Experiences in porting mini-applications to OpenACC and OpenMP on heterogeneous systems

This article studies mini-applications—Minisweep, GenASiS, GPP, and FF—that use computational methods commonly encountered in HPC. We have ported these applications to develop OpenACC and OpenMP versions, and evaluated their performance on Titan (Cray XK7 with K20x GPUs), Cori (Cray XC40 with Intel KNL), Summit (IBM AC922 with Volta GPUs), and Cori-GPU (Cray CS-Storm 500NX with Intel Skylake and Volta GPUs). Our goals are for these new ports to be useful to both application and compiler developers, to document and describe the lessons learned and the methodology to create optimized OpenMP and OpenACC versions, and to provide a description of possible migration paths between the two specifications. Cases where specific directives or code patterns result in improved performance for a given architecture are highlighted. We also include discussions of the functionality and maturity of the latest compilers available on the above platforms with respect to OpenACC or OpenMP implementations

On-the-fly memory compression for multibody algorithms.

Memory and bandwidth demands challenge developers of particle-based codes that have to scale on new architectures, as the growth of concurrency outperforms improvements in memory access facilities, as the memory per core tends to stagnate, and as communication networks cannot increase bandwidth arbitrary. We propose to analyse each particle of such a code to find out whether a hierarchical data representation storing data with reduced precision caps the memory demands without exceeding given error bounds. For admissible candidates, we perform this compression and thus reduce the pressure on the memory subsystem, lower the total memory footprint and reduce the data to be exchanged via MPI. Notably, our analysis and transformation changes the data compression dynamically, i.e. the choice of data format follows the solution characteristics, and it does not require us to alter the core simulation code

Health professions students' interprofessional experiences on a rural learning platform

HEALTH PROFESSIONS STUDENTS’ LEARNING EXPERIENCES ON A RURAL COLLABORATIVE LEARNING PLATFORM ABSTRACTA Faculty of Health Sciences launched a rural collaborative learning platform to cultivate interprofessional key competencies and to improve health outcomes. The purpose of the study was to describe health sciences students’ experiences of an rural collaborative learning platform. Health professions students created digital stories reflecting on their collaborative learning experiences. Purposive sampling resulted in 23 submissions. Qualitative analysis of content identified themes and categories. Three themes, namely, metaphor, critical consciousness and professional socialisation, were identified. The metaphor categories, Journey, Setting world ablaze, Water, and Puzzle, represent students’ desire to use visual cues to describe their experiences. Transformation, Personal development and Empathy signified critical consciousness. Collaborative practice, Values, Reflective practice, and Key competencies relate to professional socialisation. The researchers gained understanding of students’ experiences on an rural collaborative learning platform. Through digital stories, students became aware of professional interdependency, which linked their experiences to key interprofessional competencies.

Parallel Unsmoothed Aggregation Algebraic Multigrid Algorithms on GPUs

We design and implement a parallel algebraic multigrid method for isotropic graph Laplacian problems on multicore Graphical Processing Units (GPUs). The proposed AMG method is based on the aggregation framework. The setup phase of the algorithm uses a parallel maximal independent set algorithm in forming aggregates and the resulting coarse level hierarchy is then used in a K-cycle iteration solve phase with a $\ell^1$-Jacobi smoother. Numerical tests of a parallel implementation of the method for graphics processors are presented to demonstrate its effectiveness.Comment: 18 pages, 3 figure

RIPK3-mediated cell death is involved in DUX4-mediated toxicity in facioscapulohumeral dystrophy

BACKGROUND: Facioscapulohumeral dystrophy (FSHD) is caused by mutations leading to the aberrant expression of the DUX4 transcription factor in muscles. DUX4 was proposed to induce cell death, but the involvement of different death pathways is still discussed. A possible pro-apoptotic role of DUX4 was proposed, but as FSHD muscles are characterized by necrosis and inflammatory infiltrates, non-apoptotic pathways may be also involved. METHODS: We explored DUX4-mediated cell death by focusing on the role of one regulated necrosis pathway called necroptosis, which is regulated by RIPK3. We investigated the effect of necroptosis on cell death in vitro and in vivo experiments using RIPK3 inhibitors and a RIPK3-deficient transgenic mouse model. RESULTS: We showed in vitro that DUX4 expression causes a caspase-independent and RIPK3-mediated cell death in both myoblasts and myotubes. In vivo, RIPK3-deficient animals present improved body and muscle weights, a reduction of the aberrant activation of the DUX4 network genes, and an improvement of muscle histology. CONCLUSIONS: These results provide evidence for a role of RIPK3 in DUX4-mediated cell death and open new avenues of research

On-the-fly memory compression for multibody algorithms

Memory and bandwidth demands challenge developers of particle-based codes that have to scale on new architectures, as the growth of concurrency outperforms improvements in memory access facilities, as the memory per core tends to stagnate, and as communication networks cannot increase bandwidth arbitrary. We propose to analyse each particle of such a code to find out whether a hierarchical data representation storing data with reduced precision caps the memory demands without exceeding given error bounds. For admissible candidates, we perform this compression and thus reduce the pressure on the memory subsystem, lower the total memory footprint and reduce the data to be exchanged via MPI. Notably, our analysis and transformation changes the data compression dynamically, i.e. the choice of data format follows the solution characteristics, and it does not require us to alter the core simulation code

PMS20 Baseline Characteristics of Rheumatoid Arthritis Patients Starting Certolizumab Pegol Therapy And Glucocorticoid Prescription In The Eclair Study In 2012–2013

International audienc

Emerging trends in non-communicable disease mortality in South Africa, 1997 - 2010

Objectives. National trends in age-standardised death rates (ASDRs) for non communicable diseases (NCDs) in South Africa (SA) were identified between 1997 and 2010.Methods. As part of the second National Burden of Disease Study, vital registration data were used after validity checks, proportional redistribution of missing age, sex and population group, demographic adjustments for registration incompleteness, and identification of misclassified AIDS deaths. Garbage codes were redistributed proportionally to specified codes by age, sex and population group. ASDRs were calculated using mid-year population estimates and the World Health Organization world standard.Results. Of 594 071 deaths in 2010, 38.9% were due to NCDs (42.6% females). ASDRs were 287/100 000 for cardiovascular diseases (CVDs), 114/100 000 for cancers (malignant neoplasms), 58/100 000 for chronic respiratory conditions and 52/100 000 for diabetes mellitus. An overall annual decrease of 0.4% was observed resulting from declines in stroke, ischaemic heart disease, oesophageal and lung cancer, asthma and chronic respiratory disease, while increases were observed for diabetes mellitus, renal disease, endocrine and nutritional disorders, and breast and prostate cancers. Stroke was the leading NCD cause of death, accounting for 17.5% of total NCD deaths. Compared with those for whites, NCD mortality rates for other population groups were higher at 1.3 for black Africans, 1.4 for Indians and 1.4 for coloureds, but varied by condition.Conclusions. NCDs contribute to premature mortality in SA, threatening socioeconomic development. While NCD mortality rates have decreased slightly, it is necessary to strengthen prevention and healthcare provision and monitor emerging trends in cause-specific mortality to inform these strategies if the target of 2% annual decline is to be achieved

Ultraviolet Imaging Polarimetry of the Large Magellanic Cloud. II. Models

Motivated by new sounding-rocket wide-field polarimetric images of the Large Magellanic Cloud, we have used a three-dimensional Monte Carlo radiation transfer code to investigate the escape of near-ultraviolet photons from young stellar associations embedded within a disk of dusty material (i.e. a galaxy). As photons propagate through the disk, they may be scattered or absorbed by dust. Scattered photons are polarized and tracked until they escape to be observed; absorbed photons heat the dust, which radiates isotropically in the far-infrared, where the galaxy is optically thin. The code produces four output images: near- UV and far-IR flux, and near-UV images in the linear Stokes parameters Q and U. From these images we construct simulated UV polarization maps of the LMC. We use these maps to place constraints on the star + dust geometry of the LMC and the optical properties of its dust grains. By tuning the model input parameters to produce maps that match the observed polarization maps, we derive information about the inclination of the LMC disk to the plane of the sky, and about the scattering phase function g. We compute a grid of models with i = 28 deg., 36 deg., and 45 deg., and g = 0.64, 0.70, 0.77, 0.83, and 0.90. The model which best reproduces the observed polarization maps has i = 36 +2/-5 degrees and g ~0.7. Because of the low signal-to-noise in the data, we cannot place firm constraints on the value of g. The highly inclined models do not match the observed centro-symmetric polarization patterns around bright OB associations, or the distribution of polarization values. Our models approximately reproduce the observed ultraviolet photopolarimetry of the western side of the LMC; however, the output images depend on many input parameters and are nonunique.Comment: Accepted to AJ. 20 pages, 7 figure

Tips for implementing multigrid methods on domains containing holes

As part of our development of a computer code to perform 3D `constrained evolution' of Einstein's equations in 3+1 form, we discuss issues regarding the efficient solution of elliptic equations on domains containing holes (i.e., excised regions), via the multigrid method. We consider as a test case the Poisson equation with a nonlinear term added, as a means of illustrating the principles involved, and move to a "real world" 3-dimensional problem which is the solution of the conformally flat Hamiltonian constraint with Dirichlet and Robin boundary conditions. Using our vertex-centered multigrid code, we demonstrate globally second-order-accurate solutions of elliptic equations over domains containing holes, in two and three spatial dimensions. Keys to the success of this method are the choice of the restriction operator near the holes and definition of the location of the inner boundary. In some cases (e.g. two holes in two dimensions), more and more smoothing may be required as the mesh spacing decreases to zero; however for the resolutions currently of interest to many numerical relativists, it is feasible to maintain second order convergence by concentrating smoothing (spatially) where it is needed most. This paper, and our publicly available source code, are intended to serve as semi-pedagogical guides for those who may wish to implement similar schemes.Comment: 18 pages, 11 figures, LaTeX. Added clarifications and references re. scope of paper, mathematical foundations, relevance of work. Accepted for publication in Classical & Quantum Gravit