Related papers: H5MD: a structured, efficient, and portable file f…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
High-level I/O libraries, such as HDF5 and PnetCDF, are commonly used by large-scale scientific applications to perform I/O tasks in parallel. These I/O libraries store the metadata such as data types and dimensionality along with the raw…
3-D shape is important to chemistry, but how important? Machine learning works best when the inputs are simple and match the problem well. Chemistry datasets tend to be very small compared to those generally used in machine learning so we…
RUMD is a general purpose, high-performance molecular dynamics (MD) simulation package running on graphical processing units (GPU's). RUMD addresses the challenge of utilizing the many-core nature of modern GPU hardware when simulating…
Modern scientific simulations and instruments generate data volumes that overwhelm memory and storage, throttling scalability. Lossy compression mitigates this by trading controlled error for reduced footprint and throughput gains, yet…
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an…
Programmable biomolecule-mediated computing is a new computing paradigm as compared to contemporary electronic computing. It employs nucleic acids and analogous biomolecular structures as information-storing and -processing substrates to…
Developing efficient path integral (PI) methods for atomistic simulations of vibrational spectra in heterogeneous condensed phases and interfaces has long been a challenging task. Here, we present the h-CMD method, short for hybrid centroid…
We present a new scalable algorithm for short-range molecular dynamics simulations on distributed memory MIMD multicomputer based on a message-passing multi-cell approach. We have implemented the algorithm on the Connection Machine 5 (CM-5)…
Machine learning (ML)-based steering can improve the performance of ensemble-based simulations by allowing for online selection of more scientifically meaningful computations. We present DeepDriveMD, a framework for ML-driven steering of…
Scientific computing applications have benefited greatly from high performance computing infrastructure such as supercomputers. However, we are seeing a paradigm shift in the computational structure, design, and requirements of these…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
Organic memories, with small dimension, fast speed and long retention features, are considered as promising candidates for massive data archiving. In order to satisfy the re-quirements for ultra-low power and high-security information…
Rapid growth in scientific data and a widening gap between computational speed and I/O bandwidth makes it increasingly infeasible to store and share all data produced by scientific simulations. Instead, we need methods for reducing data…
Large scale simulations of complex systems ranging from climate and astrophysics to crowd dynamics, produce routinely petabytes of data and are projected to reach the zettabytes level in the coming decade. These simulations enable…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
Many scientific applications are I/O intensive and generate or access large data sets, spanning hundreds or thousands of "files." Management, storage, efficient access, and analysis of this data present an extremely challenging task. We…
We develop a Python-based open-source package to analyze the results stemming from ab initio molecular-dynamics simulations of fluids. The package is best suited for applications on natural systems, like silicate and oxide melts,…
The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures, and currently holds the world record for the largest molecular…
Reproducibility in simulation-based computer architecture research requires coordinating artifacts like disk images, kernels, and benchmarks, but existing workflows are inconsistent. We improve gem5, an open-source simulator with over 1600…