Detecting Memory-Boundedness with Hardware Performance Counters

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 complementary to information about the application behavior. However, the exact meaning of the supported hardware events is often incomprehensible due to the system complexity and partially lacking or even inaccurate documentation. For most events it is also not documented whether a certain rate indicates a saturated resource usage. Therefore, it is usually diffcult to draw conclusions on the performance impact from the observed event rates. In this paper, we evaluate whether hardware performance counters can be used to measure the capacity utilization within the memory hierarchy and estimate the impact of memory accesses on the achieved performance. The presented approach is based on a small selection of micro-benchmarks that constantly stress individual components in the memory subsystem, ranging from caches to main memory. These workloads are used to identify hardware performance counters that provide good estimates for the utilization of individual components in the memory hierarchy. However, since access latencies can be interleaved with computing instructions, a high utilization of the memory hierarchy does not necessarily result in low performance. We therefore also investigate which stall counters provide good estimates for the number of cycles that are actually spent waiting for the memory hierarchy

Impact of multivalent charge presentation on peptide-nanoparticle aggregation

Strategies to achieve controlled nanoparticle aggregation have gained much interest, due to the versatility of such systems and their applications in materials science and medicine. In this article we demonstrate that coiled- coil peptide-induced aggregation based on electrostatic interactions is highly sensitive to the length of the peptide as well as the number of presented charges. The quaternary structure of the peptide was found to play an important role in aggregation kinetics. Furthermore, we show that the presence of peptide fibers leads to well-defined nanoparticle assembly on the surface of these macrostructures

Main memory and cache performance of Intel Sandy

Abstract Application performance on multicore processors is seldom constrained by the speed of floating point or integer units. Much more often, limitations are caused by the memory subsystem, particularly shared resources such as last level caches or memory controllers. Measuring, predicting and modeling memory performance becomes a steeper challenge with each new processor generation due to the growing complexity and core count. We tackle the important aspect of measuring and understanding undocumented memory performance numbers in order to create valuable insight into microprocessor details. For this, we build upon a set of sophisticated benchmarks that support latency and bandwidth measurements to arbitrary locations in the memory subsystem. These benchmarks are extended to support AVX instructions for bandwidth measurements and to integrate the coherence states (O)wned and (F)orward. We then use these benchmarks to perform an indepth analysis of current ccNUMA multiprocessor systems with Intel (Sandy Bridge-EP) and AMD (Bulldozer) processors. Using our benchmarks we present fundamental memory performance data and illustrate performance-relevant architectural properties of both designs

Extending the Functionality of Score-P through Plugins: Interfaces and Use Cases

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 supports numerous HPC platforms and parallel programming paradigms. To extend Score-P with support for different back-ends, create a common framework for measurement and tuning of HPC applications, and to enable the re-use of common software components such as implemented instrumentation techniques, this paper makes the following contributions: (I) We describe the Score-P metric plugin interface, which enables programmers to augment the event stream with metric data from supplementary data sources that are otherwise not accessible for Score-P. (II) We introduce the flexible Score-P substrate plugin interface that can be used for custom processing of the event stream according to the specific requirements of either measurement, analysis, or runtime tuning tasks. (III) We provide examples for both interfaces that extend Score-P’s functionality for monitoring and tuning purposes

NC-gestützte Fertigung von Bohrschablonen für die dentale Implantation

Einleitung Bei Zahnverlust ist das Setzen eines Implantates eine gängige und etablierte Behandlungsmethode. Zahnimplantate bieten für den Patienten viele Vorteile. Im Vergleich zum Einsatz einer klassischen Brücke müssen keine Nachbarzähne beschliffen werden. Gesunde Zahnsubstanz bleibt erhalten. Der künstliche Zahn sitzt fest und sicher im Kiefer und bietet Schutz vor Knochenverlust. Ein Implantat leitet die beim Kauen entstehenden Kräfte gleichmäßig in den Kieferknochen. Ein weiterer Vorteil ist die Sicherstellung der natürlichen Funktionen wie Kauen, Sprechen oder Lachen. Somit trägt implantatgetragener Zahnersatz erheblich zur Verbesserung der Lebensqualität bei. Zur Planung des chirurgischen Eingriffs und dem eigentlichen Setzen des Implantates sind die Zahnärzte und Zahntechniker auf Softwarelösungen angewiesen, welche nicht nur die Möglichkeit der Befundung, Analyse und Diagnostik bieten, sondern gleichermaßen die Informationen liefern, die erforderlich sind, um mit Hilfe eines Computers die Fertigung einer Bohrschablone zu planen (CAM-System) und mittels CNC-Fertigung herzustellen

Sea ice extent and seasonality for the Early Pliocene northern Weddell Sea

Growth increment analysis coupled with stable isotopic data (δ18O/δ13C) from Early Pliocene (ca 4.7 Ma) Austrochlamys anderssoni from shallow marine sediments of the Cockburn Island Formation, northern Antarctic Peninsula, suggest these bivalves grew through much of the year, even during the coldest parts of winter recorded in the shells. The high frequency fluctuation in growth increment width of A. anderssoni appears to reflect periodic, but year-round, agitation of the water column enhancing benthic food supply from organic detritus. This suggests that Austrochlamys favoured waters that were largely sea ice free. Our data support interpretation of the Cockburn Island Formation as an interglacial marine deposit and the previous hypothesis that Austrochlamys retreated from the Antarctic as sea ice extent expanded, this transition occurring during climate cooling in the Late Pliocene

The Democratic Biopolitics of PrEP

PrEP (Pre-Exposure Prophylaxis) is a relatively new drug-based HIV prevention technique and an important means to lower the HIV risk of gay men who are especially vulnerable to HIV. From the perspective of biopolitics, PrEP inscribes itself in a larger trend of medicalization and the rise of pharmapower. This article reconstructs and evaluates contemporary literature on biopolitical theory as it applies to PrEP, by bringing it in a dialogue with a mapping of the political debate on PrEP. As PrEP changes sexual norms and subjectification, for example condom use and its meaning for gay subjectivity, it is highly contested. The article shows that the debate on PrEP can be best described with the concepts ‘sexual-somatic ethics’ and ‘democratic biopolitics’, which I develop based on the biopolitical approach of Nikolas Rose and Paul Rabinow. In contrast, interpretations of PrEP which are following governmentality studies or Italian Theory amount to either farfetched or trivial positions on PrEP, when seen in light of the political debate. Furthermore, the article is a contribution to the scholarship on gay subjectivity, highlighting how homophobia and homonormativity haunts gay sex even in liberal environments, and how PrEP can serve as an entry point for the destigmatization of gay sexuality and transformation of gay subjectivity. ‘Biopolitical democratization’ entails making explicit how medical technology and health care relates to sexual subjectification and ethics, to strengthen the voice of (potential) PrEP users in health politics, and to renegotiate the profit and power of Big Pharma

Causes and Consequences of Past and Projected Scandinavian Summer Temperatures, 500–2100 AD

Tree rings dominate millennium-long temperature reconstructions and many records originate from Scandinavia, an area for which the relative roles of external forcing and internal variation on climatic changes are, however, not yet fully understood. Here we compile 1,179 series of maximum latewood density measurements from 25 conifer sites in northern Scandinavia, establish a suite of 36 subset chronologies, and analyse their climate signal. A new reconstruction for the 1483–2006 period correlates at 0.80 with June–August temperatures back to 1860. Summer cooling during the early 17th century and peak warming in the 1930s translate into a decadal amplitude of 2.9°C, which agrees with existing Scandinavian tree-ring proxies. Climate model simulations reveal similar amounts of mid to low frequency variability, suggesting that internal ocean-atmosphere feedbacks likely influenced Scandinavian temperatures more than external forcing. Projected 21st century warming under the SRES A2 scenario would, however, exceed the reconstructed temperature envelope of the past 1,500 years