O2ATH: An OpenMP Offloading Toolkit for the Sunway Heterogeneous Manycore Platform

The next generation Sunway supercomputer employs the SW26010pro processor, which features a specialized on-chip heterogeneous architecture. Applications with significant hotspots can benefit from the great computation capacity improvement of Sunway many-core architectures by carefully making intensive manual many-core parallelization efforts. However, some legacy projects with large codebases, such as CESM, ROMS and WRF, contain numerous lines of code and do not have significant hotspots. The cost of manually porting such applications to the Sunway architecture is almost unaffordable. To overcome such a challenge, we have developed a toolkit named O2ATH. O2ATH forwards GNU OpenMP runtime library calls to Sunway's Athread library, which greatly simplifies the parallelization work on the Sunway architecture.O2ATH enables users to write both MPE and CPE code in a single file, and parallelization can be achieved by utilizing OpenMP directives and attributes. In practice, O2ATH has helped us to port two large projects, CESM and ROMS, to the CPEs of the next generation Sunway supercomputers via the OpenMP offload method. In the experiments, kernel speedups range from 3 to 15 times, resulting in 3 to 6 times whole application speedups.Furthermore, O2ATH requires significantly fewer code modifications compared to manually crafting CPE functions.This indicates that O2ATH can greatly enhance development efficiency when porting or optimizing large software projects on Sunway supercomputers.Comment: 15 pages, 6 figures, 5 tables

Using creative co-design to develop a decision support tool for people with malignant pleural effusion

Abstract: Background: Malignant pleural effusion (MPE) is a common, serious problem predominantly seen in metastatic lung and breast cancer and malignant pleural mesothelioma. Recurrence of malignant pleural effusion is common, and symptoms significantly impair people’s daily lives. Numerous treatment options exist, yet choosing the most suitable depends on many factors and making decisions can be challenging in pressured, time-sensitive clinical environments. Clinicians identified a need to develop a decision support tool. This paper reports the process of co-producing an initial prototype tool. Methods: Creative co-design methods were used. Three pleural teams from three disparate clinical sites in the UK were involved. To overcome the geographical distance between sites and the ill-health of service users, novel distributed methods of creative co-design were used. Local workshops were designed and structured, including video clips of activities. These were run on each site with clinicians, patients and carers. A joint national workshop was then conducted with representatives from all stakeholder groups to consider the findings and outputs from local meetings. The design team worked with participants to develop outputs, including patient timelines and personas. These were used as the basis to develop and test prototype ideas. Results: Key messages from the workshops informed prototype development. These messages were as follows. Understanding and managing the pleural effusion was the priority for patients, not their overall cancer journey. Preferred methods for receiving information were varied but visual and graphic approaches were favoured. The main influences on people’s decisions about their MPE treatment were personal aspects of their lives, for example, how active they are, what support they have at home. The findings informed the development of a first prototype/service visualisation (a video representing a web-based support tool) to help people identify personal priorities and to guide shared treatment decisions. Conclusion: The creative design methods and distributed model used in this project overcame many of the barriers to traditional co-production methods such as power, language and time. They allowed specialist pleural teams and service users to work together to create a patient-facing decision support tool owned by those who will use it and ready for implementation and evaluation

Robot graphic simulation testbed

The objective of this research was twofold. First, the basic capabilities of ROBOSIM (graphical simulation system) were improved and extended by taking advantage of advanced graphic workstation technology and artificial intelligence programming techniques. Second, the scope of the graphic simulation testbed was extended to include general problems of Space Station automation. Hardware support for 3-D graphics and high processing performance make high resolution solid modeling, collision detection, and simulation of structural dynamics computationally feasible. The Space Station is a complex system with many interacting subsystems. Design and testing of automation concepts demand modeling of the affected processes, their interactions, and that of the proposed control systems. The automation testbed was designed to facilitate studies in Space Station automation concepts

Application of Physiologically Based Pharmacokinetic Models in Chemical Risk Assessment

Post-exposure risk assessment of chemical and environmental stressors is a public health challenge. Linking exposure to health outcomes is a 4-step process: exposure assessment, hazard identification, dose response assessment, and risk characterization. This process is increasingly adopting “in silico” tools such as physiologically based pharmacokinetic (PBPK) models to fine-tune exposure assessments and determine internal doses in target organs/tissues. Many excellent PBPK models have been developed. But most, because of their scientific sophistication, have found limited field application—health assessors rarely use them. Over the years, government agencies, stakeholders/partners, and the scientific community have attempted to use these models or their underlying principles in combination with other practical procedures. During the past two decades, through cooperative agreements and contracts at several research and higher education institutions, ATSDR funded translational research has encouraged the use of various types of models. Such collaborative efforts have led to the development and use of transparent and user-friendly models. The “human PBPK model toolkit” is one such project. While not necessarily state of the art, this toolkit is sufficiently accurate for screening purposes. Highlighted in this paper are some selected examples of environmental and occupational exposure assessments of chemicals and their mixtures

Toward understanding I/O behavior in HPC workflows

Scientific discovery increasingly depends on complex workflows consisting of multiple phases and sometimes millions of parallelizable tasks or pipelines. These workflows access storage resources for a variety of purposes, including preprocessing, simulation output, and postprocessing steps. Unfortunately, most workflow models focus on the scheduling and allocation of com- putational resources for tasks while the impact on storage systems remains a secondary objective and an open research question. I/O performance is not usually accounted for in workflow telemetry reported to users. In this paper, we present an approach to augment the I/O efficiency of the individual tasks of workflows by combining workflow description frameworks with system I/O telemetry data. A conceptual architecture and a prototype implementation for HPC data center deployments are introduced. We also identify and discuss challenges that will need to be addressed by workflow management and monitoring systems for HPC in the future. We demonstrate how real-world applications and workflows could benefit from the approach, and we show how the approach helps communicate performance-tuning guidance to users

Design considerations for workflow management systems use in production genomics research and the clinic

Abstract The changing landscape of genomics research and clinical practice has created a need for computational pipelines capable of efficiently orchestrating complex analysis stages while handling large volumes of data across heterogeneous computational environments. Workflow Management Systems (WfMSs) are the software components employed to fill this gap. This work provides an approach and systematic evaluation of key features of popular bioinformatics WfMSs in use today: Nextflow, CWL, and WDL and some of their executors, along with Swift/T, a workflow manager commonly used in high-scale physics applications. We employed two use cases: a variant-calling genomic pipeline and a scalability-testing framework, where both were run locally, on an HPC cluster, and in the cloud. This allowed for evaluation of those four WfMSs in terms of language expressiveness, modularity, scalability, robustness, reproducibility, interoperability, ease of development, along with adoption and usage in research labs and healthcare settings. This article is trying to answer, which WfMS should be chosen for a given bioinformatics application regardless of analysis type?. The choice of a given WfMS is a function of both its intrinsic language and engine features. Within bioinformatics, where analysts are a mix of dry and wet lab scientists, the choice is also governed by collaborations and adoption within large consortia and technical support provided by the WfMS team/community. As the community and its needs continue to evolve along with computational infrastructure, WfMSs will also evolve, especially those with permissive licenses that allow commercial use. In much the same way as the dataflow paradigm and containerization are now well understood to be very useful in bioinformatics applications, we will continue to see innovations of tools and utilities for other purposes, like big data technologies, interoperability, and provenance

A Bayesian Abduction Model For Sensemaking

This research develops a Bayesian Abduction Model for Sensemaking Support (BAMSS) for information fusion in sensemaking tasks. Two methods are investigated. The first is the classical Bayesian information fusion with belief updating (using Bayesian clustering algorithm) and abductive inference. The second method uses a Genetic Algorithm (BAMSS-GA) to search for the k-best most probable explanation (MPE) in the network. Using various data from recent Iraq and Afghanistan conflicts, experimental simulations were conducted to compare the methods using posterior probability values which can be used to give insightful information for prospective sensemaking. The inference results demonstrate the utility of BAMSS as a computational model for sensemaking. The major results obtained are: (1) The inference results from BAMSS-GA gave average posterior probabilities that were 103 better than those produced by BAMSS; (2) BAMSS-GA gave more consistent posterior probabilities as measured by variances; and (3) BAMSS was able to give an MPE while BAMSS-GA was able to identify the optimal values for kMPEs. In the experiments, out of 20 MPEs generated by BAMSS, BAMSS-GA was able to identify 7 plausible network solutions resulting in less amount of information needed for sensemaking and reducing the inference search space by 7/20 (35%). The results reveal that GA can be used successfully in Bayesian information fusion as a search technique to identify those significant posterior probabilities useful for sensemaking. BAMSS-GA was also more robust in overcoming the problem of bounded search that is a constraint to Bayesian clustering and inference state space in BAMSS