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Supported software

To see all available packages on Hoffman2 cluster, issue the command:

module available
When you identify the one you want to load into your environment, issue the command:

module load name_of_package
For example, if you want to use package “gsl”, issue the command:

module load gsl
to load “gsl” into your environment.

For more details about using modules to modify your environment, see the modules page.

The following is a (partial) list of some of the popular packages.

Compilers

Intel and GNU compilers

Language and Debuggers

  • ActivePerl
  • ActiveTcl
  • ddd
  • GDC
  • Java
  • mno
  • POP-c++
  • Python
  • Ruby
  • Tcl/tk
  • valgrind

Integrated development environments

  • Eclipse
  • Netbeans

Programming libraries

  • arpack
  • atlas
  • blas
  • boost c++
  • cernlib
  • clhelp
  • cuda
  • fftw
  • GNU gsl
  • hdf
  • hdf5
  • jpeg
  • lapack
  • Intel MKL
  • NetCDF
  • OpenMotif
  • PETSc
  • Scalapack
  • Trilinos

Application packages

Bioinfomation

  • affymetrix power tools (apt)
  • annovar
  • bamtools
  • bedtools
  • bowtie
  • bwa
  • cufflinks
  • galaxy
  • gatk
  • impute
  • inspect
  • MAQ Mapping Assembly
  • Picard Tools
  • Plink
  • SAMtools sequence Alignment/Map
  • SOLAR sequential oligogenic linkage analysis
  • TopHat
  • Treemix
  • Vegas

Chemistry

  • amber 12
  • castep
  • cp2k
  • cpmd
  • quantum
  • gamess
  • gaussian09
  • grace
  • gromacs
  • lammps
  • mopac
  • namd
  • nwchem
  • OMSSA Open Mass Spectrometry
  • OpenBabel
  • Qchem
  • RasMol
  • RosettaMatch
  • XMD

Engineering and Math

  • Abaqus
  • COMSOL
  • netcdf
  • Octave
  • OpenSees
  • opensees162

Visualization

  • atomeye 3
  • gasssview
  • gnuplot
  • GrADS Grid Analysis and Display System
  • Graphiviz
  • IDL
  • ImageMagick
  • Jmol
  • Maple
  • Mathematica
  • Matlab
  • Molden
  • NCL and PyNCL
  • OpenDX
  • Paraview
  • POV-ray
  • R
  • Stata
  • tecplot360
  • VMD
  • VTK
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