How can I accelerate an LCAO-based NVT molecular dynamics calculation on CPU nodes?

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Details

Current setup

• ABACUS: develop branch, CPU build
• Hardware: 2 nodes, 64 physical cores per node
• Parallel layout: 64 MPI processes with 2 OpenMP threads per process
• System size: 322 atoms
• Basis: LCAO DZP
• Exchange-correlation: PBE
• van der Waals correction: D3(BJ)
• k-points: Gamma-only
• Plane-wave cutoff: ecutwfc = 100 Ry
• MD ensemble: NVT with a Nose–Hoover chain
• Temperature: 300 K
• Time step: currently 0.2 fs
• SCF threshold: 1e-6
• SCF solver: Broyden mixing
• mixing_beta = 0.6
• mixing_ndim = 8
• Charge density restarted from a previous converged calculation

Performance

With this setup, one MD step takes approximately 339 seconds. A typical step requires about 23 electronic iterations, with each iteration taking approximately 7 seconds.

I also added an ion-only restraint force to the code. Direct timing shows that the restraint calculation takes approximately 22 microseconds per MD step, so it has no measurable
impact on the total runtime and is not the performance bottleneck.

Have you read FAQ on the online manual http://abacus.deepmodeling.com/en/latest/community/faq.html

• Yes, I have read the FAQ part on online manual.

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