PSC staff prepare a large number of scientific software packages for use by researchers on Bridges-2. The diversity of installation methods and individual preferences has established a complex mix of software management strategies, leading to duplicated effort in preparing new and updated packages, inconsistent deployment across multiple kinds of compute nodes, and many other behind-the-scenes issues. Recent efforts have developed a new package management framework to organize these software packages into a single coherent system. This internship will involve converting existing software deployment strategies into automated scripts to function within a package management framework.
PSC also provides web-based documentation explaining how to run popular software packages on Bridges-2. This internship will also include developing, extending, and refining this documentation to include run-time optimization guidelines and software performance expectations. Initial efforts may focus on computational biochemistry packages, such as molecular dynamics simulation engines (e.g., GROMACS, NAMD, Amber, LAMMPS) and the AlphaFold protein structure prediction AI system.
Responsibilities may include:
- Referencing Linux packaging documentation (Autotools, CMake, etc.) to configure, compile, optimize, install, and test Linux software packages.
- Preparing and refining automated scripts to deploy software packages in a Linux high performance computing environment.
- Referencing scientific software documentation to optimize both the package installation and the run-time configuration of each package
- Learning to prepare (and then preparing) example input data for various scientific software packages, such as GROMACS, NAMD, Amber, LAMMPS, and AlphaFold.
- Documenting usage instructions, recommended run-time configurations, and expected performance metrics for individual scientific software packages on Bridges-2.
- Automating performance testing for use with system monitoring frameworks.
Our internships offer the opportunity to:
- Gain valuable experience and knowledge in research computing.
- Network with leaders in academia and industry to form valuable relationships.
- Publish in peer-reviewed journals and at prominent conferences.
- Learn how to work effectively within the constraints of limited system privileges, which is standard practice when working on shared Linux and Unix systems.
- Gain practical experience optimizing and running multiple scientific software packages on a high performance computing system.
- Gain practical experience automating a variety of tasks and extending an existing framework to support automating additional tasks.
- Develop other core Linux/Unix skills which are applicable across many IT fields.
Job Requirements:
- Candidates must be pursuing an undergraduate (bachelor’s) or Master’s degree.Examples of relevant majors are computer science, mathematics, statistics (any major with a significant computational/programming component), physics, chemistry, biology (any scientific major involving scientific computing), etc.
- Familiarity with Bash and the Linux/Unix command line
- Familiarity with compiling and installing open source software on Linux/Unix operating systems
- Experience with the Git version control system
- Strong ability to learn independently by studying software documentation
- Familiarity with computational biology and/or molecular dynamics is helpful, but not required
- Excellent communication skills and ability to work in a team environment.
- Excellent problem-solving skills and creativity
Keywords Amber, Automation, Autotools, Bash, Biochemistry, Biophysics, Chemistry, CMake, Compiling, Documentation, GROMACS, High Performance Computing, LAMMPS, Linux, Molecular Dynamics, NAMD, Open Source, Optimization, Package Management, Performance, Physics, Python, Slurm, Software, Supercomputing, Unix
This internship is open to anyone currently enrolled in an undergraduate program or Master’s. This is a hybrid in-person/ remote or fully in-person position and all work must be conducted while in the United States. Our offices are located at 300 South Craig Street, Pittsburgh, PA.
Please send your resume to mwd@psc.edu before February 14, 2025 or apply on Handshake.