Automatic aggregation of subtask accesses for nested OpenMP-style tasks

Task-based programming is a high performance and productive model to express parallelism. Tasks encapsulate work to be executed across multiple cores or offloaded to GPUs, FPGAs, other accelerators or other nodes. In order to maintain parallelism and afford maximum freedom to the scheduler, the task dependency graph should be created in parallel and well in advance of task execution. A key limitation with OpenMP and OmpSs-2 tasking is that a task cannot be created until all its accesses and its descendents' accesses are known. Current approaches to work around this limitation either stop task creation and execution using a taskwait or they substitute “fake” accesses known as sentinels. This paper proposes the auto clause, which indicates that the task may create subtasks that access unspecified memory regions or it may allocate and return memory at addresses that are of course not yet known. Unlike approaches using taskwaits, there is no interruption to the concurrent creation and execution of tasks, maintaining parallelism and the scheduler's ability to optimize load balance and data locality. Unlike existing approaches using sentinels, all tasks can be given a precise specification of their own data accesses, so that a single mechanism is used to control task ordering, program data transfers on distributed memory and optimize data locality, e.g. on NUMA systems. The auto clause also provides an incremental path to develop programs with nested tasks, by removing the need for every parent task to have a complete specification of the accesses of its descendent tasks. This is redundant information that can be time consuming and error-prone to describe. We present a straightforward runtime implementation that achieves a 1.4 times speedup for n-body with OmpSs-2@Cluster task offloading to 32 nodes and <4% slowdown for three benchmarks with task offloading to 8 nodes. All code is open source.This research has received funding from the European Unions Horizon 2020/EuroHPC research and innovation programme under grant agreement No 955606 (DEEP- SEA) and 754337 (EuroEXA). It is supported by the Spanish State Research Agency - Ministry of Science and Innovation (contract PID2019-107255GB- C21/MCIN/AEI/10.13039/501100011033 and Ramon y Cajal fellowship RYC2018-025628-I/MCIN/AEI/ 10.13039/501100011033 and by “ESF Investing in your future”), as well as by the Generalitat de Catalunya (2017-SGR-1414).Peer ReviewedPostprint (author's final draft

Razvoj i karakterizacija in situ gelirajućih pripravaka metronidazola na bazi pluronika za vaginalnu primjenu

The purpose of this study was to develop pluronic-based in situ gelling formulations of metronidazole (MTZ) for treatment of bacterial vaginosis, aimed at prolonging the residence time, controlling drug release, enhancing efficacy, decreasing recurrence, and increasing patient compliance. The in situ gel formulations were prepared using different concentrations of pluronic F-127 (PF-127) alone and in combination with pluronic F-68 (PF-68). The prepared formulations were evaluated for their gelation temperature (Tgel), in vitro drug release, rheological properties, mucoadhesion properties and tolerability by vaginal mucosa in tissue levels. The Tgel decreased with increasing PF-127 concentration. The Tgel was modulated by addition of PF-68 to be within the acceptable range of 25–37 ºC. With increasing pluronic concentration, the in vitro drug release decreased, viscosity and mucoadhesive force increased. Histopathological examination of rabbit vaginas from the control and treated groups revealed normal histology of the vagina and cervix. Based on the in vitro evaluation of prepared formulations, the in situ gelling liquid formulated with PF-127/PF-68 (20/10 %, m/m) was selected for further clinical evaluation.Cilj rada bio je razviti pripravke metronidazola (MTZ) za liječenje bakterijske vaginoze koji imaju sposobnost geliranja in situ, produljeno vrijeme zadržavanja na mjestu primjene, kontrolirano oslobađanje ljekovite tvari, povećanu učinkovitost te smanjiti ponovnu pojavu vaginoze i povećati suradljivost pacijenta. Pripravci koji geliraju in situ pripravljeni su koristeći različite koncentracije pluronika F-127 (PF-127), samog ili u kombinaciji s pluronikom F-68 (PF-68). Ispitivana je temperatura geliranja (Tgel) formulacija, in vitro oslobađanje ljekovite tvari, reološka svojstva, mukoadhezijska svojstva te kako ih podnaša vaginalna sluznica u slojevima tkiva. Uočeno je da se s povećanjem koncentracije PF-127 snižava Tgel. Dodatkom različitih količina PF-68 dobiveni su pripravci s rasponom Tgel od 25 do 37 ºC. S povećanjem koncentracije pluronika smanjilo se oslobađanje ljekovite tvari in vitro, a povećala se viskoznost i mukoadhezivnost. Histopatološka ispitivanja na zečicama ispitivane i kontrolne skupine dala su normalni histološki nalaz njihovih vagina i cerviksa. Na temelju in vitro evaluacije, formulacija s PF-127/PF-68 (20/10 %, m/m) izabrana je za daljnja klinička ispitivanja

Transparent load balancing of MPI programs using OmpSs-2@Cluster and DLB

Load imbalance is a long-standing source of inefficiency in high performance computing. The situation has only got worse as applications and systems increase in complexity, e.g., adaptive mesh refinement, DVFS, memory hierarchies, power and thermal management, and manufacturing processes. Load balancing is often implemented in the application, but it obscures application logic and may need extensive code refactoring. This paper presents an automated and transparent dynamic load balancing approach for MPI applications with OmpSs-2 tasks, which relieves applications from this burden. Only local and trivial changes are required to the application. Our approach exploits the ability of OmpSs-2@Cluster to offload tasks for execution on other nodes, and it reallocates compute resources among ranks using the Dynamic Load Balancing~(DLB) library. It employs LeWI to react to fine-grained load imbalances and DROM to address coarse-grained load imbalances by reserving cores on other nodes that can be reclaimed on demand. We use an expander graph to limit the amount of point-to-point communication and state. The results show 46% reduction in time-to-solution for micro-scale solid mechanics on 32 nodes and a 20% reduction beyond DLB for $n$-body on 16 nodes, when one node is running slow. A synthetic benchmark shows that performance is within 10% of optimal for an imbalance of up to 2.0 on 8 nodes. All software is released open source.This research has received funding from the European Union’s Horizon 2020/EuroHPC research and innovation programme under grant agreement No 955606 (DEEP-SEA) and 754337 (EuroEXA). It is supported by the Spanish State Research Agency - Ministry of Science and Innovation (contract PID2019-107255GB and Ramon y Cajal fellowship RYC2018-025628-I) and by the Generalitat de Catalunya (2017-SGR-1414).Peer ReviewedPostprint (author's final draft

EuroEXA - D2.6: Final ported application software

This document describes the ported software of the EuroEXA applications to the single CRDB testbed and it discusses the experiences extracted from porting and optimization activities that should be actively taken into account in future redesign and optimization. This document accompanies the ported application software, found in the EuroEXA private repository (https://github.com/euroexa). In particular, this document describes the status of the software for each of the EuroEXA applications, sketches the redesign and optimization strategy for each application, discusses issues and difficulties faced during the porting activities and the relative lesson learned. A few preliminary evaluation results have been presented, however the full evaluation will be discussed in deliverable 2.8

Impact of opioid-free analgesia on pain severity and patient satisfaction after discharge from surgery: multispecialty, prospective cohort study in 25 countries

Background: Balancing opioid stewardship and the need for adequate analgesia following discharge after surgery is challenging. This study aimed to compare the outcomes for patients discharged with opioid versus opioid-free analgesia after common surgical procedures.Methods: This international, multicentre, prospective cohort study collected data from patients undergoing common acute and elective general surgical, urological, gynaecological, and orthopaedic procedures. The primary outcomes were patient-reported time in severe pain measured on a numerical analogue scale from 0 to 100% and patient-reported satisfaction with pain relief during the first week following discharge. Data were collected by in-hospital chart review and patient telephone interview 1 week after discharge.Results: The study recruited 4273 patients from 144 centres in 25 countries; 1311 patients (30.7%) were prescribed opioid analgesia at discharge. Patients reported being in severe pain for 10 (i.q.r. 1-30)% of the first week after discharge and rated satisfaction with analgesia as 90 (i.q.r. 80-100) of 100. After adjustment for confounders, opioid analgesia on discharge was independently associated with increased pain severity (risk ratio 1.52, 95% c.i. 1.31 to 1.76; P &lt; 0.001) and re-presentation to healthcare providers owing to side-effects of medication (OR 2.38, 95% c.i. 1.36 to 4.17; P = 0.004), but not with satisfaction with analgesia (beta coefficient 0.92, 95% c.i. -1.52 to 3.36; P = 0.468) compared with opioid-free analgesia. Although opioid prescribing varied greatly between high-income and low- and middle-income countries, patient-reported outcomes did not.Conclusion: Opioid analgesia prescription on surgical discharge is associated with a higher risk of re-presentation owing to side-effects of medication and increased patient-reported pain, but not with changes in patient-reported satisfaction. Opioid-free discharge analgesia should be adopted routinely

Effects of hospital facilities on patient outcomes after cancer surgery: an international, prospective, observational study

Background Early death after cancer surgery is higher in low-income and middle-income countries (LMICs) compared with in high-income countries, yet the impact of facility characteristics on early postoperative outcomes is unknown. The aim of this study was to examine the association between hospital infrastructure, resource availability, and processes on early outcomes after cancer surgery worldwide.Methods A multimethods analysis was performed as part of the GlobalSurg 3 study-a multicentre, international, prospective cohort study of patients who had surgery for breast, colorectal, or gastric cancer. The primary outcomes were 30-day mortality and 30-day major complication rates. Potentially beneficial hospital facilities were identified by variable selection to select those associated with 30-day mortality. Adjusted outcomes were determined using generalised estimating equations to account for patient characteristics and country-income group, with population stratification by hospital.Findings Between April 1, 2018, and April 23, 2019, facility-level data were collected for 9685 patients across 238 hospitals in 66 countries (91 hospitals in 20 high-income countries; 57 hospitals in 19 upper-middle-income countries; and 90 hospitals in 27 low-income to lower-middle-income countries). The availability of five hospital facilities was inversely associated with mortality: ultrasound, CT scanner, critical care unit, opioid analgesia, and oncologist. After adjustment for case-mix and country income group, hospitals with three or fewer of these facilities (62 hospitals, 1294 patients) had higher mortality compared with those with four or five (adjusted odds ratio [OR] 3.85 [95% CI 2.58-5.75]; p&lt;0.0001), with excess mortality predominantly explained by a limited capacity to rescue following the development of major complications (63.0% vs 82.7%; OR 0.35 [0.23-0.53]; p&lt;0.0001). Across LMICs, improvements in hospital facilities would prevent one to three deaths for every 100 patients undergoing surgery for cancer.Interpretation Hospitals with higher levels of infrastructure and resources have better outcomes after cancer surgery, independent of country income. Without urgent strengthening of hospital infrastructure and resources, the reductions in cancer-associated mortality associated with improved access will not be realised

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection

OmpSs-2@Cluster: Distributed memory execution of nested OpenMP-style tasks

State-of-the-art programming approaches generally have a strict division between intra-node shared memory parallelism and inter-node MPI communication. Tasking with dependencies offers a clean, dependable abstraction for a wide range of hardware and situations within a node, but research on task offloading between nodes is still relatively immature. This paper presents a flexible task offloading extension of the OmpSs-2 programming model, which inherits task ordering from a sequential version of the code and uses a common address space to avoid address translation and simplify the use of data structures with pointers. It uses weak dependencies to enable work to be created concurrently. The program is executed in distributed dataflow fashion, and the runtime system overlaps the construction of the distributed dependency graph, enforces dependencies, transfers data, and schedules tasks for execution. Asynchronous task parallelism avoids synchronization that is often required in MPI+OpenMP tasks. Task scheduling is flexible, and data location is tracked through the dependencies. We wish to enable future work in resiliency, scalability, load balancing and malleability, and therefore release all source code and examples open source.This research has received funding from the European Union’s Horizon 2020/EuroHPC research and innovation programme under grant agreement No 955606 (DEEP-SEA) and 754337 (EuroEXA). It is supported by the Spanish State Research Agency - Ministry of Science and Innovation (contract PID2019-107255GB and Ramon y Cajal fellowship RYC2018-025628-I) and by the Generalitat de Catalunya (2017-SGR-1414).Peer ReviewedPostprint (author's final draft

Global variation in postoperative mortality and complications after cancer surgery: a multicentre, prospective cohort study in 82 countries

Background: 80% of individuals with cancer will require a surgical procedure, yet little comparative data exist on early outcomes in low-income and middle-income countries (LMICs). We compared postoperative outcomes in breast, colorectal, and gastric cancer surgery in hospitals worldwide, focusing on the effect of disease stage and complications on postoperative mortality. Methods: This was a multicentre, international prospective cohort study of consecutive adult patients undergoing surgery for primary breast, colorectal, or gastric cancer requiring a skin incision done under general or neuraxial anaesthesia. The primary outcome was death or major complication within 30 days of surgery. Multilevel logistic regression determined relationships within three-level nested models of patients within hospitals and countries. Hospital-level infrastructure effects were explored with three-way mediation analyses. This study was registered with ClinicalTrials.gov, NCT03471494. Findings: Between April 1, 2018, and Jan 31, 2019, we enrolled 15 958 patients from 428 hospitals in 82 countries (high income 9106 patients, 31 countries; upper-middle income 2721 patients, 23 countries; or lower-middle income 4131 patients, 28 countries). Patients in LMICs presented with more advanced disease compared with patients in high-income countries. 30-day mortality was higher for gastric cancer in low-income or lower-middle-income countries (adjusted odds ratio 3·72, 95% CI 1·70–8·16) and for colorectal cancer in low-income or lower-middle-income countries (4·59, 2·39–8·80) and upper-middle-income countries (2·06, 1·11–3·83). No difference in 30-day mortality was seen in breast cancer. The proportion of patients who died after a major complication was greatest in low-income or lower-middle-income countries (6·15, 3·26–11·59) and upper-middle-income countries (3·89, 2·08–7·29). Postoperative death after complications was partly explained by patient factors (60%) and partly by hospital or country (40%). The absence of consistently available postoperative care facilities was associated with seven to 10 more deaths per 100 major complications in LMICs. Cancer stage alone explained little of the early variation in mortality or postoperative complications. Interpretation: Higher levels of mortality after cancer surgery in LMICs was not fully explained by later presentation of disease. The capacity to rescue patients from surgical complications is a tangible opportunity for meaningful intervention. Early death after cancer surgery might be reduced by policies focusing on strengthening perioperative care systems to detect and intervene in common complications. Funding: National Institute for Health Research Global Health Research Unit