MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

ADVANCED SEARCH

APPLIED FILTERS: NAMD3 _____ _____ _____ _____ _____ _____ _____ _____

  • EXPLORING THE DATABASE

    Default view
    When this page is viewed no filters are initially applied. All benchmarks are selected and sorted by simulation speed. The chart on the right displays only top 30 benchmarks for clarity.
  • Selecting benchmarks
    A subset of benchmarks can be selected using a custom chain of filters. Selected database entries can be downloaded as CSV files for further analysis or viewed in the Benchmark Details table at the bottom of the page.
  • Detailed views
    A detailed view of each database entry can be accessed from Benchmark ID and Software ID search forms. Detailed views include submission commands and simulation input files. View example: PMEMD @Narval (benchmark ID=46).
  • Parallel efficiency
    Efficiency is computed as PS/(SS * N) where PS is speed of the parallel program, SS is speed of the serial program, and N is the number of CPUs or GPUs.
  • Viewing parallel speedup and efficiency
    To view the graph of the dependence of parallel speedup and efficiency on the number of CPU/GPU equivalents select only one software and one cluster. View example: GROMACS @Narval .

  • Viewing QM/MM benchmarks
    To view QM/MM benchmarks select simulation system 4cg1 .

Performance Chart For Selected Benchmarks

*Data updated Aug. 26, 2025

Cost Of GPU-accelerated Simulations

*Data updated Aug. 26, 2025

  • OPTIMIZING GPU USAGE

    Parallel scaling to multiple GPUs
    Parallel scaling to multiple GPUs strongly depends on the compibation of software, hardware and simulation parameters. Often simulations do not run faster on multiple GPUs (PMEMD @Cedar example). Simulations on nodes with direct interconnect between GPUs (NVLink) are more likely to benefit from multiple GPUs, but efficiency decreases and cost goes up with the number of GPUs (NAMD3 @Cedar example ).
  • Benchmarking GPU accelerated MD Engines
    For benchmarking we use the optimal number of cores per GPU (the number needed for the fastest simulation time but not exceeding the maximum number of CPU cores per GPU in a GPU equivalent).

BENCHMARK RESULTS

CPUY: CPU years per 1 microsecond long simulation. GPUY: GPU years per 1 microsecond long simulation. | T: tasks | C: cores | N: nodes. Speed is in ns/day. Integration step = 1 fs. Measured with dataset 6n40 (239,131 atoms).

*More information is available by clicking ID in the table above
ID Software Module Toolch Arch Data Speed CPU CPUeff CPUY GPUY T C N GPU NVLink Site
234 NAMD3.cuda binary_pack/3.0b3 - - 6n4o 2.46e+01 Xeon Gold 6148 100.0 0.0 0.111 1 1 1 1V100-PCIE No Siku
28 NAMD3.cuda binary_pack/3.0a9 - - 6n4o 2.27e+01 Xeon Gold 6148 56.3 0.0 0.241 1 2 1 2V100-PCIE No Siku
39 NAMD3.cuda binary_pack/3.0a9 - - 6n4o 2.25e+01 Xeon Gold 6148 100.0 0.0 0.122 1 1 1 1V100-SXM2 Yes Beluga
75 NAMD3.cuda binary_pack/3.0a9 - - 6n4o 2.20e+01 Xeon Gold 6248 100.0 0.0 0.125 1 1 1 1V100-SXM2 Yes Graham
27 NAMD3.cuda binary_pack/3.0a9 - - 6n4o 2.02e+01 Xeon Gold 6148 100.0 0.0 0.136 1 1 1 1V100-PCIE No Siku
33 NAMD3.cuda binary_pack/3.0a9 - - 6n4o 2.01e+01 Xeon Gold 5120 100.0 0.0 0.136 1 1 1 1V100-PCIE No Graham
50 NAMD3.cuda binary_pack/3.0a9 - - 6n4o 1.85e+01 Xeon Silver 4216 100.0 0.0 0.148 1 1 1 1V100-SXM2 Yes Cedar
54 NAMD3.cuda binary_pack/3.0a9 - - 6n4o 1.85e+01 Xeon E5-2650 52.5 0.0 0.593 1 4 1 4P100-PCIE No Cedar
38 NAMD3.cuda binary_pack/3.0a9 - - 6n4o 1.79e+01 Xeon Gold 6248 62.9 0.0 0.307 1 2 1 2RTX6000 No Siku
36 NAMD3.cuda binary_pack/3.0a9 - - 6n4o 1.42e+01 Xeon Gold 6248 100.0 0.0 0.193 1 1 1 1RTX6000 No Siku
Date Updated: Aug. 26, 2025, 11:30 p.m.