Programming
We provide programming and configuration support for High Performance Computing and Visualization software (see menu at left). Our services include:
- Troubleshooting malfunctioning programs
- Parallelizing existing serial codes
- Developing new parallel codes
- Training developers in parallel-style coding techniques
- Tuning software for maximum performance
We support several implementations of MPI as well as OpenMP.
| Software | Synopsis |
|---|---|
| Blast | Basic local alignment search tool. Available via conda or use the container with Singularity. |
| GROMACS | Molecular simulation engine (see RC webpage) |
| Gaussian | Quantum chemistry calculations (see RC webpage) |
| JAX | Python library for machine learning (see GitHub repo) |
| Jenkins | Automatic testing framework (see GitHub repo) |
| Julia | Fast, flexible programming language (see RC webpage) |
| Jupyter | Interactive Python notebooks (see RC webpage) |
| LAMMPS | Particle simulation engine (see RC webpage) |
| mpi4py | Python interface to MPI (see RC webpage) |
| PETSc | Scientific library (see RC webpage) |
| PyTorch | Deep learning framework (see RC webpage) |
| Python | General-purpose scripting language (see RC webpage) |
| Quantum Espresso | Electronic structure calculations (see RC webpage) |
| Rapids | GPU-enabled analytics and machine learning (see GitHub repo) |
| R/RStudio | Programming environment (see RC webpage) |
| Scikit-learn | Python library for machine learning (see GitHub repo) |
| Singularity | Container platform (see RC webpage) |
| Spark | Processing engine for big data (see RC webpage) |
| TensorFlow | Deep learning framework (see RC webpage) |
| TurboVNC | Graphical desktop sharing (see RC webpage) |
| VEP | Variant effect predictor (use the container with Singularity) |
Licensed Software
Our licensed software support includes the deployment, installation, and configuration of the following licensed software products. This is just a sampling of the software readily available on the clusters.
| Product | Synopsis |
|---|---|
| ArcGIS | A system for people who rely on accurate geographic information to make decisions. |
| AMPL | A modeling language for mathematical programming. |
| Cadence | Provides front-to-back design tools for all aspects of semiconductor design. Cluster Usage Guidelines |
| DDT | A debugging tool for parallel computing. Usage Guidelines. |
| Imagine | Abroad collection of software tools designed specifically to process geospatial satellite imagery |
| Intel | High-performance Fortran/C/C++ compilers and MKL math library. MKL Usage Guidelines. |
| MAP | A performance profiler from Allinea. Usage Guidelines. |
| Mathematica | Fully integrated technical computing software |
| Matlab | High-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numerical computation. MATLAB on clusters: Usage Guidelines |
| Mentor ModelSim | Combines single kernel simulator (SKS) technology with a unified debug environment for Verilog, VHDL, and SystemC. |
| SAS | An integrated statistical package |
| Simics | A simulator supporting the definition, development, and deployment of digital systems |
| Stata | An interactive data analysis program |
| Synopsys | Provides tools for digital system-on-chip design. Cluster Usage Guidelines |
| VTune | A powerful graphical and command-line profiler from Intel. Usage Guidelines. |
For additional licensed software see this OIT Knowledge Base page.