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High-throughput structure-based screening of drug-like molecules has become a common tool in biomedical research. Recently, acceleration with graphics processing units (GPUs) has provided a large performance boost for molecular docking…
As software systems increase in complexity, conventional monitoring methods struggle to provide a comprehensive overview or identify performance issues, often missing unexpected problems. Observability, however, offers a holistic approach,…
We provide an overview of the software engineering efforts and their impact in QMCPACK, a production-level ab-initio Quantum Monte Carlo open-source code targeting high-performance computing (HPC) systems. Aspects included are: (i)…
High-Performance Computing (HPC) platforms enable scientific software to achieve breakthroughs in many research fields such as physics, biology, and chemistry, by employing Research Software Engineering (RSE) techniques. These include 1)…
Research processes often rely on high-performance computing (HPC), but HPC is often seen as antithetical to "reproducibility": one would have to choose between software that achieves high performance, and software that can be deployed in a…
Binary package managers install software quickly but they limit configurability due to rigid ABI requirements that ensure compatibility between binaries. Source package managers provide flexibility in building software, but compilation can…
Recent developments in the commercial open source community have catalysed the use of Linux containers for scalable deployment of web-based applications to the cloud. Scientific software can be containerized with dependencies, configuration…
Science reproducibility is a cornerstone feature in scientific workflows. In most cases, this has been implemented as a way to exactly reproduce the computational steps taken to reach the final results. While these steps are often…
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…
We describe the development of a scientific cloud computing (SCC) platform that offers high performance computation capability. The platform consists of a scientific virtual machine prototype containing a UNIX operating system and several…
The high-performance computing (HPC) community has recently seen a substantial diversification of hardware platforms and their associated programming models. From traditional multicore processors to highly specialized accelerators, vendors…
High-energy physics (HEP) experiments have developed millions of lines of code over decades that are optimized to run on traditional x86 CPU systems. However, we are seeing a rapidly increasing fraction of floating point computing power in…
High Performance Computing (HPC) clouds are becoming an alternative to on-premise clusters for executing scientific applications and business analytics services. Most research efforts in HPC cloud aim to understand the cost-benefit of…
Solving the software dependency issue under the HPC environment has always been a difficult task for both computing system administrators and application scientists. This work would like to tackle the issue by introducing the modern…
Software and hardware co-design and optimization of HPC systems has become intolerably complex, ad-hoc, time consuming and error prone due to enormous number of available design and optimization choices, complex interactions between all…
In our former works we have made serious efforts to improve the performance of medical image analysis methods with using ensemble-based systems. In this paper, we present a novel hardware-based solution for the efficient adoption of our…
Scientists rely on simulations to study natural phenomena. Trusting the simulation results is vital to develop sciences in any field. One approach to build trust is to ensure the reproducibility and traceability of the simulations through…
Containers are used by an increasing number of Internet service providers to deploy their applications in multi-access edge computing (MEC) systems. Although container-based virtualization technologies significantly increase application…
To address the growing needs for scalable High Performance Computing (HPC) and Quantum Computing (QC) integration, we present our HPC-QC full stack framework and its hybrid workload development capability with modular…
Robust execution environments are important for addressing key challenges in quantum computing, such as application development, portability, and reproducibility, and help unlock the development of modular quantum programs, driving forward…