High Performance Computing

Officially Supported Applications

These applications have been approved as HPC Maintained Applications - the application review is NOT complete; all other applications are currently under review.

Name Default Version Load Environment Description How to Use
Abaqus 2018 module load abaqus Commercial Finite Element Package View
Amber Amber18 module load amber Parallel Molecular Dynamics View
ANSYS
    Commercial Finite Element Package View
ANSYS CFD
    Commercial Fluid Dynamics Package View
cmake     Build, test, and package software View
Gaussian
    Commercial quantum chemistry code View
Java 1.8.0 module load java Programming language View
Julia 1.0.0 module load julia Efficient language for matrix computations View
LAMMPS Molecular dynamics simulator View
MAKER 2.31.10 module load maker Genome annotation pipeline View
MATLAB R2018b module load matlab Commercial language for matrix computations
View
Perl 5.28.0 [none required] General Purpose Scripting Language
Python 2.7.15
3.6.5
module load python2
module load python3
Interpreted programming language View
R 3.5.1 module load R/gcc_4.8.5_R-3.5.1 Open Source Statistics Package
View
SAS 9.4 module load sas Commercial Statistical Analysis Package View
VMD 1.9.3 module load vmd A Package for visualizing molecules View

Other Applications

These applications are under review for adding to either the Officially Supported or Obselete lists.

Name Obsolete Status Henry2 cluster Notes
Abinit   Installed
7.2.1
An ab initio quantum chemistry package
BAMTools   Installed
2.30
Manipulate BAM (genetic sequence) files
Bowtie2   Installed
2.2.5
Fast aligner for short DNA sequences
CHARMM Installed
c35b3
  A molecular dynamics program
CPLEX Installed
11.2, 12.1
Installed
12.6.3
Linear, Mixed-integer and Quadratic solvers
http://www.ilog.com/products/cplex/
CPMD  Installed
3.13.2
Ab initio molecular dynamics
CUDA-GPU Installed
6.0,7.5,9.0
  NVIDIA library for using GPUs
Cufflinks   Installed
2.2.1
Analysis of RNA-Seq samples
Cutadapt Installed
1.0.0
  Remove adapter sequences from high-throughput data
DL_POLY_4   Installed
4.07
Molecular dynamics simulation
http://www.cse.clrc.ac.uk/msi/software/DL_POLY/
EggLib   Installed
2.1.9
Evolutionary genetics and genomics
Elmer  Installed
8.0
Open Source Finite Element Software for Multiphysics Problems
http://www.csc.fi/english/pages/elmer
ESPRESSO (qe)   Installed
6.2.0,5.4.0
Electronic-structure calculations and materials modeling package (including PWscf, PHONON, CP90, FPMD, Wannier)
Falcon Installed   Hierarchical Sequencing
FastQC Installed
0.10.1
  Quality control for high throughput sequence data
fastStructure   Installed
1.0-4
An algorithm for inferring population structure from large SNP genotype data
FASTX-Toolkit   Installed
0.0.14
FASTQ/A short-reads pre-processing
Gamess Installed
18Apr20013
  ab initio quantum chemistry
http://www.msg.ameslab.gov/GAMESS/
Grass GIS   Installed
grass-7.2.0
Geographical Information System
GDB   Installed

GDB Debugger
GenomeTools   Installed
1.5.5
Genome informatics tools
GROMACS
  Installed
5.1.1
Molecular dynamics
biochemicals and polymers
InterProScan
Installed
5.3-46.0
scans protein and nucleic sequences for signatures
KmerGenie
Installed
19Mar14
aids in de novo genome assembly
MAPS (by SCIENOMICS) Installed
4.1.0
MAPS is a comprehensive software package for material modeling, simulation and analysis. It is GUI driven and is often used for quickly and easily building material models (with options of using physics that is effective for different scale ranges), running simulations, and analyzing the results. It is commonly used to facilitate LAMMPS molecular dynamics workflows.
Mathematica Installed
11.2
Commercial language for symbolic computations
Mobyle Workbench   Updated Feb. 2014 A portal with many genetic analysis programs
mrFAST   Installed
2.6.0.1
Micro read fast alignment search tool
MOOSEInstalled Nov. 1, 2018 Finite-element Multiphysics
DOE parallel package
Idea to Solution in Hours?
NAMD Molecular Dynamics  versions 2.7 and 2.9 http://www.ks.uiuc.edu/Research/namd/
NCAR Graphics 6.1.2 Installed Visualization of scientific data
NCAR Graphics Home Page
NCBI Toolbox Installed Includes BLAST, SEQUIN, FA2HTGS, ENTREZ, and CN3D
NCBI Toolbox Webpage Link
NWChem   Scalable parallel computational chemistry
www.emsl.pnl.gov/docs/nwchem/doc/user/index.html
Oases   Installed
0.2.06
De novo transcriptome assembler for very short reads
Octave Installed
3.6.3
Interpreted language for matrix computations
OpenFOAM Installed
2.2.2
  Open Source Finite Element Software
http://www.opencfd.co.uk/openfoam/doc/tutorials.html
PETSc DOE software
package to enable parallel computations
Installed
3.8.0
Portable, Extensible, Toolkit for Scientific Computation
PLINK   Installed
1.07
Whole genome association analysis
Qiime Centos7
under python2.7.9

SageMath   Installed
7.4
Sage variable precision and symbolic computations
SAMtools   Installed
1.7a
SAM (Sequence Alignment/Map) tools
SCIENOMICS - MAPS Installed
4.1.0
See MAPS above
SeaDAS (NASA SeaDAS) Installed
7.5
SeaDAS is a comprehensive software package for the processing, display, analysis, and quality control of ocean color data or satellite-based earth science data analyses
Siesta Installed
3.2,4.0.1
Open Source Pseudo Potential Package
SOAPdenovo2   240 short-read method for de novo assembly of genomes
STACKS Installed
1.08
  Building loci from short-read sequences
Stata Installed (UNCG Users only) Commercial statistical analysis package
Tophat   Installed
2.0.14
Splice junction mapper for RNA-Seq reads
TotalView Installed
8.4.1-4
https://computing.llnl.gov/tutorials/totalview/
Another full-featured parallel debugger
is the pgdbg debugger for codes compiled
with the Portland Group compilers.
VariationHunter   Installed
0.04
Find individual genomic structural variation
Velvet   Installed
1.2.10
de novo genomic assembler

Libraries

Libraries will also being sorted as Officially Supported or Obselete. The following table shows both.

Name Status
Out of Date
Status
henry2
cluster
Notes
ACML Installed
3.6.0
3.6.1
4.3.0
subdirectories of /usr/local/apps/acml
Numerical libraries provided by AMD (64 bit only). Versions for pgi, intel, and gnu compilers. Separate directories for 64 bit integer and multithreaded versions.
http://developer.amd.com/cpu/Libraries/acml/Pages/default.aspx
BLAS   Installed Part of the AMD and mkl libraries
fftw Installed
2.1.5
3.3.4
subdirectories of /usr/local/apps/fftw
Fast Fourier Transforms -- includes parallel versions
hdf   Installed
hdf5-1.8.14
hdf5-1.8.16
subdirectories of
/usr/local/apps/hdf-centos7
Intel MKL   Installed
2013,2016
mklXXX subdirectories of /usr/local/apps/intel
https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor
LAPACK Installed Part of the AMD and mkl libraries
NetCDF Installed
4.3.3
4.4.0
subdirectories of
/usr/local/apps/netcdf-centos7
ScaLAPACK   Installed
MKL 2013,2016
Distributed memory dense dense linear algebra
www.netlib.org/scalapack/
Trilinos   Installed http://software.sandia.gov/trilinos/
Parallel numeric library from Sandia
Other packages, likely unsupported, may be found in the subdirectories of /usr/local/apps. Last modified: December 05 2018 10:33:12.