriptomes from RNA-seq data.
       
Chemistry/Biochemistry ABINIT 6.12.3
Hungabee, Jasper DFT electronic structure and molecular dynamics.
  CPMD 3.15.3 Hungabee, Jasper Ab initio molecular dynamics.
  GAMESS 20110818 Checkers, Jasper General ab initio quantum chemistry package.
  Gaussian 09 B1 Hungabee, Jasper Semi-empirical and ab initio molecular orbital calculations.  U of Alberta researchers only.
  GROMACS 4.5.5, 4.6
Lattice/Parallel (4.6), Hungabee (4.5.5), Jasper (4.5.5)
Molecular dynamics. Lattice/Parallel versions features GPU acceleration.
  NWChem 6.1 Hungabee, Jasper Large scale molecular simulations.
  ORCA 2.9.1 Jasper Ab initio, DFT and semiempirical SCF-MO package.
       
Graphics ParaView 3.14.1
Lattice/Parallel General purpose data visualization software (front-end for VTK).
  VMD 1.9.1 Bugaboo Minor bug fix upgrade for this molecular visualization software.
       
Programming Blitz++ 0.9 Breezy C++ template library for dense vectors and multi-dimensional arrays.
  Boost 1.48.0 Bugaboo C++ utility library.
  dbus 1.4.20 Bugaboo Inter-application communications library.
  HDF 5 1.8.8 Orcinus Hierarchical Data Format (serial version without szip).
  ncdr4 1.6.1 and RNetCDF 1.5.3-1 Bugaboo NetCDF file format support for R.
  RStudio 0.96.122 Bugaboo Integrated development environment for R.
  Qt Bugaboo User interface development framework.
 
tvmet 1.7.2 (with CppUnit 1.12.1)
Breezy
Tiny Vector Matrix using Expression Templates, with CppUnit testing software.
       
Other Climate Data Operators (CDO) Grex Numerical weather and climate data analysis and file conversion.
  MATLAB 2012a
Bugaboo
Latest MATLAB (for SFU researchers only).
  micEcon 0.6-6 Bugaboo, Hermes/Nestor Microeconomic Analysis and Modelling - for R
  screen Bugaboo Terminal session manager.
  WRF and WPS Bugaboo Weather research and forecasting.

 

Updates for mid-March to mid-April 2012

Category Software package and version System Remarks
Bioinformatics
ALLPATHS-LG 41301
Breezy
Sequence assembly package
       
Chemistry/Biochemistry BigDFT 1.6.0 Grex Wavelet-based DFT code for nano-scale materials science
 
LAMMPS 120321
Bugaboo
Classical molecular dynamics simulator
  NWChem 6.1 Grex Large-scale molecular simulation package
  OpenMX 3.6p1 with ADPACK 2.2
Grex DFT code for nano-scale materials science
  ORCA 2.9.0
Lattice/Parallel Ab initio, DFT and semi-empirical SCF-MO package
       
Graphics Grace 5.1.22
Orcinus Charting
       
Programming Cheetah 2.4.4 Grex Python-based software to generate text/code from templates
  Cmake 2.8.7 Orcinus Software build system tool
  Git 1.7.9.4 Orcinus Version control system
  Intel 12.1 compilers
Grex C, C++ and Fortran compilers
  MPI (Message Passing Interface) Grex Intel MPI 4.0.3.008  and MVAPICH 1.2rc1
  PDFLib-Lite Lattice/Parallel Library for incorporating PDF file format support in other programs.
  Perl XML::Simple Glacier, Bugaboo Perl interface to simplify XML parsing
  pyparsing
Breezy, Grex
Grammar definition and string parsing for Python
       
Other Runtime files v716 for MATLAB R2011b
Checkers
Run MATLAB code compiled with R2011b mcc

Updates for February and early March 2012

Category Software package and version System Remarks
System Various as shown at right
Bugaboo/Snowpatch
Operating system update including various components of the Linux distribution, TORQUE (2.5.10), Intel MPI (4.0.3.008)  and Intel compilers (12.1.3)
       
Bioinformatics ABySS 1.3.2 and Trans-ABySS 1.2.0
Bugaboo/Snowpatch Sequence assembly.
  Biopython Breezy A suite of Python-based tools for bioinformatics.
  MEME Suite 4.8.1 Bugaboo/Snowpatch Motif (pattern)-based sequence analysis tools
       
Chemistry/Biochemistry
CP2K 2.2
Bugaboo/Snowpatch
Ab initio molecular dynamics package
  ORCA 2.9.0
Grex Ab initio, DFT and semi-empirical SCF-MO package
  Quantum ESPRESSO 4.3.2 Orcinus Suite of programs for electronic structure and materials modelling
  VASP 5.2 Grex Ab initio quantum mechanical molecular dynamics package (licensed users only)
       
Programming PDFLib-Lite Breezy Library for incorporating PDF file format support in other programs.
  Perl Math/Round.pm Grex Perl extension for rounding numbers
  Python MySQLdb
Bugaboo/Snowpatch MySQL support in Python
       
Miscellaneous Networkx 1.6
Python module
Breezy, Grex
Python-based software for creating and manipulating graphs (networks).

Updates for December 2011 and January 2012

Category Software package and version System Remarks
System CentOS 5.7
Breezy
Operating system update
       
Bioinformatics ALLPATHS-LG 39750 Breezy Sequence assembly.
  BEAST 1.6.2 Bugaboo/Snowpatch Bayesian Evolutionary Analysis by Sampling Trees.
  BEAGLE 1.1 Bugaboo/Snowpatch Broad-platform Evolutionary Analysis General Likelihood Evaluator - library for speeding up phylogenetic calculations such as in BEAST.
  Blast+ Bugaboo/Snowpatch
Threaded version; call with blastx.
  MIRA 3.4.0.1 Breezy Sequence assembly.
  Picard tools 1.57 Breezy Java-based tools for manipulating binary sequence alignment map (BAM) files.
  RITA 1.0.0 Bugaboo/Snowpatch Sequence analysis - Rapid identification of taxonomic assignments (RITA) - rank-specific option only.
  Velvet 1.2.01
Grex Genomic sequence assembly from short-read data.
       
Chemistry/Biochemistry
Chaste 3.0
Bugaboo/Snowpatch
Cancer Heart and Soft Tissue Environment - electophysiology and tissue modelling 
  DFTB Slater-Koster files Lattice Force field files for use with various programs, such as AMBER, ADF, etc.
 
DL_POLY4 4.02 Checkers A suite of programs for molecular dynamics.
  GAMESS Grex A general ab initio quantum chemistry package. 
  OpenBabel 2.3.1 Grex Toolkit for conversion between file formats of various electronic structure/molecular modeling codes.
  SIESTA 3.1 Grex An electronic structure and ab-initio quantum-mechanical molecular dynamics package.
       
Programming Boost 1.48.0 Breezy, Lattice C++ libraries
  GCC 4.4.4 Breezy GNU C, C++ and Fortran compilers; call with gcc44, g++44, gfortran44
  Git 1.7.3.5 Lattice Use: module load git
  Intel Compilers 12.1, MKL 1.3
Checkers
Intel C, C++ and Fortran compilers and Math Kernel Library
  Intel MPI Grex Alternative to Open MPI (module load intel/impi/4.0.1.007)
  mpi4py 1.2.2 Lattice MPI for Python; requires module load python
  Numpy 1.6.1
Checkers
Python scientific add-on library
  Ruby 1.93p0, libyaml 0.1.4 Lattice Scripting language
       
Data Visualization
Paraview 3.12.0
Bugaboo/Snowpatch General purpose visualization

VMD 1.9
Grex
Molecular visualization
       
Miscellaneous PETSc 3.2-p5 Bugaboo/Snowpatch
Toolkit for parallel solution of differential equations.

 


Updated 2013-04-08.