Related papers: Building a Virtual HPC Cluster with Auto Scaling b…
High-performance computing (HPC) is reshaping computational drug discovery by enabling large-scale, time-efficient molecular simulations. In this work, we explore HPC-driven pipelines for Alzheimer's disease drug discovery, focusing on…
The emergence of large-scale AI models, like GPT-4, has significantly impacted academia and industry, driving the demand for high-performance computing (HPC) to accelerate workloads. To address this, we present HPCClusterScape, a…
We present a convex optimization framework for overcoming the limitations of Kubernetes Cluster Autoscaler by intelligently allocating diverse cloud resources while minimizing costs and fragmentation. Current Kubernetes scaling mechanisms…
Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation…
Data-based classification is fundamental to most branches of science. While recent years have brought enormous progress in various areas of statistical computing and clustering, some general challenges in clustering remain: model selection,…
The increasing prevalence of cloud-native technologies, particularly containers, has led to the widespread adoption of containerized deployments in data centers. The advancement of deep neural network models has increased the demand for…
Different departments of a large organization often run dedicated cluster systems for different computing loads, like HPC (high performance computing) jobs or Web service applications. In this paper, we have designed and implemented a cloud…
The drug discovery process involves several tasks to be performed in vivo, in vitro and in silico. Molecular docking is a task typically performed in silico. It aims at finding the three-dimensional pose of a given molecule when it…
We discuss some specific software engineering challenges in the field of high-performance computing, and argue that the slow adoption of SE tools and techniques is at least in part caused by the fact that these do not address the HPC…
Software design patterns present general code solutions to common software design problems. Modern software systems rely heavily on containers for running their constituent service components. Yet, despite the prevalence of ready-to-use…
Cloud computing has become the ubiquitous computing and storage paradigm. It is also attractive for scientists, because they do not have to care any more for their own IT infrastructure, but can outsource it to a Cloud Service Provider of…
Cloud computing recently developed into a viable alternative to on-premises systems for executing high-performance computing (HPC) applications. With the emergence of new vendors and hardware options, there is now a growing need to…
High Performance Computing (HPC) aims at providing reasonably fast computing solutions to scientific and real life problems. The advent of multicore architectures is noticeable in the HPC history, because it has brought the underlying…
Docker has gained attention as a lightweight container-based virtualization platform. The process for building a Docker image is defined in a text file called a Dockerfile. A Dockerfile can be considered as a kind of source code that…
Compute infrastructure hosted by a cloud provider allows an application to scale without limit. The application developer no longer needs to worry about the up-front investment in a server farm provisioned for a worst-case load scenario.…
Web applications are on the rise and rapidly evolve into more and more mature replacements for their native counterparts. This disruptive trend is mainly driven by the attainment of platform-independence and instant deployability. On top of…
As a broader set of applications from simulations to data analysis and machine learning require more parallel computational capability, the demand for interactive and urgent high performance computing (HPC) continues to increase. This paper…
Reliable Docker-based environment construction is a dominant bottleneck for scaling execution-grounded training and evaluation of software engineering agents. We introduce DockSmith, a specialized agentic Docker builder designed to address…
Virtual clusters are widely used computing platforms than can be deployed in multiple cloud platforms. The ability to dynamically grow and shrink the number of nodes has paved the way for customised elastic computing both for High…
Containerization has revolutionized software deployment, with Docker leading the way due to its ease of use and consistent runtime environment. As Docker usage grows, optimizing Dockerfile performance, particularly by reducing rebuild time,…