HPC Software and Programming Tools

The following scientific computing software is available on our HPC cluster systems under directory /share1/

  1. Licensed/Open Source Software Applications
  2. Utilities and Libraries

Licensed/Open Source Software Applications

Software/Applications HPC2015 HPC2021
Bioinformatics and Genomics
Bowtie2 2.2.9 2.4.2
CD-HIT 4.6.8 4.8.1
GARLI 2.1  
GATK 4.0.8.1 4.1.8.1
HyPhy 2.2.7  
PHYML 2.4.5  
MEME 4.11.2 4.11.2
MEGAHIT 1.1.1 1.1.4
BLAST mpiBLAST and other BLAST  
SAMtools 1.3.1, 1.4* 1.12
Chemistry and Molecular Modeling
ADF 2014 2019
AMBER 16, 18, 20 20
CFOUR 1.0  
CP2K 6.1  
CPMD 4.1 4.3
Gaussian g09, g16 g09, g16
GAMESS 20141205R1, 20170420R1, 20180214R1*  
GROMACS 5.1.1, 2018.2* 2020.5
LAMMPS 16 Feb 2016 29 Sep 2021
NAMD 2.12  
NWChem 6.6 7.0.2
ORCA 3.0.3, 4.0.0, 4.2.0* 5.0.0
SIESTA 3.2 4.0.1
Physics and Materials Science
Abaqus 6.13-4, 6.14-1, 2016, 2017, 2018* 2020, 2021*
ParaDiS 2.3.5.1  
Quantum ESPRESSO 6.1, 6.3* 6.7
VASP 4.6, 5.3, 5.4.1, 5.4.4, 6.1.2 5.4.4, 6.1.2, 6.2.0
Mathematics and Statistics
MATLAB R2015a, R2015b, R2016b, R2017b, R2018b* R2021b
Octave 3.4.3, 4.0.0*  
R 3.2.2, 3.2.5, 3.4.1, 3.5.1, 3.6.1, 4.0.1* 4.0.4
STATA   16.1, 17.0
Data Analysis and Machine Learning
Anaconda Available Available
Caffe 1.0.0 Available
TensorFlow 2.3.1 Available
Theano / Aesara 1.0.2 Available

* Several versions are installed; listed is the default version.

Utilities and Libraries

Utilities HPC2015 HPC2021
Compilers and programming languages
GNU Compiler 4.4.7*, 4.9.3, 5.2.0, 6.3.0, 8.2.0 8.3.1*, 10.2.0
Intel Compiler 2013, 2015, 2016, 2017, 2018*, 2019 2019,2020,2021*
PGI Compiler 15.7, 16.10, 17.7, 18.5, 19.7*  
CUDA 7.0, 7.5, 8.0, 9.0, 10.0* 11.2
Python 2.6.6*, 2.7.11, 3.6.3, 3.7.3, 3.8.3 3.9.2, 3.9.7*
Julia 0.5.2, 0.6.2*, 0.7.0, 1.0.2, 1.3.1 1.6.1*
Ruby 2.4 2.7.1, 3.0.2
Parallel Libraries
MPICH Available 3.4.2
MVAPICH Available  
Intel MPI 4.1.3, 5.0.3, 5.1.1, 5.1.3, 2017.7, 2018.4* 2019, 2020,2021*
Open MPI Available 4.1.0
MPI for Python (mpi4py) 2.0.0  
Math Libraries
ACML Available  
FFTW 3.3.4, 3.3.7 3.3.9
GMP 6.1.0  
GSL 2.1, 2.5 2.7
IMSL fnl710, cnl860  
Intel MKL Available Available
BLAS, LAPACK and ScaLAPACK Available Available
NAG NPL6A62NA, FSL6I26DC, FSL6I24DD, FSLM626DC,
CSL6I26DD, CSLM626DD, CLL6I262C, CLL6I262D, MBL6I25DN
 
Programming Utilities
HDF5 1.8.16, 1.10.1*, 1.10.5 1.10.7
MPC 1.0.3  
MPFR 3.1.3  
NETCDF 4.3.3.1  
Visualization and Plotting
Gnuplot 4.2.6  
Grace/Xmgr 5.1.25  
GrADS 2.0.2  
Molden 5.4  
ParaView 5.2.0 5.9.0
VMD 1.9.2  
VisIt 2.12.1  

* Several versions are installed; listed is the default version.