Software engineering to sustain a high-performance computing scientific application: QMCPACK

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) strategic expansion of continuous integration (CI) targeting CPUs, using GitHub Actions runners, and NVIDIA and AMD GPUs in pre-exascale systems, using self-hosted hardware; (ii) incremental reduction of memory leaks using sanitizers, (iii) incorporation of Docker containers for CI and reproducibility, and (iv) refactoring efforts to improve maintainability, testing coverage, and memory lifetime management. We quantify the value of these improvements by providing metrics to illustrate the shift towards a predictive, rather than reactive, sustainable maintenance approach. Our goal, in documenting the impact of these efforts on QMCPACK, is to contribute to the body of knowledge on the importance of research software engineering (RSE) for the sustainability of community HPC codes and scientific discovery at scale.Comment: Accepted at the first US-RSE Conference, USRSE2023, https://us-rse.org/usrse23/, 8 pages, 3 figures, 4 table

Investigation on Data Adaptation Techniques for Neural Named Entity Recognition

Data processing is an important step in various natural language processing tasks. As the commonly used datasets in named entity recognition contain only a limited number of samples, it is important to obtain additional labeled data in an efficient and reliable manner. A common practice is to utilize large monolingual unlabeled corpora. Another popular technique is to create synthetic data from the original labeled data (data augmentation). In this work, we investigate the impact of these two methods on the performance of three different named entity recognition tasks.Comment: ACL SRW 2021 - camera read

A new multi-criteria approach for sustainable material selection problem

Sustainable material selection is a crucial problem given the new demands of society and novel production strategies that consider the concepts of sustainability. Multi-criteria decision-making methods have been extensively used to help decision-makers select alternatives in different fields of knowledge. Nonetheless, these methods have been criticized due to the rank reversal problem, where the independence of the irrelevant alternative principle is violated after the initial decision problem is changed. Over the course of this study, we observed that the solutions that are proposed for this problem, in the context of sustainable material selection, are insufficient. Thus, we present a new material selection approach that is based on the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) method, which is immune to rank reversal. We also demonstrate the causes of rank reversal in the TOPSIS method, how the R-TOPSIS method was designed to solve them, and how it can be applied to sustainable material selection

Exploring the dynamics of gene drive mosquitoes within wild populations using an agent-based simulation

Gene drive technology is emerging as a potentially powerful tool in combating vector-borne diseases – notably malaria. This study introduces an agent-based model (ABM) focused on the deployment of genetically engineered mosquitoes with gene drive (GEM) in Príncipe Island, Republic of São Tomé and Príncipe, an island nation in the Gulf of Guinea, West Africa. Grounded in empirical data from laboratory and field studies, our model forecasts the dynamics of mosquito populations central to devising efficacious GEM release strategies. The core objective is to evaluate the time required for GEMs to constitute 90% of the mosquito population and to elucidate their dispersal throughout the island. This research is instrumental in understanding GEM potential in controlling malaria vectors

Towards enhancing coding productivity for GPU programming using static graphs

The main contribution of this work is to increase the coding productivity of GPU programming by using the concept of Static Graphs. GPU capabilities have been increasing significantly in terms of performance and memory capacity. However, there are still some problems in terms of scalability and limitations to the amount of work that a GPU can perform at a time. To minimize the overhead associated with the launch of GPU kernels, as well as to maximize the use of GPU capacity, we have combined the new CUDA Graph API with the CUDA programming model (including CUDA math libraries) and the OpenACC programming model. We use as test cases two different, well-known and widely used problems in HPC and AI: the Conjugate Gradient method and the Particle Swarm Optimization. In the first test case (Conjugate Gradient) we focus on the integration of Static Graphs with CUDA. In this case, we are able to significantly outperform the NVIDIA reference code, reaching an acceleration of up to 11× thanks to a better implementation, which can benefit from the new CUDA Graph capabilities. In the second test case (Particle Swarm Optimization), we complement the OpenACC functionality with the use of CUDA Graph, achieving again accelerations of up to one order of magnitude, with average speedups ranging from 2× to 4×, and performance very close to a reference and optimized CUDA code. Our main target is to achieve a higher coding productivity model for GPU programming by using Static Graphs, which provides, in a very transparent way, a better exploitation of the GPU capacity. The combination of using Static Graphs with two of the current most important GPU programming models (CUDA and OpenACC) is able to reduce considerably the execution time w.r.t. the use of CUDA and OpenACC only, achieving accelerations of up to more than one order of magnitude. Finally, we propose an interface to incorporate the concept of Static Graphs into the OpenACC Specifications.his research was funded by EPEEC project from the European Union’s Horizon 2020 Research and Innovation program under grant agreement No. 801051. This manuscript has been authored by UT-Battelle, LLC, under contract DE-AC05-00OR22725 with the US Department of Energy (DOE). The US government retains and the publisher, by accepting the article for publication, acknowledges that the US government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for US government purposes. DOE will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan, accessed on 13 April 2022).Peer ReviewedPostprint (published version

Wearable Movement Sensors for Rehabilitation: From Technology to Clinical Practice

This Special Issue shows a range of potential opportunities for the application of wearable movement sensors in motor rehabilitation. However, the papers surely do not cover the whole field of physical behavior monitoring in motor rehabilitation. Most studies in this Special Issue focused on the technical validation of wearable sensors and the development of algorithms. Clinical validation studies, studies applying wearable sensors for the monitoring of physical behavior in daily life conditions, and papers about the implementation of wearable sensors in motor rehabilitation are under-represented in this Special Issue. Studies investigating the usability and feasibility of wearable movement sensors in clinical populations were lacking. We encourage researchers to investigate the usability, acceptance, feasibility, reliability, and clinical validity of wearable sensors in clinical populations to facilitate the application of wearable movement sensors in motor rehabilitation