Pittsburgh Supercomputing Center is a joint computational research center with Carnegie Mellon University and the University of Pittsburgh. Established in 1986, PSC is supported by several federal agencies, the Commonwealth of Pennsylvania and private industry.

PSC provides university, government and industrial researchers with access to several of the most powerful systems for high-performance computing, communications and data storage available to scientists and engineers nationwide for unclassified research. PSC advances the state of the art in high-performance computing, communications and data analytics and offers a flexible environment for solving the largest and most challenging problems in computational science.

Molecular dynamics simulations are very popular on PSC’s flagship supercomputer, Bridges-2. However, the corresponding software engines are very complex, and there are many parameters that a researcher can adjust to tune a simulation’s performance. If a researcher does not have experience running similar simulations on a similar supercomputer, it is very difficult to evaluate whether the observed performance is reasonable. The primary objective of this internship is to document reasonable performance metrics for a variety of chemical systems under several different simulation engines.

Responsibilities may include:

  • Learning to prepare and preparing model systems for molecular dynamics simulation
  • Learning to use and using the GROMACS, NAMD, Amber, and/or LAMMPS molecular dynamics engines on a high performance computing resource
  • Optimizing molecular dynamics simulation performance on Bridges-2
  • Visualizing molecular dynamics simulations using VMD
  • Collecting and organizing simulation performance data
  • Documenting simulation performance in a manner appropriate for publishing on the PSC website
  • Automate simulation 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.
  • Develop core Linux/Unix skills which are applicable across many IT fields

Job Requirements     
Successful candidates will have the following:

  • Candidates must be pursuing an undergraduate (bachelor’s) or Master’s degree.Examples of relevant majors are computer science, statistics, or any major with a significant computational component
  • 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
  • Excellent communication skills and ability to work in a team environment.
  • Excellent problem-solving skills and creativity.

Keywords: Amber, Automation, Bash, Biochemistry, Biology, Biophysics, Chemistry, Documentation, GROMACS, High Performance Computing, LAMMPS, Linux, Molecular Dynamics, NAMD, Optimization, Performance, Physics, Slurm, Supercomputing

This internship is open to anyone currently enrolled in an undergraduate program. 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 29, 2024.