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Related Experiment Video

Updated: Jul 26, 2025

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
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Experiences Porting NAMD to the Data Parallel C++ Programming Model.

David J Hardy1, Jaemin Choi2, Wei Jiang3

  • 1University of Illinois at Urbana-Champaign, Beckman Institute for Advanced Science and Technology, Urbana, Illinois, USA.

International Workshop on Opencl
|June 19, 2023
PubMed
Summary
This summary is machine-generated.

Data Parallel C++ (DPC++) enables High-Performance Computing (HPC) applications to use diverse hardware through vendor-neutral programming. Porting the NAMD application to DPC++ successfully demonstrated its correctness for GPU-offload force kernels.

Keywords:
DPC++Molecular DynamicsNAMDSYCLoneAPI

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Area of Science:

  • Computer Science
  • Computational Science
  • Scientific Computing

Background:

  • High-Performance Computing (HPC) increasingly requires heterogeneous resources (CPUs, GPUs, etc.).
  • Vendor-neutral programming paradigms are essential for broad hardware compatibility.
  • Data Parallel C++ (DPC++), based on the open SYCL standard, offers a vendor-neutral solution.

Purpose of the Study:

  • To evaluate the feasibility and correctness of porting a complex HPC application to DPC++.
  • To demonstrate the utility of SYCL/DPC++ for heterogeneous computing in scientific applications.
  • To assess the performance implications of using DPC++ for GPU-offload kernels.

Main Methods:

  • Porting the NAMD molecular dynamics application, including its GPU-offload force kernels, to SYCL/DPC++.
  • Utilizing the Data Parallel C++ programming language, which adheres to open SYCL standards.
  • Verification of the ported application's functional correctness.

Main Results:

  • Successful porting of NAMD's GPU-offload force kernels to SYCL/DPC++.
  • Demonstrated correctness of the porting effort, validating the approach.
  • Established a pathway for leveraging heterogeneous computing resources with a vendor-neutral paradigm.

Conclusions:

  • SYCL/DPC++ provides a viable vendor-neutral solution for modern HPC applications.
  • Porting complex scientific applications like NAMD to DPC++ is achievable.
  • This work validates the use of DPC++ for heterogeneous computing in scientific domains.