GPU Acceleration Demonstrated for Density Functional Theory Calculations in OpenMX Code
A team from Niigata University, JAEA, and the University of Tokyo has implemented GPU acceleration for both collinear and noncollinear density functional theory (DFT) calculations in the widely used OpenMX code, achieving speedups of up to 2.60 times over CPU-only runs. The work offloads computationally intensive matrix operations to NVIDIA H100 GPUs via cuBLAS, cuSOLVER, and OpenACC on the Pegasus supercomputer. Faster DFT calculations could significantly reduce the time and cost of simulating magnetic and electronic properties of materials at the quantum level.
Researchers from Niigata University, the Japan Atomic Energy Agency, and the University of Tokyo have developed GPU-accelerated versions of collinear and noncollinear density functional theory calculations within OpenMX, a numerical atomic orbital (NAO)-based DFT code. The implementation offloads matrix multiplications, eigenvalue solves, and selected auxiliary steps to NVIDIA H100 GPUs using the cuBLAS and cuSOLVER libraries alongside OpenACC directives. Benchmarks conducted on the Pegasus supercomputer showed that a 512-atom collinear calculation running on two nodes with two GPUs achieved a 2.02x speedup compared to a CPU-only run using 96 cores across the same two nodes. For a more computationally demanding 384-atom noncollinear case — relevant to systems with spin-orbit coupling and complex magnetic structures — the GPU-accelerated run delivered a 2.60x speedup under equivalent conditions. The results, published in the Journal of the Physical Society of Japan, demonstrate that practical GPU acceleration is achievable in NAO-based DFT codes, which have historically lagged behind plane-wave codes in GPU adoption. This advance is particularly significant for noncollinear calculations, which are essential for modeling topological materials, heavy-element compounds, and exotic magnetic phases.
What's missing
Performance on other GPU architectures (e.g., AMD, older NVIDIA generations) or multi-GPU scaling beyond two nodes is not reported. Energy efficiency (performance per watt) of GPU vs. CPU runs is also not addressed.
What different sources said
- arXiv physicsCenter
Multi-GPU MBE(3)-OSV-MP2 for Performant Large-Scale ab initio Calculations
Related
Gut Bacteria Enzyme Found to Break Down Heat-Processed Food Compounds, Producing Novel Biogenic Amines
Researchers have discovered that an enzyme in common gut bacteria can degrade N-epsilon-carboxymethyllysine (CML), a compound formed during thermal food processing, producing previously unknown biogenic amines. The enzyme, ornithine decarboxylase SpeC from enterobacteria, acts on CML and related modified lysine derivatives through a low-level 'underground' catalytic activity. This finding suggests a previously unrecognized communication axis between thermally processed dietary compounds and gut microbial physiology, with potential implications for host health.
Full-Length Gene Sequencing Reveals Two Distinct Bacterial Communities in Black-Legged Ticks Expanding Into Canada
Researchers used Oxford Nanopore full-length 16S rRNA gene sequencing to characterize the microbiome of Ixodes scapularis black-legged ticks collected in Nova Scotia, Canada, distinguishing between tick-adapted bacteria and environmentally acquired bacteria. The study comes as I. scapularis — the primary vector of Lyme disease — is rapidly expanding northward into Canada due to climate change. The findings suggest that environmentally derived bacteria in tick microbiomes are not mere contamination, which has implications for how tick microbiome data is collected and interpreted across surveillance studies.
Study Identifies Metabolic Link Between Cell Envelope Stress and Biofilm Formation in Bacteria
Researchers have discovered that the metabolite acetyl-CoA directly inhibits enzymes that degrade the bacterial signaling molecule c-di-GMP, connecting cell envelope biosynthesis stress to biofilm formation in Pseudomonas aeruginosa. The study found that sub-inhibitory concentrations of antibiotics targeting early peptidoglycan biosynthesis — but not other antibiotic classes — elevate c-di-GMP levels by reducing phosphodiesterase activity, with acetyl-CoA competing for the enzyme active site. Because the relevant enzyme domain is broadly conserved across bacterial species, this checkpoint mechanism may be widespread and could have implications for understanding antibiotic-induced biofilm responses.