Scientific Application Requirements for Leadership Computing at the Exascale

The Department of Energy s Leadership Computing Facility, located at Oak Ridge National Laboratory s National Center for Computational Sciences, recently polled scientific teams that had large allocations at the center in 2007, asking them to identify computational science requirements for future exascale systems (capable of an exaflop, or 1018 floating point operations per second). These requirements are necessarily speculative, since an exascale system will not be realized until the 2015 2020 timeframe, and are expressed where possible relative to a recent petascale requirements analysis of similar science applications [1]. Our initial findings, which beg further data collection, validation, and analysis, did in fact align with many of our expectations and existing petascale requirements, yet they also contained some surprises, complete with new challenges and opportunities. First and foremost, the breadth and depth of science prospects and benefits on an exascale computing system are striking. Without a doubt, they justify a large investment, even with its inherent risks. The possibilities for return on investment (by any measure) are too large to let us ignore this opportunity. The software opportunities and challenges are enormous. In fact, as one notable computational scientist put it, the scale of questions being asked at the exascale is tremendous and the hardware has gotten way ahead of the software. We are in grave danger of failing because of a software crisis unless concerted investments and coordinating activities are undertaken to reduce and close this hardwaresoftware gap over the next decade. Key to success will be a rigorous requirement for natural mapping of algorithms to hardware in a way that complements (rather than competes with) compilers and runtime systems. The level of abstraction must be raised, and more attention must be paid to functionalities and capabilities that incorporate intent into data structures, are aware of memory hierarchy, possess fault tolerance, exploit asynchronism, and are power-consumption aware. On the other hand, we must also provide application scientists with the ability to develop software without having to become experts in the computer science components. Numerical algorithms are scattered broadly across science domains, with no one particular algorithm being ubiquitous and no one algorithm going unused. Structured grids and dense linear algebra continue to dominate, but other algorithm categories will become more common. A significant increase is projected for Monte Carlo algorithms, unstructured grids, sparse linear algebra, and particle methods, and a relative decrease foreseen in fast Fourier transforms. These projections reflect the expectation of much higher architecture concurrency and the resulting need for very high scalability. The new algorithm categories that application scientists expect to be increasingly important in the next decade include adaptive mesh refinement, implicit nonlinear systems, data assimilation, agent-based methods, parameter continuation, and optimization. The attributes of leadership computing systems expected to increase most in priority over the next decade are (in order of importance) interconnect bandwidth, memory bandwidth, mean time to interrupt, memory latency, and interconnect latency. The attributes expected to decrease most in relative priority are disk latency, archival storage capacity, disk bandwidth, wide area network bandwidth, and local storage capacity. These choices by application developers reflect the expected needs of applications or the expected reality of available hardware. One interpretation is that the increasing priorities reflect the desire to increase computational efficiency to take advantage of increasing peak flops [floating point operations per second], while the decreasing priorities reflect the expectation that computational efficiency will not increase. Per-core requirements appear to be relatively static, while aggregate requirements will grow with the system. This projection is consistent with a relatively small increase in performance per core with a dramatic increase in the number of cores. Leadership system software must face and overcome issues that will undoubtedly be exacerbated at the exascale. The operating system (OS) must be as unobtrusive as possible and possess more stability, reliability, and fault tolerance during application execution. As applications will be more likely at the exascale to experience loss of resources during an execution, the OS must mitigate such a loss with a range of responses. New fault tolerance paradigms must be developed and integrated into applications. Just as application input and output must not be an afterthought in hardware design, job management, too, must not be an afterthought in system software design. Efficient scheduling of those resources will be a major obstacle faced by leadership computing centers at the exas..

Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis

: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes several proteins that inhibit host interferon responses. Among these, ORF6 antagonizes interferon signaling by disrupting nucleocytoplasmic trafficking through interactions with the nuclear pore complex components Nup98-Rae1. However, the roles and contributions of ORF6 during physiological infection remain unexplored. We assessed the role of ORF6 during infection using recombinant viruses carrying a deletion or loss-of-function (LoF) mutation in ORF6. ORF6 plays key roles in interferon antagonism and viral pathogenesis by interfering with nuclear import and specifically the translocation of IRF and STAT transcription factors. Additionally, ORF6 inhibits cellular mRNA export, resulting in the remodeling of the host cell proteome, and regulates viral protein expression. Interestingly, the ORF6:D61L mutation that emerged in the Omicron BA.2 and BA.4 variants exhibits reduced interactions with Nup98-Rae1 and consequently impairs immune evasion. Our findings highlight the role of ORF6 in antagonizing innate immunity and emphasize the importance of studying the immune evasion strategies of SARS-CoV-2

Modeling the Office of Science Ten Year Facilities Plan: The PERI Architecture Tiger Team

The Performance Engineering Institute (PERI) originally proposed a tiger team activity as a mechanism to target significant effort optimizing key Office of Science applications, a model that was successfully realized with the assistance of two JOULE metric teams. However, the Office of Science requested a new focus beginning in 2008: assistance in forming its ten year facilities plan. To meet this request, PERI formed the Architecture Tiger Team, which is modeling the performance of key science applications on future architectures, with S3D, FLASH and GTC chosen as the first application targets. In this activity, we have measured the performance of these applications on current systems in order to understand their baseline performance and to ensure that our modeling activity focuses on the right versions and inputs of the applications. We have applied a variety of modeling techniques to anticipate the performance of these applications on a range of anticipated systems. While our initial findings predict that Office of Science applications will continue to perform well on future machines from major hardware vendors, we have also encountered several areas in which we must extend our modeling techniques in order to fulfill our mission accurately and completely. In addition, we anticipate that models of a wider range of applications will reveal critical differences between expected future systems, thus providing guidance for future Office of Science procurement decisions, and will enable DOE applications to exploit machines in future facilities fully

Future and potential spending on health 2015-40: Development assistance for health, and government, prepaid private, and out-of-pocket health spending in 184 countries

Background: The amount of resources, particularly prepaid resources, available for health can affect access to health care and health outcomes. Although health spending tends to increase with economic development, tremendous variation exists among health financing systems. Estimates of future spending can be beneficial for policy makers and planners, and can identify financing gaps. In this study, we estimate future gross domestic product (GDP), all-sector government spending, and health spending disaggregated by source, and we compare expected future spending to potential future spending. Methods: We extracted GDP, government spending in 184 countries from 1980-2015, and health spend data from 1995-2014. We used a series of ensemble models to estimate future GDP, all-sector government spending, development assistance for health, and government, out-of-pocket, and prepaid private health spending through 2040. We used frontier analyses to identify patterns exhibited by the countries that dedicate the most funding to health, and used these frontiers to estimate potential health spending for each low-income or middle-income country. All estimates are inflation and purchasing power adjusted. Findings: We estimated that global spending on health will increase from US$9.21 trillion in 2014 to$24.24 trillion (uncertainty interval [UI] 20.47-29.72) in 2040. We expect per capita health spending to increase fastest in upper-middle-income countries, at 5.3% (UI 4.1-6.8) per year. This growth is driven by continued growth in GDP, government spending, and government health spending. Lower-middle income countries are expected to grow at 4.2% (3.8-4.9). High-income countries are expected to grow at 2.1% (UI 1.8-2.4) and low-income countries are expected to grow at 1.8% (1.0-2.8). Despite this growth, health spending per capita in low-income countries is expected to remain low, at $154 (UI 133-181) per capita in 2030 and$195 (157-258) per capita in 2040. Increases in national health spending to reach the level of the countries who spend the most on health, relative to their level of economic development, would mean $321 (157-258) per capita was available for health in 2040 in low-income countries. Interpretation: Health spending is associated with economic development but past trends and relationships suggest that spending will remain variable, and low in some low-resource settings. Policy change could lead to increased health spending, although for the poorest countries external support might remain essential

Future and potential spending on health 2015-40 : development assistance for health, and government, prepaid private, and out-of-pocket health spending in 184 countries

Background The amount of resources, particularly prepaid resources, available for health can affect access to health care and health outcomes. Although health spending tends to increase with economic development, tremendous variation exists among health financing systems. Estimates of future spending can be beneficial for policy makers and planners, and can identify financing gaps. In this study, we estimate future gross domestic product (GDP), all-sector government spending, and health spending disaggregated by source, and we compare expected future spending to potential future spending. Methods We extracted GDP, government spending in 184 countries from 1980-2015, and health spend data from 1995-2014. We used a series of ensemble models to estimate future GDP, all-sector government spending, development assistance for health, and government, out-of-pocket, and prepaid private health spending through 2040. We used frontier analyses to identify patterns exhibited by the countries that dedicate the most funding to health, and used these frontiers to estimate potential health spending for each low-income or middle-income country. All estimates are inflation and purchasing power adjusted. Findings We estimated that global spending on health will increase from US$9.21 trillion in 2014 to$24.24 trillion (uncertainty interval [UI] 20.47-29.72) in 2040. We expect per capita health spending to increase fastest in upper-middle-income countries, at 5.3% (UI 4.1-6.8) per year. This growth is driven by continued growth in GDP, government spending, and government health spending. Lower-middle income countries are expected to grow at 4.2% (3.8-4.9). High-income countries are expected to grow at 2.1% (UI 1.8-2.4) and low-income countries are expected to grow at 1.8% (1.0-2.8). Despite this growth, health spending per capita in low-income countries is expected to remain low, at $154 (UI 133-181) per capita in 2030 and$195 (157-258) per capita in 2040. Increases in national health spending to reach the level of the countries who spend the most on health, relative to their level of economic development, would mean $321 (157-258) per capita was available for health in 2040 in low-income countries. Interpretation Health spending is associated with economic development but past trends and relationships suggest that spending will remain variable, and low in some low-resource settings. Policy change could lead to increased health spending, although for the poorest countries external support might remain essential.Peer reviewe

The global, regional, and national burden of stomach cancer in 195 countries, 1990-2017 : a systematic analysis for the Global Burden of Disease study 2017

Background: Stomach cancer is a major health problem in many countries. Understanding the current burden of stomach cancer and the differential trends across various locations is essential for formulating effective preventive strategies. We report on the incidence, mortality, and disability-adjusted life-years (DALYs) due to stomach cancer in 195 countries and territories from 21 regions between 1990 and 2017. Methods: Estimates from GBD 2017 were used to analyse the incidence, mortality, and DALYs due to stomach cancer at the global, regional, and national levels. The rates were standardised to the GBD world population and reported per 100 000 population as age-standardised incidence rates, age-standardised death rates, and age-standardised DALY rates. All estimates were generated with 95% uncertainty intervals (UIs). Findings: In 2017, more than 1·22 million (95% UI 1·19–1·25) incident cases of stomach cancer occurred worldwide, and nearly 865 000 people (848 000–885 000) died of stomach cancer, contributing to 19·1 million (18·7–19·6) DALYs. The highest age-standardised incidence rates in 2017 were seen in the high-income Asia Pacific (29·5, 28·2–31·0 per 100 000 population) and east Asia (28·6, 27·3–30·0 per 100 000 population) regions, with nearly half of the global incident cases occurring in China. Compared with 1990, in 2017 more than 356 000 more incident cases of stomach cancer were estimated, leading to nearly 96 000 more deaths. Despite the increase in absolute numbers, the worldwide age-standardised rates of stomach cancer (incidence, deaths, and DALYs) have declined since 1990. The drop in the disease burden was associated with improved Socio-demographic Index. Globally, 38·2% (21·1–57·8) of the age-standardised DALYs were attributable to high-sodium diet in both sexes combined, and 24·5% (20·0–28·9) of the age-standardised DALYs were attributable to smoking in males. Interpretation: Our findings provide insight into the changing burden of stomach cancer, which is useful in planning local strategies and monitoring their progress. To this end, specific local strategies should be tailored to each country's risk factor profile. Beyond the current decline in age-standardised incidence and death rates, a decrease in the absolute number of cases and deaths will be possible if the burden in east Asia, where currently almost half of the incident cases and deaths occur, is further reduced. Funding: Bill & Melinda Gates Foundation

Burden of cardiovascular diseases in the Eastern Mediterranean Region, 1990-2015 : findings from the Global Burden of Disease 2015 study

To report the burden of cardiovascular diseases (CVD) in the Eastern Mediterranean Region (EMR) during 1990-2015. We used the 2015 Global Burden of Disease study for estimates of mortality and disability-adjusted life years (DALYs) of different CVD in 22 countries of EMR. A total of 1.4 million CVD deaths (95% UI: 1.3-1.5) occurred in 2015 in the EMR, with the highest number of deaths in Pakistan (465,116) and the lowest number of deaths in Qatar (723). The age-standardized DALY rate per 100,000 decreased from 10,080 in 1990 to 8606 in 2015 (14.6% decrease). Afghanistan had the highest age-standardized DALY rate of CVD in both 1990 and 2015. Kuwait and Qatar had the lowest age-standardized DALY rates of CVD in 1990 and 2015, respectively. High blood pressure, high total cholesterol, and high body mass index were the leading risk factors for CVD. The age-standardized DALY rates in the EMR are considerably higher than the global average. These findings call for a comprehensive approach to prevent and control the burden of CVD in the region.Peer reviewe

Transport injuries and deaths in the Eastern Mediterranean Region : findings from the Global Burden of Disease 2015 Study

Transport injuries (TI) are ranked as one of the leading causes of death, disability, and property loss worldwide. This paper provides an overview of the burden of TI in the Eastern Mediterranean Region (EMR) by age and sex from 1990 to 2015. Transport injuries mortality in the EMR was estimated using the Global Burden of Disease mortality database, with corrections for ill-defined causes of death, using the cause of death ensemble modeling tool. Morbidity estimation was based on inpatient and outpatient datasets, 26 cause-of-injury and 47 nature-of-injury categories. In 2015, 152,855 (95% uncertainty interval: 137,900-168,100) people died from TI in the EMR countries. Between 1990 and 2015, the years of life lost (YLL) rate per 100,000 due to TI decreased by 15.5%, while the years lived with disability (YLD) rate decreased by 10%, and the age-standardized disability-adjusted life years (DALYs) rate decreased by 16%. Although the burden of TI mortality and morbidity decreased over the last two decades, there is still a considerable burden that needs to be addressed by increasing awareness, enforcing laws, and improving road conditions.Peer reviewe

Neonatal, infant, and under-5 mortality and morbidity burden in the Eastern Mediterranean region: findings from the Global Burden of Disease 2015 study

Objectives Although substantial reductions in under-5 mortality have been observed during the past 35 years, progress in the Eastern Mediterranean Region (EMR) has been uneven. This paper provides an overview of child mortality and morbidity in the EMR based on the Global Burden of Disease (GBD) study. Methods We used GBD 2015 study results to explore under-5 mortality and morbidity in EMR countries. Results In 2015, 755,844 (95% uncertainty interval (UI) 712,064–801,565) children under 5 died in the EMR. In the early neonatal category, deaths in the EMR decreased by 22.4%, compared to 42.4% globally. The rate of years of life lost per 100,000 population under 5 decreased 54.38% from 177,537 (173,812–181,463) in 1990 to 80,985 (76,308–85,876) in 2015; the rate of years lived with disability decreased by 0.57% in the EMR compared to 9.97% globally. Conclusions Our findings call for accelerated action to decrease child morbidity and mortality in the EMR. Governments and organizations should coordinate efforts to address this burden. Political commitment is needed to ensure that child health receives the resources needed to end preventable deaths