High Performance Computing

Software

Henry2 has a mixture of staff maintained software and user maintained software. The list of supported software is under construction. The tables below contains both supported and obselete software. Staff cannot install and maintain custom software for each of Henry2's many users. For executables that are too large for a home directory, users may request space for custom software.

Space for User Maintained Executables

Acceptable Use Policy
  Directory /usr/local/usrapps provides space for user installed and maintained applications
  Space is not to be used for data or working space from which to execute jobs
  Applications must be maintained/patched to minimize potential security vulnerabilities
  Access should be managed via Linux group permissions to comply with license restrictions
  Applications that require root access to install are not permitted.

Procedure to request use of space under /usr/local/usrapps
  Submit request via email to oit_hpc@help.ncsu.edu
  Request should include:
    Name of HPC Project that will be responsible for the application
    Name of the application to be installed
    Statement that the group is authorized to install the application on the HPC Linux cluster
  A directory will be created with group read/write access for the requesting project
  Project group will be responsible for installing and maintaining the application

The list of supported software is under construction. The tables below contain both supported and obselete 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@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.

Compilers

Name Status
henry2
cluster
Notes
Intel   2013, 2016, 2017, 2018 Intel Linux Compilers Web Site
Intel MPI   Installed
openmpi-2013,2016
mvapich2-2016
intelmpi2016
intelmpi2018
module load PrgEnv-intel
module load intel
module load intel_mpi
Portland
Group
MPI
  Installed
14.3,15.1
http://www.pgroup.com/
Portland
Group
 
OpenMPI 14.3
http://www.pgroup.com/
Gnu   4.8,3,4.9.4,6,2,0,7.2.0


The following list of applications is not complete. Other packages may be found in the subdirectories of /usr/local/apps. Send e-mail to "oit_help at help.ncsu.edu" to suggest additional general-use applications or to request application upgrades.

Applications

Name Obsolete Status Henry2 cluster Notes
Abinit   Installed
7.2.1
An ab initio quantum chemistry package
ABAQUS   Installed
6.16
Commercial Finite Element Package
AMBER   Installed
12 14
Parallel Molecular Dynamics
ANSYS
  Installed
170
Commercial Finite Elment Package
ANSYS CDF
  Installed
170
Commercial Fluid Dyamics 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
cmake Installed
3.3.2
  An altermative to make
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 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)
Falcon Installed   Heirarchical 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/
Gaussian
  Installed
g09, g16
Commerical quantum chemistry code
http://gaussian.com
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
Java Installed
See the Howto for access to some newer versions
Julia Installed
v1.0
Efficient language for matrix computations
KmerGenie
Installed
19Mar14
aids in de novo genome assembly
LAMMPS Installed
5Mar13
16Mar18
Molecular dynamics
MAKER   Installed
2.10, 2.31
Genome annotation pipeline
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
Matlab Installed
2014a,2016a,2017a,2017b
Commercial language for matrix 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   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
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
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
3.4.3
Open Source Statistics Package
SageMath   Installed
7.4
Sage variable precision and symbolic computations
SAMtools   Installed
1.7a
SAM (Sequence Alignment/Map) tools
SAS Installed
9.4
Commerical Statistical Analysis Package
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 analyis 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 varation
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: October 14 2018 17:58:00.