Related papers: H5MD: a structured, efficient, and portable file f…
With the availability of hybrid DRAM-NVRAM memory on the memory bus of CPUs, a number of file systems on NVRAM have been designed and implemented. In this paper we present the design and implementation of a file system on NVRAM called…
Computer simulations are an essential pillar of knowledge generation in science. Exploring, understanding, reproducing, and sharing the results of simulations relies on tracking and organizing the metadata describing the numerical…
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the…
Processing cores and the accompanying main memory working in tandem enable the modern processors. Dissipating heat produced from computation, memory access remains a significant problem for processors. Therefore, processor thermal…
The Starlink Hierarchical Data System has been a very successful niche astronomy file format and library for over 30 years. Development of the library was frozen ten years ago when funding for Starlink was stopped and almost no-one remains…
There are many ways to represent a molecule as input to a machine learning model and each is associated with loss and retention of certain kinds of information. In the interest of preserving three-dimensional spatial information, including…
The discovery and study of new material systems rely on molecular simulations that often come with significant computational expense. We propose MDDM, a Molecular Dynamics Diffusion Model, which is capable of predicting a valid output…
Multimodal embedding models have gained significant attention for their ability to map data from different modalities, such as text and images, into a unified representation space. However, the limited labeled multimodal data often hinders…
To address the computational and storage challenges posed by large-scale datasets in deep learning, dataset distillation has been proposed to synthesize a compact dataset that replaces the original while maintaining comparable model…
We propose a novel Hamming distance tolerant content-addressable memory (HD-CAM) for energy-efficient in memory approximate matching applications. HD-CAM implements approximate search using matchline charge redistribution rather than its…
The dynamic mode decomposition (DMD) is a simple and powerful data-driven modeling technique that is capable of revealing coherent spatiotemporal patterns from data. The method's linear algebra-based formulation additionally allows for a…
A range of computational biology software (GROMACS, AMBER, NAMD, LAMMPS, OpenMM, Psi4 and RELION) was benchmarked on a representative selection of HPC hardware, including AMD EPYC 7742 CPU nodes, NVIDIA V100 and AMD MI250X GPU nodes, and an…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
HOOMD-blue is a particle simulation engine designed for nano- and colloidal-scale molecular dynamics and hard particle Monte Carlo simulations. It has been actively developed since March 2007 and available open source since August 2008.…
Traditional process monitoring methods, such as PCA, PLS, ICA, MD et al., are strongly dependent on continuous variables because most of them inevitably involve Euclidean or Mahalanobis distance. With industrial processes becoming more and…
Yamdb (Yet another materials data base) addresses the need to provide thermophysical properties of liquid metals and molten salts in an easily accessible manner. Mathematical relations describing material properties - usually determined by…
We developed a portable code for dissipative particle dynamics (DPD) simulations. This Fortran program named CAMUS has a couple of notable features. One is the omission of constructing the so-called neighboring particles list, providing a…
Organizations that make use of large quantities of information require the ability to store and process data from central locations so that the product can be shared or distributed across a heterogeneous group of users. However, recent…
We specify a file-oriented data format suitable for parallel, partition-independent disk I/O. Here, a partition refers to a disjoint and ordered distribution of the data elements between one or more processes. The format is designed such…
We aim to model unknown file processing. As the content of log files often evolves over time, we established a dynamic statistical model which learns and adapts processing and parsing rules. First, we limit the amount of unstructured text…