The TSCC runs CentOS version 6.3. PGI and Intel compilers are available, as are mvapich2 and openmpi. Over 50 additional software applications and libraries are installed on the system, and system administrators regularly work with researchers to extend this set as time/costs allow.
This is a partial list, based on current software from Triton Resource. The TSCC software installation is being assembled and this information may change accordingly. Specifics of installed location, version and other details may change as the development process concludes.
| Package | Topic Area | Version | License Type | Package Home Page | User Install Location | Installed on: (L)ogin, (C)ompute, (B)oth |
|---|---|---|---|---|---|---|
| bbcp | Data Transfer | 12.08.17 | Private License | bbcp Home Page | /opt/bbcp | B |
| ATLAS (Automatically Tuned Linear Algebra Software) | Mathematics | 3.10.0 | BSD | ATLAS Home Page | /opt/atlas | B |
| AMOS (A Modular, Open-Source whole genome assembler) | Genomics | 3.1.0 | OSI | AMOS Home Page | /opt/amos | B |
| Amber (Assisted Model Building with Energy Refinement) | Molecular Dynamics | 12 | Amber 12 Software License | Amber Home Page | /opt/amber | C |
| ABySS (Assembly by Short Sequences) | Genomics | 1.3.4 | BC Cancer Agency academic | ABySS Home Page | /opt/abyss | B |
| APBS (Adaptive Poisson-Boltzmann Solver) | Bioinformatics | 1.3 | BSD, MIT | APBS Home Page | /opt/apbs | C |
| BEAST | Bioinformatics, Phylogenetics | 1.7.4 | GNU LGPL | BEAST Home Page | /opt/beast | C |
| BLAT | Bioinformatics, Genetics | 35 | Free Non-commercial | BLAT User Guide | /opt/biotools/blat | B |
| bbFTP | Large Parallel File Transfer | 3.2.0 | GNU GPL | bbFTP Home Page | /opt/bbftp | B |
| Boost | C++ Library | 1.50.0 | Boost Software License | Boost Home Page | /opt/boost | B |
| Bowtie Short Read Aligner | Bioinformatics | 0.12.9 | GNU GPL | Bowtie Home Page | /opt/biotools/bowtie | B |
| Burrows-Wheeler Aligner (BWA) | Bioinformatics | 0.6.2 | GNU GPL | BWA Home Page | /opt/biotools/bwa | B |
| Cilk | Parallel Programming | 5.4.6 | GNU GPL | Cilk Home Page | /opt/cilk | B |
| CPMD | Molecular Dynamics |
3.15.3 |
Free for noncommercial research | CPMD Home Page | /opt/cpmd/bin | B |
| DDT | Graphical Parallel Debugger | 3.2 | Licensed | DDT Home Page | /opt/ddt | B |
| Package | Topic Area | Version | License Type | Package Home Page | User Install Location | Installed on: (L)ogin, (C)ompute, (B)oth |
| FFTW | General | 2.1.5 –or– 3.3.3 |
GNU GPL | FFTW Home Page | /opt/fftw | B |
| FPMPI | MPI Programming | 2.2 | Licenced | FPMPI Home Page | /opt/mvapich2 –and– /opt/openmpi |
B |
| FSA (Fast Statistical Alignment) | Genetics | 1.15.7 | Licensed | FSA Home Page | /opt/fsa | TBD |
| GAMESS | Chemistry | 5.2012 | No-cost Site License | GAMESS Home Page | /opt/gamess | B |
| Gaussian | Structure Modeling | 09.c.01 | Commercial | Gaussian Home Page | /opt/gaussian | B |
| Genome Analysis Toolkit (GATK) | Bioinformatics | 2.3.9 | BSD Open Source | GATK Home Page | /opt/biotools/GenomeAnalysisTK | B |
| GROMACS (Groningen Machine for Chemical Simulations) | Molecular Dynamics | 4.6.2 | GNU GPL | Gromacs Home Page | /opt/gromacs | B |
| GSL (GNU Scientific Library) | C/C++ Library | 1.15 | GNU GPL | GSL Home Page | /opt/gsl | B |
| IDL | Visualization | 8.2.r1 | Licensed | IDL Home Page | /opt/idl | B |
| IPython | Parallel Computing | 0.13.1 | BSD | IPython Home Page | /opt/ipython | B |
| JAGS (Just Another Gibbs Sampler) | Statistical Analysis | 3.3.0 | GNU GPL, MIT | JAGS Home Page | /opt/jags | B |
| LAPACK (Linear Algebra PACKage) | Mathematics | 3.4.2 | BSD | LAPACK Home Page | /opt/lapack | B |
| matplotlib | Python Graphing Library | 1.1.1 | PSF (Python Software Foundation) | matplotlib Home Page | /opt/scipy/lib64/python2.4/site-packages | B |
| LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) | Molecular Dynamics Simulator | 12Jan13 | GPL | LAMMPS Home Page | /opt/lammps | C |
| MATLAB | Parallel Development Environment | 7.9 | Licensed | MATLAB Home Page | /opt/matlab.2011a –and– /opt/matlab_server_2012b |
B |
| Package | Topic Area | Version | License Type | Package Home Page | User Install Location | Installed on: (L)ogin, (C)ompute, (B)oth |
| Mono | Development Framework | 3.0.2 | MIT, GNU GPL | Mono Home Page | /opt/mono | B |
| MUMmer | Bioinformatics | 3.23 | Artistic License | MUMmer Home Page | /opt/mummer | B |
| mxml (Mini-XML) | Bioinformatics | 2.7 | GNU GPL | Mini-XML Home Page | /opt/mxml | B |
| Octave | Numerical Computation | 3.6.2 | GNU GPL | Octave Home Page | /opt/octave | B |
| openmpi | Parallel Library | 1.6.3 | Generic | Open MPI Home Page | /opt/openmpi/intel/mx –or– /opt/openmpi/pgi/mx –or– /opt/openmpi/gnu/mx |
B |
| NAMD | Molecular Dynamics, BioInformatics | 2.9 | Non-Exclusive, Non-Commercial Use | NAMD Home Page | /opt/namd | C |
| NCO | NetCDF Support | 4.2.3 | Generic | NCO Home Page | /opt/nco/intel –or– /opt/nco/pgi –or– /opt/nco/gnu |
B |
| NetCDF | General | 4.2.1.1 | Licensed (free) | NetCDF Home | Environment Module | B |
| NoSE (Network Simulation Environment) | Networking | 1.2.1 | GNU GPL | NoSE Home | Perl Module | B |
| NumPy (Numerical Python) | Scientific Calculation | 1.6.2 | BSD | NumPy Home | /opt/scipy/lib64/python2.4/site-packages | B |
| NWChem | Chemistry | 6.1.1 | EMSL (free) | NWChem Home Page | /opt/nwchem | B |
| ParMETIS (Parallel Graph Partitioning and Fill-reducing Matrix Ordering) | Numerical Computation | 4.0.2 | Open | ParMETIS Home Page | /opt/parmetis | B |
| PDT (Program Database Toolkit) | Software Engineering | 3.18.1 | Open | PDT Home Page | /opt/pdt | B |
| PETSc (Portable, Extensible Toolkit for Scientific Computation) | Mathematics | 3.3.p5 | Open | PETSc Home Page | /opt/petsc | B |
| PyFITS | Astrophysics | 3.1.1 | BSD | PyFITS Home Page | /opt/scipy/lib64/python2.4/site-packages | B |
| Python | General Scripting | 2.7 | BSD | Python Home Page | /opt/python/bin | B |
| pytz | Python TimeZone Module | 2012j | MIT | PyTZ Home Page | /opt/scipy/lib64/python2.4/site-packages | B |
| R | Statistical Computing and Graphics | 3.0.1 | GNU GPL | R Home Page | /opt/R | B |
| RapidMiner | Data Mining | 5.2.008 | Open Source under AGPL3 | RapidMiner Home Page | /opt/rapidminer | B |
| SAMTools (Sequence Alignment/Map) | Bioinformatics | 0.1.18 | BSD, MIT | SAMtools Home Page | /opt/biotools/samtools | B |
| ScaLAPACK (Scalable Linear Algebra PACKage) | Mathematics | 2.0.2 | modified BSD | ScaLAPACK Home Page | /opt/scalapack | B |
| SciPy (Scientific Python) | Scientific Computing | 0.11.0rc1 | BSD | SciPy Home Page | /opt/scipy | B |
| SIESTA | Molecular Dynamics | 3.1 | SIESTA LICENCE for COMPUTER CENTRES | SIESTA Home Page | /opt/siesta | B |
| SOAPdenovo (Short Oligonucleotide Analysis Package) | Bioinformatics | 1.05 | GNU GPLv3 | SOAPdenovo Home Page | /opt/biotools/soapdenovo | B |
| SPRNG (The Scalable Parallel Random Number Generators Library) | General Scientific | 2.0b | None | SPRNG Home Page | /opt/sprng | B |
| SuperLU | Mathematics | 3.2 | Regents of the University of California | SuperLU Home Page | /opt/superlu | B |
| TAU | Tuning and Analysis Utilities | 2.22.p1 | GNU GPL | TAU Home Page | /opt/tau/intel –or– /opt/tau/pgi –or– /opt/tau/gnu |
B |
| Tecplot | Simulation Analytics | 2012 | Tecplot License | Tecplot Home Page | /opt/tecplot | B |
| Trilinos | Software Engineering | 11.0.3 | BSD and LGPL | Trilinos Home Page | /opt/trilinos | B |
| VASP (Vienna Ab initio Simulation Package) | Molecular Dynamics | 5.2.12 | University of Vienna | VASP Home Page | /opt/vasp | B |
| Velvet (Short read de novo assembler using de Bruijn graphs) | Bioinformatics | 1.2.08 | GNU GPL | Velvet Home Page | /opt/biotools/velvet | B |
| WEKA (Waikato Environment for Knowledge Analysis) | Data Mining | 3.7.7 | GNU GPL | WEKA Home Page | /opt/weka | B |
| Package | Topic Area | Version | License Type | Package Home Page | User Install Location | Installed on: (L)ogin, (C)ompute, (B)oth |
System Software |
||||||
| Package | Topic Area | Version | License Type | Package Home Page | User Install Location | Installed on: (L)ogin, (C)ompute, (B)oth |
|---|---|---|---|---|---|---|
| CentOS | Operating System | 6.3 | Open Source | CentOS Home Page | N/A | B |
| Ganglia | N/A | 2.5.7 | Open Source | Ganglia Home Page | /opt/ganglia | B |
| Gold | Allocation Manager | 2.2.0.5 | Open Source | Gold Home Page | /opt/gold | L |
| Hadoop | Distributed Processing Framework | 1.1.1 | Apache License | Hadoop Home Page | /opt/hadoop | B |
| HDF4 (Hierarchical Data Format) | Data Management | 2.8 | BSD License | HDF4 Home Page | /opt/hdf4 | B |
| HDF5 (Hierarchical Data Format) | Data Management | 1.8.10 | BSD License | HDF5 Home Page | /opt/hdf5 | B |
| IPM (Integrated Performance Modeling) | Profiling | 2.0.0 | Free | IPM Home Page | /opt/ipm | B |
| Lustre | Scalable File System | 1.8 | GNU GPL | Lustre Home Page | /opt/lustre | B |
| Maui | Workload Scheduler | 3.2.5 | GNU Lesser GPL | Maui Scheduler SourceForge Page | /opt/maui | L |
| Modules | Environment Variable Management | 3.2.7 | GNU GPL | Modules Home Page | /opt/modules | B |
| mvapich2 | Message Passing Interface | 1.9a2 | Open Source | MVAPICH2 Home Page | /opt/mvapich2/gnu/ib/bin –or– /opt/mvapich2/intel/ib/bin –or– /opt/mvapich2/pgi/ib/bin |
B |
| myHadoop | System Administration | 0.2a | BSD | myHadoop Home Page | /opt/myhadoop | B |
| Nagios | System Monitor | 3.4.3 | GNU GPL | Nagios Home Page | /opt/nagios | Management Node Only |
| Nagios Plugins | System Monitor | 1.4.16 | GNU GPL | Nagios Plugins Home Page | /opt/nagios | Management Node Only |
| NSCA (Nagios Service Check Acceptor) | System Monitor | 2.9.1 | GNU GPL | NSCA Home Page | /opt/nagios | B |
| PAPI (Performance Application Programming Interface) | Performance Monitor | 5.0.1 | Unknown | PAPI Home Page | /opt/papi | B |
| TORQUE | Resource Manager | 2.3.6 | Open Source | TORQUE Home Page | /opt/torque | B |
| Package | Topic Area | Version | License Type | Package Home Page | User Install Location | Installed on: (L)ogin, (C)ompute, (B)oth |
Compilers |
||||||
| Package | Topic Area | Version | License Type | Package Home Page | User Install Location | Installed on: (L)ogin, (C)ompute, (B)oth |
|---|---|---|---|---|---|---|
| CMake | Cross Platform Makefile Generator | 2.8.10.2 | Open | CMake Home Page | /opt/cmake | B |
| GNU Compilers | C and Fortran Compilers | 4.4.6 | CentOS Core License | GNU Compiler Collection Home Page | /usr/bin/gcc –and– /usr/bin/gfortran |
B |
| Intel Compilers | C and Fortran Compilers | 2013.1.117 | Licensed (flexlm) | Intel Compilers Home Page | /opt/intel | B |
| Java | Compiler | 1.6.0_07 | Open | Java Home Page | /usr/bin/javac | B |
| PGI Compilers | C and Fortran Compilers | 12.10 | Licensed (flexlm) | PGI Compilers Home Page | /opt/pgi | B |
| UPC (Unified Parallel C) Compiler | Parallel Computing | 2.16 | BSD | UPC Home Page | /opt/upc | B |
Users can install software in their home directories. If interest is shared with other users, requested installations can become part of the core software repository. Please subscribe to the TSCC Mailing List and submit new software requests there.