Wolfgang E. Nagel

• Technische Universität Dresden

Substance use disorders (SUDs) are seen as a continuum ranging from goal‐directed and hedonic drug use to loss of control over drug intake with aversive consequences for mental and physical health and social functioning. The main goals of our interdisciplinary German collaborative research centre on Losing and Regaining Control over Drug Intake (Re...

Importance: Alcohol consumption (AC) leads to death and disability worldwide. Ongoing discussions on potential negative effects of the COVID-19 pandemic on AC need to be informed by real-world evidence. Objective: To examine whether lockdown measures are associated with AC and consumption-related temporal and psychological within-person mechanis...

With today’s top supercomputers consuming several megawatts of power, optimization of energy consumption has become one of the major challenges on the road to exascale computing. The EU Horizon 2020 project READEX provides a tools-aided auto-tuning methodology to dynamically tune HPC applications for energy-efficiency. READEX is a two-step methodol...

This book presents the proceedings of the 12th International Parallel Tools Workshop, held in Stuttgart, Germany, during September 17-18, 2018, and of the 13th International Parallel Tools Workshop, held in Dresden, Germany, during September 2-3, 2019. The workshops are a forum to discuss the latest advances in parallel tools for high-performance c...

This book presents the state-of-the-art in supercomputer simulation. It includes the latest findings from leading researchers using systems from the High Performance Computing Center Stuttgart (HLRS) in 2019. The reports cover all fields of computational science and engineering ranging from CFD to computational physics and from chemistry to compute...

This book presents the state-of-the-art in supercomputer simulation. It includes the latest findings from leading researchers using systems from the High Performance Computing Center Stuttgart (HLRS) in 2020. The reports cover all fields of computational science and engineering ranging from CFD to computational physics and from chemistry to compute...

The FFMK project designs, builds and evaluates a system-software architecture to address the challenges expected in Exascale systems. In particular, these challenges include performance losses caused by the much larger impact of runtime variability within applications, hardware, and operating system (OS), as well as increased vulnerability to failu...

As in the embedded systems domain, energy efficiency has recently become one of the main design criteria in high performance computing. The European Union Horizon 2020 project READEX (Run-time Exploitation of Application Dynamism for Energy-efficient eXascale computing) has developed a tools-aided auto-tuning methodology inspired by system scenario...

One of the major risk factors for global death and disability is alcohol, tobacco, and illicit drug use. While there is increasing knowledge with respect to individual factors promoting the initiation and maintenance of substance use disorders (SUDs), disease trajectories involved in losing and regaining control over drug intake (ReCoDe) are still...

Nowadays, the daily work of many research communities is characterized by an increasing amount and complexity of data. This makes it increasingly difficult to manage, access and utilize the data to ultimately gain scientific insights based on it. At the same time, domain scientists want to focus on their science instead of IT. The solution is resea...

The rising concern for power consumption of large-scale computer systems puts a research focus on the respective measurement methods. Varying workload patterns and energy efficiency optimizations cause highly dynamic power consumption on today’s compute nodes—a challenge for every measurement infrastructure. We identify five partly contradictory re...

The mean time between failures (MTBF) of HPC systems is rapidly reducing, and that current failure recovery mechanisms e.g., checkpoint-restart, will no longer be able to recover the systems from failures. Early failure detection is a new class of failure recovery methods that can be beneficial for HPC systems with short MTBF. System logs (syslogs)...

This book presents the proceedings of the 11th International Parallel Tools Workshop, a forum to discuss the latest advances in parallel tools, held September 11-12, 2017 in Dresden, Germany. High-performance computing plays an increasingly important role for numerical simulation and modeling in academic and industrial research. At the same time, u...

Since its launch in October 2014, the Competence Center for Scalable Data Services and Solutions (ScaDS) Dresden/Leipzig carries out collaborative research on Big Data methods and their use in challenging data science applications of different domains, leading to both general, and application-specific solutions and services. In this article, we giv...

With the explosion of the number of compute nodes, the bottleneck of future computing systems lies in the network architecture connecting the nodes. Addressing the bottleneck requires replacing current backplane-based network topologies. We propose to revolutionize computing electronics by realizing embedded optical waveguides for onboard networkin...

The efficient and intelligent handling of large, often distributed and heterogeneous data sets increasingly determines the scientific and economic competitiveness in most application areas. Mobile applications, social networks, multimedia collections, sensor networks, data intense scientific experiments, and complex simulations nowadays generate a...

This book presents the state-of-the-art in supercomputer simulation. It includes the latest findings from leading researchers using systems from the High Performance Computing Center Stuttgart (HLRS) in 2017. The reports cover all fields of computational science and engineering ranging from CFD to computational physics and from chemistry to compute...

Parallel and high performance computing experts are obsessed with performance and scalability. Performance analysis and tuning are important and complex but there are a number of software tools to support this. One methodology is the detailed recording of parallel runtime behavior in event traces and their subsequent analysis. This regularly produc...

Energy efficiency is an important aspect of future exascale systems, mainly due to rising energy cost. Although High performance computing (HPC) applications are compute centric, they still exhibit varying computational characteristics in different regions of the program, such as compute-, memory-, and I/O-bound code regions. Some of today’s cluste...

Biological research is increasingly dependent on analyzing vast amounts of microscopy datasets. Technologies such as Fiji/ImageJ2 and KNIME support knowledge extraction from biological data by providing a large set of configurable algorithms and an intuitive pipeline creation and execution interface. The increasing complexity of required analysis p...

Performance measurement and runtime tuning tools are both vital in the HPC software ecosystem and use similar techniques: the analyzed application is interrupted at specific events and information on the current system state is gathered to be either recorded or used for tuning. One of the established performance measurement tools is Score-P. It sup...

Load balance is one of the major challenges for efficient supercomputing, especially for applications that exhibit workload variations. Various dynamic load balancing and workload partitioning methods have been developed to handle this issue by migrating workload between nodes periodically during the runtime. However, on today’s top HPC systems–and...

Modern processors incorporate several performance monitoring units, which can be used to count events that occur within different components of the processor. They provide access to information on hardware resource usage and can therefore be used to detect performance bottlenecks. Thus, many performance measurement tools are able to record them com...

Science gateways are employed to hide increasingly complex IT infrastructures from users via easy-to-use graphical interfaces while enabling IT-driven research not possible before. The science gateway MoSGrid (Molecular Simulation Grid) is a valuable and user-friendly workbench to submit and process molecular simulation studies on a large scale. Wi...

Nowadays, the daily work of many research communities is characterized by an increasing amount and complexity of data. This makes it increasingly difficult to manage, access and utilize to ultimately gain scientific insights based on it. At the same time, domain scientists want to focus on their science instead of IT. The solution is research data...

Nowadays, the daily work of many research communities is characterized by an increasing amount and complexity of data. This makes it increasingly difficult to manage, access and utilize to ultimately gain scientific insights based on it. At the same time, domain scientists want to focus on their science instead of IT. The solution is research data...

This book presents the proceedings of the 10th International Parallel Tools Workshop, held October 4-5, 2016 in Stuttgart, Germany – a forum to discuss the latest advances in parallel tools. High-performance computing plays an increasingly important role for numerical simulation and modelling in academic and industrial research. At the same time, u...

Nowadays, the daily work of many research communities is characterized by an increasing amount and complexity of data. This makes it increasingly difficult to manage, access and utilize to ultimately gain scientific insights based on it. At the same time, domain scientists want to focus on their science instead of IT. The solution is research data...

Research data management is of the utmost importance in a world where research data is created with an ever increasing amount and rate and with a high variety across all scientific disciplines. This paper especially discusses software engineering challenges stemming from creating a long-living software system. It aims at providing a reference imple...

In event-based performance analysis the amount of collected data is one of the most urgent challenges. It can massively slow down application execution, overwhelm the underlying file system and introduce significant measurement bias due to intermediate memory buffer flushes. To address these issues we propose an in-memory event tracing approach tha...

Intraoperative thermal imaging is an emerging technology to analyse cortical perfusion in neurosurgery. Neural activity monitoring represents one important application which can be achieved by exploiting neurovascular coupling. Increased metabolism caused by neural activity leads to local perfusion changes in eloquent areas of the brain that also c...

The Message Passing Interface (MPI) includes nonblocking collective operations that support additional overlap between computation and communication. These new operations enable complex data movement between large numbers of processes. However, their asynchronous behavior hides and complicates the detection of defects in their use. We highlight a l...

Dynamic load balancing with diffusive methods is known to provide minimal load transfer and requires communication between neighbor nodes only. These are very attractive properties for highly parallel systems. We compare diffusive methods with state-of-the-art geometrical and graph-based partitioning methods on thousands of nodes. When load balanci...

In this paper we address the problem of locating race conditions among synchronization primitives in execution traces of hybrid parallel programs. In hybrid parallel programs collective and point-to-point synchronization can’t be analyzed separately. We introduce a model for synchronization primitives and formally define synchronization races with...

With the appearance of the heterogeneous platform OpenPower, many-core accelerator devices have been coupled with Power host processors for the first time. Towards utilizing their full potential, it is worth investigating performance portable algorithms that allow to choose the best-fitting hardware for each domain-specific compute task. Suiting ev...

With the appearance of the heterogeneous platform OpenPower,many-core accelerator devices have been coupled with Power host processors for the first time. Towards utilizing their full potential, it is worth investigating performance portable algorithms that allow to choose the best-fitting hardware for each domain-specific compute task. Suiting eve...

Porting applications to new hardware or programming models is a tedious and error prone process. Every help that eases these burdens is saving developer time that can then be invested into the advancement of the application itself instead of preserving the status-quo on a new platform. The Alpaka library defines and implements an abstract hierarchi...

The utility of simulations depends on the confidence in the simulation implementation and its results. This study discusses the verification of the communication models in the parallel trace-driven simulation framework HAEC-SIM. As simulation input, a parallel application is executed and recorded on an existing HPC system. The simulation focuses on...

Porting applications to new hardware or programming models is a tedious and error prone process. Every help that eases these burdens is saving developer time that can then be invested into the advancement of the application itself instead of preserving the status-quo on a new platform. The Alpaka library defines and implements an abstract hierarchi...

This extension enables KNIME 3.2 and newer to execute (sub-)workflows remotely on cluster systems with Unicore and Unity. Hereby, a single subworkflow can be executed remotely. In case of data-parallel workflows it is also possible to split input to the workflow into several non-overlapping chunks with each chunk being submitted as seperate job to...

This book presents the state-of-the-art in supercomputer simulation. It includes the latest findings from leading researchers using systems from the High Performance Computing Center Stuttgart (HLRS) in 2015. The reports cover all fields of computational science and engineering ranging from CFD to computational physics and from chemistry to compute...

In this paper we describe the hardware and application-inherent challenges that future exascale systems pose to high-performance computing (HPC) and propose a system architecture that addresses them. This architecture is based on proven building blocks and few principles: (1) a fast light-weight kernel that is supported by a virtualized Linux for t...

This is the archive containing the software used for evaluations in the publication "Performance-Portable Many-Core Plasma Simulations: Porting PIConGPU to OpenPower and Beyond" submitted to the international workshop on OpenPOWER for HPC 2016. The archive has the following content: PIConGPU Kelvin-Helmholtz Simulation code (picongpu-alpaka/): Remo...

High Performance Computing (HPC) remains a driver that offers huge potentials and benefits for science and society. However, a profound understanding of the computational matters and specialized software is needed to arrive at effective and efficient simulations. Dedicated software tools are important parts of the HPC software landscape, and suppor...

This book presents the state-of-the-art in supercomputer simulation. It includes the latest findings from leading researchers using systems from the High Performance Computing Center Stuttgart (HLRS) in 2016. The reports cover all fields of computational science and engineering ranging from CFD to computational physics and from chemistry to compute...

A major challenge in the design of contemporary microprocessors is the increasing number of cores in conjunction with the persevering need for cache coherence. To achieve this, the memory subsystem steadily gains complexity that has evolved to levels beyond comprehension of most application performance analysts. The Intel Haswell-EP architecture is...

Zusammenfassung Große zylindrische Stahlprüflinge werden mittels der Methode der finiten Differenzen im Zeitbereich (engl.

Practical experiments on the flow in a lid-driven cavity are carried out to compare the performance of a second-order finite volume Navier-Stokes solver for incompressible fluids employing a projection method, when using various linear solver libraries on central processing units (CPUs) and graphical processing units (GPUs). The goal of the paper i...

Distributed data life cycles consist of data sources, data and computing components as well as data sinks and user facing elements. The complexity of the underlying systems is ever rising with the increasing heterogeneity and distribution of components and environments. Researchers would like to focus on their specific research topic without the ne...

The popular and diverse hardware accelerator ecosystem makes apples-to-apples comparisons between platforms rather difficult. SPEC ACCEL tries to offer a yardstick to compare different accelerator hardware and software ecosystems. This paper uses this SPEC benchmark to compare an AMD GPU, an NVIDIA GPU and an Intel Xeon Phi with respect to performa...

This work presents a new trace-based parallel discrete event simulation framework designed for predicting the behavior of a novel computing platform running energy-aware parallel applications. Discrete event traces capture the runtime be- havior of parallel applications on existing systems and form the basis for the simulation. The simulation frame...

The sheer volume of data accumulated in many scientific disciplines as well as in industry is a critical point that requires immediate attention. The handling of large data sets will become a limiting factor-even for data intensive applications running on future Exascale systems. Nowadays, Big Data can be more a collection of challenges for data pr...

Proceedings of the 8th International Workshop on Parallel Tools for High Performance Computing, October 2014, HLRS, Stuttgart, Germany

Hybrid nodes with hardware accelerators are becoming very common in systems today. Users often find it di to characterize and understand the performance advantage of such accelerators for their applications. The SPEC High Performance Group (HPG) has developed a set of performance metrics to evaluate the performance and power consumption of accelera...

Accurate and fine-grained power measurements of computing systems are essential for energy-aware performance optimizations of HPC systems and applications. Although cluster wide instrumentation options are available, fine spatial granularity and temporal resolution are not supported by the system vendors and extra hardware is needed to capture the...

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA Glioblastoma multiforme (GBM) is the most prevalent malignant primary brain tumor in adults. GBM is classified as primary if it is assumed to have arisen de novo or as secondary if it progressed from lower grade astrocytoma. Previous studies have found that primary and secondary...

In this paper, we propose a holistic approach for the analysis of parallel applications on a high performance–low energy computer (called the HAEC platform). The HAEC platform is currently under design and refers to an architecture in which multiple 3-D stacked massively parallel processor chips are optically interconnected on a single board and mu...

During the execution of parallel applications, there might be a very large number of exchanged messages between the computing nodes. Hence, the communication delays crucially influence the execution time of the whole application and a suitable communication approach should be selected to minimize the execution time. Selecting a suitable communicati...

High performance computing (HPC) systems are getting more and more powerful but also more and more complex. Supportive environments such as performance analysis tools are essential to assist developers in utilizing the computing resources of such complex systems. One of the most urgent challenges in event based performance analysis is the enormous...

State-of-the-art research in a variety of natural sciences depends heavily on methods of computational chemistry, for example, the calculation of the properties of materials, proteins, catalysts, and drugs. Applications providing such methods require a lot of expertise to handle their complexity and the usage of high-performance computing. The MoSG...

Scientific data life cycles are becoming more and more demanding. Data amounts are seen to be ever increasing while at the same time advanced IT infrastructures become more common resulting in a much broader user group demanding a high usability. These challenges are met with a distributed science gateway infrastructure, which in turn is complex in...

The decomposition of one-dimensional workload arrays into consecutive partitions is a core problem of many load balancing methods, especially those based on space-filling curves. While previous work has shown that heuristics can be parallelized, only sequential algorithms exist for the optimal solution. However, centralized partitioning will become...

Virtual high-throughput screening (vHTS) is an invaluable method in modern drug discovery. It permits screening large datasets or databases of chemical structures for those structures binding possibly to a drug target. Virtual screening is typically performed by docking code, which often runs sequentially. Processing of huge vHTS datasets can be pa...

MoSGrid (Molecular Simulation Grid) is a user-friendly and highly efficient science gateway which contains three domains for the different methodologies used in chemistry: quantum chemistry, molecular dynamics, and docking. Workflows are implemented by using the WS-PGRADE technology. By adding an abstraction layer, we are able to develop meta-metaw...

The MoSGrid portal offers an approach to carry out high-quality molecular simulations on distributed compute infrastructures to scientists with all kinds of background and experience levels. A user friendly web interface guarantees the ease-of-use of modern chemical simulation applications well established in the field. The usage of well-defined wo...

We introduce novel ideas involving aspect-oriented instrumentation, Multi-Faceted Program Monitoring, as well as novel techniques for a selective and detailed event-based application performance analysis, with an eye toward exascale. We give special attention to the spatial, temporal, and level-of-detail aspects of the three important phases of com...

Tools are essential for application developers and system support personnel during tasks such as performance optimization and debugging of massively parallel applications. An important class are event-based tools that analyze relevant events during the runtime of an application, e.g., function invocations or communication operations. We develop a p...

Programming development tools are a vital component for understanding the behavior of parallel applications. Event tracing is a principal ingredient to these tools, but new and serious challenges place event tracing at risk on extreme-scale machines. As the quantity of captured events increases with concurrency, the additional data can overload the...

We propose a spectral element multigrid method for the two-dimensional Helmholtz equation discretized on regular grids. Combining p-multigrid with static condensation the method achieves nearly linear complexity with an order-independent convergence rate for solving the condensed equations. For smoothing we consider two groups of edge-based relaxat...

This book presents the state-of-the-art in simulation on supercomputers. Leading researchers present results achieved on systems of the High Performance Computing Center Stuttgart (HLRS) for the year 2012. The reports cover all fields of computational science and engineering ranging from CFD via computational physics and chemistry to computer scien...

The widely used Message Passing Interface (MPI) with its multitude of communication functions is prone to usage errors. Runtime error detection tools aid in the removal of these errors. We develop MUST as one such tool that provides a wide variety of automatic correctness checks. Its correctness checks can be run in a distributed mode, except for i...

We present a particle-in-cell simulation of the relativistic Kelvin-Helmholtz Instability (KHI) that for the first time delivers angularly resolved radiation spectra of the particle dynamics during the formation of the KHI. This enables studying the formation of the KHI with unprecedented spatial, angular and spectral resolution. Our results are of...

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