Software
The following tables show the status of software that has been requested and/or installed on HPC systems for general use. Tables are divided between Compilers, Applications, and Libraries. 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 at help dot ncsu dot edu" and we will (if the software license permits), add you to the list of users. For ANSYS and ANSYS CFD (previously CFX), please request access using the button provided below (you have to agree to some software licensing terms). For Gaussian a license acknowledgement needs to be signed and returned to obtain access.
Compilers
| Name | Status henry2 cluster |
Notes | |
|---|---|---|---|
| Intel | 2013, 2016 | Intel Linux Compilers Web Site | |
| Intel MPI | Installed openmpi-2013,2016 mvapich2-2016 intelmpi2016 |
||
| Portland Group MPI |
Installed 14.3,15.1 |
http://www.pgroup.com/ | |
| Portland Group |
OpenMPI 14.3 |
http://www.pgroup.com/ |
The following list of applications is not complete. If you look in subdirectories of /usr/local/apps, you'll see many other packages. If you need an application you think would be appropriate for general use, or a more up-to-date version of an existing package, please send an e-mail to "oit_help at help dot ncsu dot edu".
Applications
| Name | Obsolete | Status henry2 cluster | Notes |
|---|---|---|---|
| Abinit | Installed 7.2.1 |
An ab initio quantum chemistry package | |
| ABAQUS | Installed 6.16 |
http://www.abaqus.com/ Commercial Finite Element Package |
|
| AMBER | Installed 12 14 |
http://amber.scripps.edu/ Parallel Molecular Dynamics |
|
| ANSYS |
Installed 170 |
http://www.ansys.com/ Commercial Finite Elment Package |
|
| ANSYS CFX |
Installed 170 |
http://www.ansys.com/cfx Commercial Fluid Dyaamics Package |
|
| BAMTools | Installed 2.30 |
Manipulate BAM (genetic sequence) files | |
| bioperl | Installed 1.6.1 |
Perl modules for DNA sequence analysis | |
| mpiBLAST | Installed | A parallel version of the NCBI program BLAST | |
| 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 |
||
| CUDA-GPU | Installed 6.0,7.5 |
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 Multiphysical 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) | |
| 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/ |
|
| Gaussian |
Installed g09 |
Commerical quantum chemistry code http://gaussian.com |
|
| Grass GIS | Installed grass-7.2.0 |
Geographical Information System | |
| 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 | |
| Java | Installed | See the Howto for access to some newer versions |
|
| Julia | Installed 0.5.2 |
Efficient language for matrix computations |
|
| KmerGenie | Installed 19Mar14 |
aids in de novo genome assembly | |
| LAMMPS | Installed 9Dec14 5Mar13 |
Molecular dynamics | |
| MAKER | Installed 2.10, 2.31 |
Genome annotation pipeline | |
| Mathematica | Installed 11.2 |
Commercial language for symbolic computations |
|
| Matlab | Installed 2014a,2016a,2017a |
Commercial language for matrix computations |
|
| MITE-Hunter | Installed Version of November 2011 |
Find transposable elements in DNA datasets | |
| Mobyle Workbench | Updated Feb. 2014 | A portal with many genetic analysis programs |
|
| Mr Bayes | Installed 3.1.1 3.1.2 |
Construct evolutionary trees from genetic sequences http://mrbayes.csit.fsu.edu |
|
| mrFAST | Installed 2.6.0.1 |
Micro read fast alignment search tool | |
| MOOSE | Installed 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 http://ngwww.ucar.edu/ng4.3/ |
|
| NCBI Toolbox | Installed | Includes BLAST, SEQUIN, FA2HTGS, ENTREZ, and CN3D | |
| NWChem | Scalably 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 |
|
| PBJelly | Installed 14.1.14 |
Aligns long sequencing reads to high-confidence draft assembles | |
| Perl | Installed v5.16.3 |
General Purpose Scripting Language |
|
| 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 |
|
| PSPP | Installed 0.8.0-g13bf3f |
Tool for statistical analysis of sampled data | |
| Python | Installed 2.7.13, 3.4.0 |
2.7.13 includes numpy, scipy, and some additional modules, 3.4.0 has somewhat fewer modules. |
|
| Qiime | centos7 under python2.7.9 |
||
| R | Installed 3.1.2 3.3.0 3.4.2 |
Open Source Statistics Package |
|
| RAxML | Installed 8.1.17 |
Phylogenetic Analysis |
|
| RepeatModeler | 1-0-7 | de novo repeat (genomic) family identification and modeling |
|
| SageMath | Installed 7.4 |
Sage variable precision and symbolic computations |
|
| SAMtools | Installed 1.12 |
SAM (Sequence Alignment/Map) tools | |
| SAS | Installed 9.3 |
Commerical Statistical Analysis Package |
|
| 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 analyis package |
|
| Tophat | Installed 2.0.14 |
Splice junction mapper for RNA-Seq reads | |
| TotalView | Installed 8.4.1-4 |
http://www.etnus.com/ 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 varation | |
| VASP | Installed 5.2 |
Commercial molecular dynamics code |
|
| Velvet | Installed 1.2.10 |
de novo genomic assembler |
|
| VMD | Installed 1.9.1 |
A Package for visualizing molecules http://www.ks.uiuc.edu/Research/vmd/ |
|
Libraries
| 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 subdirectores 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 |
Last modified: December 12 2017 14:58:38.
