Henry2 has a mixture of staff maintained software and user maintained software. The list of supported software below is currently under construction.
The following tables show the status of software that has been requested and/or installed on HPC systems for general use. Many of the applications require group membership for access. If you encounter a permission denied error for one of the packages, please contact oit_hpc@help.ncsu.edu and, license permitting, we will add you to the list of users. For ANSYS and ANSYS CFD (previously CFX), please request access and agree to the licensing terms using the button provided below. For Gaussian, a license acknowledgement needs to be signed and returned to obtain access.
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 | 3.12.3 | module load 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 | 2.7.153.6.5 | module load python2 module load python3 |
Interpreted programming language | View |
| R | 3.5.1 | module load R | Open source statistics package | View |
| SAS | 9.4 | module load sas | Commercial statistical analysis package | View |
| Tecplot 360 | 2018 R2 | module load tecplot | Commerial application for CFD visualization and analysis | View |
| VMD | 1.9.3 | module load vmd | Software package for visualizing molecules | View |
These libraries have been approved as HPC Maintained Applications - the library review is NOT complete; all other libraries are currently under review.
| Name | Default Version | Load Environment | Description | How to Use |
|---|---|---|---|---|
| CUDA | 9.0 | module load cuda | NVIDIA library for using GPUs | View |
These applications are under review for adding to either the Officially Supported or Obselete lists.
| Name | Latest Installed Version | Location | Notes |
|---|---|---|---|
| Abinit | 7.10.2 | /usr/local/abinit | An ab initio quantum chemistry package |
| BAMTools | 2.30 | /usr/local/apps/bam | Manipulate BAM (genetic sequence) files |
| Bowtie2 | 2.2.5 | /usr/local/bowtie2 | Fast aligner for short DNA sequences |
| CHARMM | 35b3 | /usr/local/apps/c35b3 | A molecular dynamics program |
| CPLEX | 12.6.3 | /usr/local/apps/cplex | Linear, Mixed-integer and Quadratic solvers |
| Cufflinks | 2.2.1 | /usr/local/apps/cufflinks | Analysis of RNA-Seq samples |
| EggLib | 2.1.9 | /usr/local/apps/egglib | Evolutionary genetics and genomics |
| Elmer | 8.0 | /usr/local/apps/elmer | Open Source Finite Element Software for Multiphysics Problems |
| ESPRESSO | 5.4.0 | /usr/local/apps/espresso | Electronic-structure calculations and materials modeling package (including PWscf, PHONON, CP90, FPMD, Wannier) |
| Falcon | 0.5 | /usr/local/apps/falcon | Hierarchical Sequencing |
| FastQC | 0.10.1 | /usr/local/apps/FastQC | Quality control for high throughput sequence data |
| fastStructure | 1.0-4 | /usr/local/apps/fastStructure | An algorithm for inferring population structure from large SNP genotype data |
| FASTX-Toolkit | 0.0.14 | /usr/local/apps/fastx_toolkit | FASTQ/A short-reads pre-processing |
| Gamess | 2013 | /usr/local/apps/GAMESS | ab initio quantum chemistry |
| Grass GIS | 7.2.0 | /usr/local/apps/grass | Open Source Geographical Information System |
| GDB | x86_64-redhat-linux-gnu | System installed | GDB Debugger |
| GenomeTools | 1.5.5 | /usr/local/apps/genometools | Genome informatics tools |
| GROMACS | 5.1.1 | /usr/local/apps/gromacs | Molecular dynamics of biochemicals and polymers |
| InterProScan | 5.3-46.0 | /usr/local/apps/interproscan | Scans protein and nucleic sequences for signatures |
| KmerGenie | 2014 | /usr/local/apps/kmergenie | Aids in de novo genome assembly |
| MAPS | 4.1.0 | /usr/local/apps/scienomics | Software package for material modeling, simulation and analysis |
| Mathematica | 11.2 | /usr/local/apps/mathematica | Commercial language for symbolic computations |
| mrFAST | 2.6.0.1 | /usr/local/apps/mrfast | Micro read fast alignment search tool |
| MOOSE | /usr/local/moose | Finite-element Multiphysics DOE parallel package | |
| NAMD Molecular Dynamics | 2.10 | /usr/local/apps/NAMD | |
| Oases | 0.2.08 | /usr/local/apps/oases | De novo transcriptome assembler for very short reads |
| Octave | 3.8.2 | System installed | Interpreted language for matrix computations |
| OpenFOAM | v1706 | /usr/local/apps/OpenFOAM | Open Source Finite Element Software |
| PETSc | 3.8.4 | /usr/local/apps/PETSc | DOE software package to enable parallel computations |
| PLINK | 1.07 | /usr/local/apps/plink | Whole genome association analysis |
| SageMath | 7.4 | /usr/local/apps/sage | Sage variable precision and symbolic computations |
| SAMtools | 0.1.7.a | /usr/local/apps/samtools | SAM (Sequence Alignment/Map) tools |
| SeaDAS | 7.5 | /usr/local/apps/seadas-7.5 | For the processing, display, analysis, and quality control of ocean color data or satellite-based earth science data analyses |
| Siesta | 4.0.1 | /usr/local/apps/siesta | Open Source Pseudo Potential Package |
| SOAPdenovo2 | 2.04 | /usr/local/apps/SOAPdenovo2 | short-read method for de novo assembly of genomes |
| Stata | UNCG Users only | Commercial statistical analysis package |
|
| Tophat | 2.0.14 | /usr/local/apps/tophat | Splice junction mapper for RNA-Seq reads |
| TotalView | 8.4.1-4 | /usr/local/apps/totalview | Parallel debugger with GUI interface |
| VariationHunter | 0.04 | /usr/local/apps/variationhunter | Find individual genomic structural variation |
| Velvet | 1.2.10 | /usr/local/apps/velvet | de novo genomic assembler |
These libraries are under review for adding to either the Officially Supported or Obselete lists.
| Name | Latest Installed Version | Location or Load Environment |
Notes |
|---|---|---|---|
| ACML | 4.3.0 | /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. |
| BLAS | Part of the AMD and mkl libraries | ||
| fftw | 3.3.4 | /usr/local/apps/fftw | Fast Fourier Transforms -- includes parallel versions |
| hdf | 1.8.16 | /usr/local/apps/hdf-centos7 | |
| Intel MKL | 2017 | module load mkl | Intel math kernel libraries |
| LAPACK | Part of the AMD and mkl libraries | ||
| NetCDF | 4.4.0 | /usr/local/apps/netcdf-centos7 | |
| ScaLAPACK | 2017 | module load mkl | Distributed memory dense dense linear algebra |
| Trilinos | Parallel numeric library from Sandia |