Available Software

Available Software

The site provides the list of software applications available at HPC System. To get more information on how to use the software please refer to Software Guide.

Important Notes

  • (Imp) Some of the Software may only be available in SLURM cluster (e.g. hpc1/hpc2). For the SLURM cluster (hpc1/hpc2), we currently don't have SLURM script for individual Software. Please visit HPC transitioning to SLURM GUIDE. This is the work in progress.
  • To get the versions of the software installed in HPC, use the command "module avail". To check the dependency modules such as cmake, boost etc, load the depends module first "module load depends"
  • The path of the executable and libraries of the <software> can be obtained using the comamd "module display <software>"
  • The default binaries/executable (compiler or software) are available at /usr/bin and /usr/local/bin
  • The default libraries are available at /usr/lib, /usr/lib64, /usr/local/lib, /usr/local/lib64
  • In case of specific software, you can install it on your home directory. Check the Software Installation GuideIf it is a generic software and you are having trouble installing it after following the instructions at Software Installation Guide, please contact us at 
  • If the Software available in HPC is the licensed one (see Software Guide), you need to explicitly request for it via email 
  • To maintain the licensed software for you, you would need to contact the vendor and find out about the software and its feasibility on the HPC (license model and control). We would ask that your PI would get the HPC membership (see  HPC access policy).

Software List


 Browser/ PDF reader
   
Firefox browser
Evince pdf/document reader


 
Text File Editor
Gvim/ VI editor
Emacs
Gedit
Nano
 
Compiler suites (C, C++, Fortran)
Gnu compilers 
Intel compilers 
PGI compilers 
Java
Python
Code Synthesis XSD
 
MPI Versions
openmpi (compiled with gcc)
openmpi-intel (compiled with intel) -> this is the default module
mpich (compiled with gcc)
mpich-intel (compiled with intel)
OpenMP (gnu, intel, pgi)

Data Bases:
SqLite
 
Applications

NAMD
Gromacs
Mathematica(need to install math font on local machines)
Matlab 
R statistical package
Charmm/qchem 
ABINIT
CPMD
Rosetta
Schrodinger
LAMMPS (parallel)
Gaussian 
Neuron
Qhull
Sundials
cmake
qt 
EMAN2
PHYLIP
Desmond
NumPy
OpenMMPreview
Torch 
PEDSYS
Parser
Gadgetron
Siesta
Relion
Mitoseek
Tophat
Plink
SPIDER
Mothur
MotionCorr
Xqilla
GitHub
Genetorrent
Eigensoft
King
OpenFoam
charm++
Merlin
BSoft
BWA
Perl
SHAPEIT
GIT
Mercurial
BidDFT
pigz
atompaw
LS-DYNA
cufflinks
Julia
Caffe
FLACS


Libraries


fftw 
hdf5 
mkl
gnu gsl 
ATLAS  (yum install atlas-devel)
BLAS
BLACS
LAPACK
ScaLAPACK
CULA
libxml2
libxslt
Global Arrays
CLHEP
ffmpeg
MAGMA
VORO++
APR/APR-util
MPFR
ncurses
GStreamer
OpenCV
libxc

Python Libraries:
numpy, PyQt4, matplotlib, sip, OpenGL
 
Visualization Software
Gnuplot
ParaView
Visit
VMD

vtk
InterViews (IV)
ImageMagick
Circos
GraphicsMagick

 Debugger

Gnu gdb
Intel idb

GPU Applications

CUDA

JACKET
MotionCorr