What You Should Know About NAMD and Charm++ But Were Hoping to Ignore

ABSTRACT

The biomolecular simulation program NAMD is used heavily at many HPC centers. Supporting NAMD users requires knowledge of the Charm++ parallel runtime system on which NAMD is built. Introduced in 1993, Charm++ supports message-driven, task-based, and other programming models and has demonstrated its portability across generations of architectures, interconnects, and operating systems. While Charm++ can use MPI as a portable communication layer, specialized high-performance layers are preferred for Cray, IBM, and InfiniBand networks and a new OFI layer supports Omni-Path. NAMD binaries using some specialized layers can be launched directly with mpiexec or its equivalent, or mpiexec can be called by the charmrun program to leverage system job-launch mechanisms. Charm++ supports multi-threaded parallelism within each process, with a single thread dedicated to communication and the rest for computation. The optimal balance between thread and process parallelism depends on the size of the simulation, features used, memory limitations, nodes count, and the core count and NUMA structure of each node. It is also important to enable the Charm++ built-in CPU affinity settings to bind worker and communication threads appropriately to processor cores. Appropriate execution configuration and CPU affinity settings are particularly non-intuitive on Intel KNL processors due to their high core counts and flat NUMA hierarchy. Rules and heuristics for default settings can provide good default performance in most cases and dramatically reduce the search space when optimizing for a specific simulation on particular machine. Upcoming Charm++ and NAMD releases will simplify and automate launch configuration and affinity settings.

References

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Index Terms

• Applied computing

  • Life and medical sciences

    • Computational biology

      • Molecular structural biology

  • Physical sciences and engineering

    • Chemistry

    • Physics

• Computing methodologies

  • Parallel computing methodologies

    • Parallel programming languages

• Social and professional topics

  • Professional topics

    • Management of computing and information systems

      • Implementation management

        • Computing equipment management

      • Project and people management

        • Computer and information systems training

      • Software management

        • Software selection and adaptation