TY - JOUR A1 - Ziegler, Alexander A1 - Ogurreck, Malte A1 - Steinke, Thomas A1 - Beckmann, Felix A1 - Prohaska, Steffen A1 - Ziegler, Andreas T1 - Opportunities and challenges for digital morphology JF - Biology Direct Y1 - 2010 U6 - https://doi.org/10.1186/1745-6150-5-45 VL - 5 IS - 1 SP - 45 ER - TY - JOUR A1 - Zhong, Xin A1 - Höfling, Felix A1 - John, Timm T1 - Hydrogen diffusion in garnet: insights from atomistic simulations JF - Geochemistry Geophysics Geosystems N2 - Garnet has been widely used to decipher the pressure-temperature-time history of rocks, but its physical properties such as elasticity and diffusion are strongly affected by trace amounts of hydrogen. Experimental measurements of H diffusion in garnet are limited to room pressure. We use atomistic simulations to study H diffusion in perfect and defective garnet lattices, focusing on protonation defects at the Si and Mg sites, which are shown to be energetically favored. Transient trapping of H renders ab-initio simulations of H diffusion computationally challenging, which is overcome with machine learning techniques by training a deep neural network that encodes the interatomic potential. Our results from such deep potential molecular dynamics (DeePMD) simulations show high mobility of hydrogen in defect-free garnet lattices, whereas H diffusivity is significantly diminished in defective lattices. Tracer simulations focusing on H alone highlight the vital role of atomic vibrations of heavier atoms like Mg on the release of H atoms. Two regimes of H diffusion are identified: a diffuser-dominated regime at high hydrogen content with low activation energies due to saturation of vacancies by hydrogen, and a vacancy-dominated regime at low hydrogen content with high activation energies due to trapping of H atoms at vacancy sites. These regimes account for experimental observations, such as a H-concentration dependent diffusivity and the discrepancy in activation energy between deprotonation and D-H exchange experiments. This study underpins the crucial role of vacancies in H diffusion and demonstrates the utility of machine-learned interatomic potentials in studying kinetic processes in the Earth's interior. Y1 - 2025 U6 - https://doi.org/10.1029/2024GC011951 VL - 26 SP - e2024GC011951 ER - TY - CHAP A1 - Zhao, Zhengji A1 - Marsman, Martijn A1 - Wende, Florian A1 - Kim, Jeongnim T1 - Performance of Hybrid MPI/OpenMP VASP on Cray XC40 Based on Intel Knights Landing Many Integrated Core Architecture N2 - With the recent installation of Cori, a Cray XC40 system with Intel Xeon Phi Knights Landing (KNL) many integrated core (MIC) architecture, NERSC is transitioning from the multi-core to the more energy-efficient many-core era. The developers of VASP, a widely used materials science code, have adopted MPI/OpenMP parallelism to better exploit the increased on-node parallelism, wider vector units, and the high bandwidth on-package memory (MCDRAM) of KNL. To achieve optimal performance, KNL specifics relevant for the build, boot and run time setup must be explored. In this paper, we present the performance analysis of representative VASP workloads on Cori, focusing on the effects of the compilers, libraries, and boot/run time options such as the NUMA/MCDRAM modes, Hyper-Threading, huge pages, core specialization, and thread scaling. The paper is intended to serve as a KNL performance guide for VASP users, but it will also benefit other KNL users. Y1 - 2017 N1 - Availability: https://cug.org/conference-proceedings ER - TY - JOUR A1 - Zander, Thomas A1 - Dreischarf, Marcel A1 - Timm, Anne-Katrin A1 - Baumann, Wolfgang A1 - Schmidt, Hendrik T1 - Impact of material and morphological parameters on the mechanical response of the lumbar spine - A finite element sensitivity study JF - Journal of Biomechanics KW - finite element modelling KW - lumbar spine KW - sensitivity analysis KW - model validation KW - coefficient of determination Y1 - 2016 U6 - https://doi.org/10.1016/j.jbiomech.2016.12.014 VL - 53 SP - 185 EP - 190 ER - TY - CHAP A1 - Yi, Sangho A1 - Kondo, Derrick A1 - Andrzejak, Artur T1 - Reducing Costs of Spot Instances via Checkpointing in the Amazon Elastic Compute Cloud T2 - Cloud Computing (CLOUD), 2010 IEEE 3rd International Conference on Y1 - 2010 U6 - https://doi.org/10.1109/CLOUD.2010.35 SP - 236 EP - 243 ER - TY - JOUR A1 - Xiao, Li A1 - Zhang, Xiaodong A1 - Andrzejak, Artur A1 - Chen, Songqing T1 - Building a Large and Efficient Hybrid Peer-to-Peer Internet Caching System JF - IEEE Trans. Knowl. Data Eng. Y1 - 2004 U6 - https://doi.org/10.1109/TKDE.2004.1 VL - 16 IS - 6 SP - 754 EP - 769 ER - TY - CHAP A1 - Witzke, Joel A1 - Schintke, Florian A1 - Lößer, Ansgar A1 - Scheuermann, Björn T1 - Proactive Resource Management to Optimize Distributed Workflow Executions T2 - IEEE International Conference on Big Data, BigData 2023, Sorrento, Italy, December 15-18, 2023 Y1 - 2023 U6 - https://doi.org/10.1109/BigData59044.2023.10386493 SP - 6305 EP - 6307 PB - IEEE ER - TY - CHAP A1 - Witzke, Joel A1 - Lößer, Ansgar A1 - Bountris, Vasilis A1 - Schintke, Florian A1 - Scheuermann, Björn T1 - I/O of Scientific Workflows Monitored in Detail T2 - 20th IEEE International Conference on e-Science, e-Science 2024, Osaka, Japan, September 16-20, 2024 Y1 - 2024 U6 - https://doi.org/10.1109/E-SCIENCE62913.2024.10678728 N1 - Best Poster Award SP - 1 EP - 2 ER - TY - JOUR A1 - Witzke, Joel A1 - Lößer, Ansgar A1 - Bountris, Vasilis A1 - Schintke, Florian A1 - Scheuermann, Björn T1 - Low-level I/O Monitoring for Scientific Workflows JF - CoRR Y1 - 2024 U6 - https://doi.org/10.48550/ARXIV.2408.00411 VL - abs/2408.00411 SP - 1 EP - 10 ER - TY - THES A1 - Witte, Jochen T1 - Implementierung einer NFS Schnittstelle im Kontext eines Grid-Datenmanagement-Systems N2 - Diese Arbeit dokumentiert den Entwurf und die Implementierung einer NFS-Schnittstelle zum ZIBDMS. Das ZIBDMS, welches derzeit am Zuse-Institut Berlin entwickelt wird, ist ein Managementsystem für verteilte Daten in heterogenen Umgebungen [10]. Es soll die einfache Benutzung von Mechanismen zur Replikation sowie neue Möglichkeiten des Zugriffs und der Verwaltung von Metadaten und Datenobjekten ermöglichen. Dem Nutzer bietet das System verschiedene Sichten: Neben der klassischen, hierarchischen Sicht mit Verzeichnissen und Dateien wird auch eine attributbasierte Zugriffsmethode angeboten, in der Datenobjekte ausschließlich über Attribut/Wert-Paare referenziert werden. Für den Benutzer transparent, soll sich das System im Hinblick auf die Verfügbarkeit von Daten und Metadaten selbsttätig optimieren. Um Skalierbarkeit gew¨ahrleisten zu können, werden intern Peer-to-Peer- Techniken entwickelt und benutzt. Die NFS-Schnittstelle erhöht die Nutzbarkeit des Systems, da Client- Implementierungen für nahezu alle Betriebssysteme zur Verfügung stehen. Der Benutzer kann so über das gewohnte Dateisystem Daten und Metadaten pflegen, ohne spezifisches Vorwissen zu benötigen. In dieser Arbeit wird untersucht, inwiefern sich die Semantik des ZIBDMS auf jene des NFS-Protokolls übertragen läßt. Weiterhin wird das Konzept von Pseudodateien beschrieben und diskutiert, inwiefern es eine brauchbare Lösung darstellt, den im Vergleich zur NFS-Semantik wesentlich größeren Funktionsumfang des ZIBDMS für den Anwender nutzbar zu machen. Pseudodateien sind nicht-persistente Objekte, welche für den Benutzer als reguläre Datei sichtbar werden und die erweiterte Funktionalitäten wie die Bearbeitung von Metadaten oder die Platzierung von Replikaten über die Dateisystem-Sicht des NFS zur Verfügung stellen sollen. Schließlich werden Leistungsmessungen an den benutzten Komponenten des ZIBDMS vorgenommen und vergleichbaren Systemen gegen übergestellt. Die Aufmerksamkeit liegt hier auf der zugrundeliegenden Katalog-Technologie sowie dem durch das NFS-Protokoll verursachten Overhead. Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10081 ER - TY - CHAP A1 - Wendler, Jan A1 - Schintke, Florian T1 - Grid-Enabled Computational Fluid Dynamics using FlowGrid T2 - Cracow Grid Workshop ’03 Proceedings Y1 - 2004 SP - 59 EP - 66 PB - Academic Computer Centre CYFRONET AGH CY - ul. Nawojki 11, 30-950 Krakow 61, P.O.Box 386, Poland ER - TY - JOUR A1 - Wendler, Jan A1 - Schintke, Florian T1 - Executing and observing CFD applications on the Grid JF - Future Generation Computer Systems the International Journal of Grid Computing: Theory, Methods and Applications Y1 - 2005 U6 - https://doi.org/10.1016/j.future.2004.09.026 VL - 21 IS - 1 SP - 11 EP - 18 PB - Elsevier Science Publishers ER - TY - CHAP A1 - Wendler, Jan A1 - Bach, Joscha ED - Polani, Daniel ED - Browning, Brett ED - Bonarini, Andrea ED - Yoshida, Kazuo T1 - Recognizing and Predicting Agent Behavior with Case Based Reasoning T2 - RoboCup 2003: Robot Soccer World Cup VII Y1 - 2003 U6 - https://doi.org/10.1007/978-3-540-25940-4_72 VL - 3020 SP - 729 EP - 738 PB - Springer ER - TY - GEN A1 - Wende, Florian A1 - Steinke, Thomas A1 - Reinefeld, Alexander T1 - The Impact of Process Placement and Oversubscription on Application Performance: A Case Study for Exascale Computing N2 - With the growing number of hardware components and the increasing software complexity in the upcoming exascale computers, system failures will become the norm rather than an exception for long-running applications. Fault-tolerance can be achieved by the creation of checkpoints during the execution of a parallel program. Checkpoint/Restart (C/R) mechanisms allow for both task migration (even if there were no hardware faults) and restarting of tasks after the occurrence of hardware faults. Affected tasks are then migrated to other nodes which may result in unfortunate process placement and/or oversubscription of compute resources. In this paper we analyze the impact of unfortunate process placement and oversubscription of compute resources on the performance and scalability of two typical HPC application workloads, CP2K and MOM5. Results are given for a Cray XC30/40 with Aries dragonfly topology. Our results indicate that unfortunate process placement has only little negative impact while oversubscription substantially degrades the performance. The latter might be only (partially) beneficial when placing multiple applications with different computational characteristics on the same node. T3 - ZIB-Report - 15-05 KW - Fault-tolerance KW - Process placement KW - Oversubscription Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53560 SN - 1438-0064 ER - TY - CHAP A1 - Wende, Florian A1 - Steinke, Thomas A1 - Reinefeld, Alexander ED - Gray, A. ED - Smith, L. ED - Weiland, M. T1 - The Impact of Process Placement and Oversubscription on Application Performance: A Case Study for Exascale Computing T2 - Proceedings of the 3rd International Conference on Exascale Applications and Software, EASC 2015 Y1 - 2015 SN - 978 -0-9 926615 -1-9 SP - 13 EP - 18 PB - The University of Edinburgh ER - TY - GEN A1 - Wende, Florian A1 - Steinke, Thomas A1 - Klemm, Michael A1 - Reinefeld, Alexander ED - Reinders, James ED - Jeffers, Jim T1 - Concurrent Kernel Offloading T2 - High Performance Parallelism Pearls Y1 - 2014 UR - http://store.elsevier.com/High-Performance-Parallelism-Pearls/James-Reinders/isbn-9780128021187/ SN - 978-0128021187 N1 - Target publication date: Nov, 2014 PB - Morgan Kaufman, Elsevier ER - TY - GEN A1 - Wende, Florian A1 - Steinke, Thomas A1 - Cordes, Frank T1 - Multi-threaded Kernel Offloading to GPGPU Using Hyper-Q on Kepler Architecture N2 - Small-scale computations usually cannot fully utilize the compute capabilities of modern GPGPUs. With the Fermi GPU architecture Nvidia introduced the concurrent kernel execution feature allowing up to 16 GPU kernels to execute simultaneously on a shared GPU device for a better utilization of the respective resources. Insufficient scheduling capabilities in this respect, however, can significantly reduce the theoretical concurrency level. With the Kepler GPU architecture Nvidia addresses this issue by introducing the Hyper-Q feature with 32 hardware managed work queues for concurrent kernel execution. We investigate the Hyper-Q feature within heterogeneous workloads with multiple concurrent host threads or processes offloading computations to the GPU each. By means of a synthetic benchmark kernel and a hybrid parallel CPU-GPU real-world application, we evaluate the performance obtained with Hyper-Q on GPU and compare it against a kernel reordering mechanism introduced by the authors for the Fermi architecture. T3 - ZIB-Report - 14-19 KW - GPGPU KW - Hyper-Q KW - Concurrent Kernel Execution Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50362 SN - 1438-0064 ER - TY - GEN A1 - Wende, Florian A1 - Steinke, Thomas T1 - Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU N2 - Simulations of the critical Ising model by means of local update algorithms suffer from critical slowing down. One way to partially compensate for the influence of this phenomenon on the runtime of simulations is using increasingly faster and parallel computer hardware. Another approach is using algorithms that do not suffer from critical slowing down, such as cluster algorithms. This paper reports on the Swendsen-Wang multi-cluster algorithm on Intel Xeon Phi coprocessor 5110P, Nvidia Tesla M2090 GPU, and x86 multi-core CPU. We present shared memory versions of the said algorithm for the simulation of the two- and three-dimensional Ising model. We use a combination of local cluster search and global label reduction by means of atomic hardware primitives. Further, we describe an MPI version of the algorithm on Xeon Phi and CPU, respectively. Significant performance improvements over known im plementations of the Swendsen-Wang algorithm are demonstrated. T3 - ZIB-Report - 13-44 KW - Swendsen-Wang Multi-Cluster Algorithm KW - Ising Model KW - Xeon Phi KW - GPGPU KW - Connected Component Labeling Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42187 SN - 1438-0064 ER - TY - CHAP A1 - Wende, Florian A1 - Steinke, Thomas T1 - Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU T2 - Proceeding SC '13 Proceedings of SC13: International Conference for High Performance Computing, Networking, Storage and Analysis Article No. 83 ACM New York, NY, USA, 2013 Y1 - 2013 U6 - https://doi.org/http://dx.doi.org/10.1145/2503210.2503254 ER - TY - CHAP A1 - Wende, Florian A1 - Noack, Matthias A1 - Steinke, Thomas A1 - Klemm, Michael A1 - Zitzlsberger, Georg A1 - Newburn, Chris J. ED - Dutot, Pierre-Francois ED - Trystram, Denis T1 - Portable SIMD Performance with OpenMP* 4.x Compiler Directives N2 - Effective vectorization is becoming increasingly important for high performance and energy efficiency on processors with wide SIMD units. Compilers often require programmers to identify opportunities for vectorization, using directives to disprove data dependences. The OpenMP 4.x SIMD directives strive to provide portability. We investigate the ability of current compilers (GNU, Clang, and Intel) to generate SIMD code for microbenchmarks that cover common patterns in scientific codes and for two kernels from the VASP and the MOM5/ERGOM application. We explore coding strategies for improving SIMD performance across different compilers and platforms (Intel® Xeon® processor and Intel® Xeon Phi™ (co)processor). We compare OpenMP* 4.x SIMD vectorization with and without vector data types against SIMD intrinsics and C++ SIMD types. Our experiments show that in many cases portable performance can be achieved. All microbenchmarks are available as open source as a reference for programmers and compiler experts to enhance SIMD code generation. Y1 - 2016 SN - 978-3-319-43659-3 U6 - https://doi.org/10.1007/978-3-319-43659-3_20 VL - Euro-Par 2016: Parallel Processing: 22nd International Conference on Parallel and Distributed Computing PB - Springer International Publishing ER -