Related papers: Performance of the Cell processor for biomolecular…
The increase of existing computational capabilities has made simulation emerge as a third discipline of Science, lying midway between experimental and purely theoretical branches [1, 2]. Simulation enables the evaluation of quantities which…
Vertex models represent confluent tissue by polygonal or polyhedral tilings of space, with the individual cell interacting via force laws that depend on both the geometry of the cells and the topology of the tessellation. This dependence on…
A low-power precision-scalable processor for ConvNets or convolutional neural networks (CNN) is implemented in a 40nm technology. Its 256 parallel processing units achieve a peak 102GOPS running at 204MHz. To minimize energy consumption…
Using a realistic molecular catalyst system, we conduct scaling studies of ab initio molecular dynamics simulations using the CP2K code on both Intel Xeon CPU and NVIDIA V100 GPU architectures. We explore using process placement and…
A previous study of MD algorithms designed for GPU use is extended to cover more recent developments in GPU architecture. Algorithm modifications are described, together with extensions to more complex systems. New measurements include the…
We present a GPU implementation of LAMMPS, a widely-used parallel molecular dynamics (MD) software package, and show 5x to 13x single node speedups versus the CPU-only version of LAMMPS. This new CUDA package for LAMMPS also enables…
Power awareness is fast becoming immensely important in computing, ranging from the traditional High Performance Computing applications, to the new generation of data centric workloads. In this work we describe our efforts towards a power…
In this paper, we describe the architecture and performance of the GRAPE-6 system, a massively-parallel special-purpose computer for astrophysical $N$-body simulations. GRAPE-6 is the successor of GRAPE-4, which was completed in 1995 and…
Molecular dynamics (MD) simulations have transformed our understanding of the nanoscale, driving breakthroughs in materials science, computational chemistry, and several other fields, including biophysics and drug design. Even on exascale…
Recently, special-purpose computers have surpassed general-purpose computers in the speed with which large-scale stellar dynamics simulations can be performed. Speeds up to a Teraflops are now available, for simulations in a variety of…
Supercomputers become faster as hardware and software technologies continue to evolve. Current supercomputers are capable of 1015 floating point operations per second (FLOPS) that called Petascale system. The High Performance Computer (HPC)…
Current computers operate at enormous speeds of ~10^13 bits/s, but their principle of sequential logic operation has remained unchanged since the 1950s. Though our brain is much slower on a per-neuron base (~10^3 firings/s), it is capable…
Due to their highly parallel multi-cores architecture, GPUs are being increasingly used in a wide range of computationally intensive applications. Compared to CPUs, GPUs can achieve higher performances at accelerating the programs'…
This paper explores the potential of cryogenic semiconductor computing and superconductor electronics as promising alternatives to traditional semiconductor devices. As semiconductor devices face challenges such as increased leakage…
Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
On modern architectures, the performance of 32-bit operations is often at least twice as fast as the performance of 64-bit operations. By using a combination of 32-bit and 64-bit floating point arithmetic, the performance of many dense and…
The Intel Haswell-EP processor generation introduces several major advancements of power control and energy-efficiency features. For computationally intense applications using advanced vector extension (AVX) instructions, the processor…
The output of a 200 kHz, 34 W, 300 fs Yb amplifier is compressed to 31 fs with > 88 % efficiency to reach a peak power of 2.5 GW, which to date is a record for a single-stage bulk multi-pass cell. Despite operation 80 times above the…
We present the GPU version of DeePMD-kit, which, upon training a deep neural network model using ab initio data, can drive extremely large-scale molecular dynamics (MD) simulation with ab initio accuracy. Our tests show that the GPU version…