Experiences from Software Engineering of Large Scale AMR Multiphysics Code Frameworks

Among the present generation of multiphysics HPC simulation codes there are many that are built upon general infrastructural frameworks. This is especially true of the codes that make use of structured adaptive mesh refinement (SAMR) because of unique demands placed on the housekeeping aspects of the code. They have varying degrees of abstractions between the infrastructure such as mesh management and IO and the numerics of the physics solvers. In this experience report we summarize the experiences and lessons learned from two of such major software efforts, FLASH and Chombo.Comment: Experience Repor

UPC++ v1.0 Programmer’s Guide, Revision 2020.3.0

UPC++ is a C++11 library that provides Partitioned Global Address Space (PGAS) programming. It is designed for writing parallel programs that run efficiently and scale well on distributed-memory parallel computers. The PGAS model is single program, multiple-data (SPMD), with each separate constituent process having access to local memory as it would in C++. However, PGAS also provides access to a global address space, which is allocated in shared segments that are distributed over the processes. UPC++ provides numerous methods for accessing and using global memory. In UPC++, all operations that access remote memory are explicit, which encourages programmers to be aware of the cost of communication and data movement. Moreover, all remote-memory access operations are by default asynchronous, to enable programmers to write code that scales well even on hundreds of thousands of cores

UPC++ v1.0 Programmer’s Guide, Revision 2019.9.0

UPC++ is a C++11 library that provides Partitioned Global Address Space (PGAS) programming. It is designed for writing parallel programs that run efficiently and scale well on distributed-memory parallel computers. The PGAS model is single program, multiple-data (SPMD), with each separate constituent process having access to local memory as it would in C++. However, PGAS also provides access to a global address space, which is allocated in shared segments that are distributed over the processes. UPC++ provides numerous methods for accessing and using global memory. In UPC++, all operations that access remote memory are explicit, which encourages programmers to be aware of the cost of communication and data movement. Moreover, all remote-memory access operations are by default asynchronous, to enable programmers to write code that scales well even on hundreds of thousands of cores

UPC++ v1.0 Specification, Revision 2019.9.0

UPC++ is a C++11 library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. We are revising the library under the auspices of the DOE’s Exascale Computing Project, to meet the needs of applications requiring PGAS support. UPC++ is intended for implementing elaborate distributed data structures where communication is irregular or fine-grained. The UPC++ interfaces for moving non-contiguous data and handling memories with different optimal access methods are composable and similar to those used in conventional C++. The UPC++ programmer can expect communication to run at close to hardware speeds. The key facilities in UPC++ are global pointers, that enable the programmer to express ownership information for improving locality, one-sided communication, both put/get and RPC, futures and continuations. Futures capture data readiness state, which is useful in making scheduling decisions, and continuations provide for completion handling via callbacks. Together, these enable the programmer to chain together a DAG of operations to execute asynchronously as high-latency dependencies become satisfied

Adalimumab and infliximab survival in patients with hidradenitis suppurativa:a daily practice cohort study

Background: Biologics are often required for the treatment of hidradenitis suppurativa (HS). However, data on the drug survival of biologics in daily practice are currently lacking. Objectives: To assess the d

The PLUTO Code for Adaptive Mesh Computations in Astrophysical Fluid Dynamics

We present a description of the adaptive mesh refinement (AMR) implementation of the PLUTO code for solving the equations of classical and special relativistic magnetohydrodynamics (MHD and RMHD). The current release exploits, in addition to the static grid version of the code, the distributed infrastructure of the CHOMBO library for multidimensional parallel computations over block-structured, adaptively refined grids. We employ a conservative finite-volume approach where primary flow quantities are discretized at the cell-center in a dimensionally unsplit fashion using the Corner Transport Upwind (CTU) method. Time stepping relies on a characteristic tracing step where piecewise parabolic method (PPM), weighted essentially non-oscillatory (WENO) or slope-limited linear interpolation schemes can be handily adopted. A characteristic decomposition-free version of the scheme is also illustrated. The solenoidal condition of the magnetic field is enforced by augmenting the equations with a generalized Lagrange multiplier (GLM) providing propagation and damping of divergence errors through a mixed hyperbolic/parabolic explicit cleaning step. Among the novel features, we describe an extension of the scheme to include non-ideal dissipative processes such as viscosity, resistivity and anisotropic thermal conduction without operator splitting. Finally, we illustrate an efficient treatment of point-local, potentially stiff source terms over hierarchical nested grids by taking advantage of the adaptivity in time. Several multidimensional benchmarks and applications to problems of astrophysical relevance assess the potentiality of the AMR version of PLUTO in resolving flow features separated by large spatial and temporal disparities.Comment: 34 pages, 34 figures, accepted for publication in ApJ

Hidradenitis suppurativa/acne inversa:A practical framework for treatment optimization - systematic review and recommendations from the HS ALLIANCE working group

Hidradenitis suppurativa (HS)/acne inversa is a debilitating chronic disease that remains poorly understood and difficult to manage. Clinical practice is variable, and there is a need for international, evidence-based and easily applicable consensus on HS management. We report here the findings of a systematic literature review, which were subsequently used as a basis for the development of international consensus recommendations for the management of patients with HS. A systematic literature review was performed for each of nine clinical questions in HS (defined by an expert steering committee), covering comorbidity assessment, therapy (medical, surgical and combinations) and response to treatment. Included articles underwent data extraction and were graded according to the Oxford Centre for Evidence-based Medicine criteria. Evidence-based recommendations were then drafted, refined and voted upon, using a modified Delphi process. Overall, 5310 articles were screened, 171 articles were analysed, and 65 were used to derive recommendations. These articles included six randomized controlled trials plus cohort studies and case series. The highest level of evidence concerned dosing recommendations for topical clindamycin in mild disease (with systemic tetracyclines for more frequent/widespread lesions) and biologic therapy (especially adalimumab) as second-line agents (following conventional therapy failure). Good-quality evidence was available for the hidradenitis suppurativa clinical response (HiSCR) as a dichotomous outcome measure in inflammatory areas under treatment. Lower-level evidence supported recommendations for topical triclosan and oral zinc in mild-to-moderate HS, systemic clindamycin and rifampicin in moderate HS and intravenous ertapenem in selected patients with more severe disease. Intralesional or systemic steroids may also be considered. Local surgical excision is suggested for mild-to-moderate HS, with wide excision for more extensive disease. Despite a paucity of good-quality data on management decisions in HS, this systematic review has enabled the development of robust and easily applicable clinical recommendations for international physicians based on graded evidence

Recidivism report 2002-2008. Trends in the reconviction rate of Dutch offenders

Policy programmes in the field of Dutch criminal law often aim at the reduction of recidivism; measures are taken to lower the risk of prosecuted offenders relapsing into criminal behaviour. Some years ago, specific targets were formulated with respect to two major offender groups. For convicted juvenile offenders, and for adult ex-prisoners, the medium-term recidivism will have to be reduced by 10 percentage points between 2002 and 2010 (VbbV, 2007). The current government also endorses the need to suppress recidivism (DSP, 2011). A substantial part of crime in the Netherlands is committed by persons who have been prosecuted before. Therefore, crime prevention is also the prevention of recidivism. The Recidivism Monitor is an ongoing research project carried out by the WODC. With this instrument the realisation of the recidivism targets can be monitored. Each year, the WODC reports on the reconviction rate of Dutch offenders. Nearly all persons who were suspect in a penal case are included in the study. The standard measurements of the Recidivism Monitor relate to five offender populations: adult offenders sanctioned by court or Public Prosecutor’s Service (PPS), juvenile offenders sanctioned by court or PPS, ex-prisoners, former inmates of juvenile detention centres and former offenders placed under an entrustment order (tbs).1 The reconviction rates in the tbs-sector are reported on separately (see int. al. Bregman & Wartna, 2011). This fact sheet outlines known recidivism in the other four offender populations. Specifically, the study relates to juveniles and adults who were sanctioned by court or PPS or released from a penitentiary institution in the years between 2002, the first year of the target period, and 2008, the latest year for which statistics are currently available