High performance communication on reconfigurable clusters

High Performance Computing (HPC) has matured to where it is an essential third pillar, along with theory and experiment, in most domains of science and engineering. Communication latency is a key factor that is limiting the performance of HPC, but can be addressed by integrating communication into accelerators. This integration allows accelerators to communicate with each other without CPU interactions, and even bypassing the network stack. Field Programmable Gate Arrays (FPGAs) are the accelerators that currently best integrate communication with computation. The large number of Multi-gigabit Transceivers (MGTs) on most high-end FPGAs can provide high-bandwidth and low-latency inter-FPGA connections. Additionally, the reconfigurable FPGA fabric enables tight coupling between computation kernel and network interface. Our thesis is that an application-aware communication infrastructure for a multi-FPGA system makes substantial progress in solving the HPC communication bottleneck. This dissertation aims to provide an application-aware solution for communication infrastructure for FPGA-centric clusters. Specifically, our solution demonstrates application-awareness across multiple levels in the network stack, including low-level link protocols, router microarchitectures, routing algorithms, and applications. We start by investigating the low-level link protocol and the impact of its latency variance on performance. Our results demonstrate that, although some link jitter is always present, we can still assume near-synchronous communication on an FPGA-cluster. This provides the necessary condition for statically-scheduled routing. We then propose two novel router microarchitectures for two different kinds of workloads: a wormhole Virtual Channel (VC)-based router for workloads with dynamic communication, and a statically-scheduled Virtual Output Queueing (VOQ)-based router for workloads with static communication. For the first (VC-based) router, we propose a framework that generates application-aware router configurations. Our results show that, by adding application-awareness into router configuration, the network performance of FPGA clusters can be substantially improved. For the second (VOQ-based) router, we propose a novel offline collective routing algorithm. This shows a significant advantage over a state-of-the-art collective routing algorithm. We apply our communication infrastructure to a critical strong-scaling HPC kernel, the 3D FFT. The experimental results demonstrate that the performance of our design is faster than that on CPUs and GPUs by at least one order of magnitude (achieving strong scaling for the target applications). Surprisingly, the FPGA cluster performance is similar to that of an ASIC-cluster. We also implement the 3D FFT on another multi-FPGA platform: the Microsoft Catapult II cloud. Its performance is also comparable or superior to CPU and GPU HPC clusters. The second application we investigate is Molecular Dynamics Simulation (MD). We model MD on both FPGA clouds and clusters. We find that combining processing and general communication in the same device leads to extremely promising performance and the prospect of MD simulations well into the us/day range with a commodity cloud

OFDMA/SC-FDMA aided space-time shift keying for dispersive multi-user scenarios

Motivated by the recent concept of Space-Time Shift Keying (STSK) developed for achieving a flexible diversity versus multiplexing gain trade-off, we propose a novel Orthogonal Frequency Division Multiple Access (OFDMA)/Single Carrier Frequency Division Multiple Access (SC-FDMA) aided multi-user STSK scheme for frequency-selective channels. The proposed OFDMA/SC-FDMA STSK scheme is capable of providing an improved performance in dispersive channels, while supporting multiple users in a multiple antenna aided wireless system. Furthermore, the scheme has the inherent potential of benefitting from the low-complexity single-stream Maximum-likelihood (ML) detector. Both an uncoded and a sophisticated near-capacity coded OFDMA/SC-FDMA STSK scheme were studied and their performances were compared in multiuser wideband Multiple-Input Multiple-Output (MIMO) scenarios. Explicitly, OFDMA/SC-FDMA aided STSK exhibits an excellent performance even in the presence of channel impairments due to the frequency-selectivity of wideband channels and proves to be a beneficial choice for high capacity multi-user MIMO systems

Printability and Applicability of 3D Printing System Loaded with Chlorogenic Acid Hydrogel

Three-dimensional food printing (3DFP) is an efficient way of food processing in line with the future lifestyle. As a delivery system, hydrogel has become a research hotspot because of its remarkable characteristics such as directed delivery. The purpose of this study was to explore the effects of 3DFP on the structure, physical properties and functions of hydrogels containing methylcellulose (MC), chlorogenic acid (CA) and hyaluronic acid (HA) for the purpose of revealing the printability and applicability of hydrogels in 3DFP processing. Texture properties, rheological properties, microstructure, embedding rate and digestive properties of the 3D printed products were measured. The results showed that the best CA-loaded hydrogel system for 3DFP processing consisted of MC, HA and CA at a mass ratio of 8:0.5:0.5. Its printed product showed the smallest width deviation (13.40%), the highest hardness, the maximum elasticity, and the minimum adhesiveness, had compact structure and uniform porosity, was not easy to collapse, and had good supportability and the best printing moldability. 3DFP well optimized the physical structure of hydrogel without changing its chemical properties. The embedding rate of CA was 22.09 percentage points higher than that before 3D printing. In simulated gastrointestinal digestion test, the release rate of CA from the printed product was significantly higher than that of the unprinted samples, showing a good sustained release effect, and the in vitro release of CA was fitted to the Ritger-Peppas model. These results showed that the hydrogel system had good printability and applicability, and 3DFP could significantly improve the targeted release of CA loaded in hydrogel

Core/Shell Metal Halide Perovskite Nanocrystals for Optoelectronic Applications

© 2021 Wiley-VCH GmbH Core/shell structured metal halide perovskite nanocrystals (NCs) are emerging as a type of material with remarkable optical and electronic properties. Research into this field has been developing and expanding rapidly in recent years, with significant advances in the studies of the shell growth mechanism and in understanding of properties of these materials. Significant enhancement of both the stability and the optical performance of core/shell perovskite NCs are of particular importance for their applications in optoelectronic technologies. In this review, the recent advances in core/shell structured perovskite NCs are summarized. The band structures and configurations of core/shell perovskite NCs are elaborated, the shell classification and shell engineering approaches, such as perovskites and their derivative shells, semiconductor shell, oxide shell, polymer shell, etc. are reviewed, and the shell growth mechanisms are discussed. The prospective of these NCs in lighting and displays, solar cells, photodetectors, and other devices is discussed in the light of current knowledge, remaining challenges, and future opportunities

Can antibiotics for enteritis or for urinary tract infection disrupt the urinary microbiota in rats?

BackgroundTo establish antibiotic preregimes and administration routes for studies on urinary microbiota.Methods and materialsAntibiotics for enteritis (Abx-enteritis) and UTIs (Abx-UTI) were administered via gavage and/or urinary catheterisation (UC) for 1 and/or 2 weeks. The effects of these Abx on the urinary microbiota of rats were examined via 16S rRNA sequencing and urine culture, including anaerobic and aerobic culture. Additionally, the safety of the Abx was examined.ResultsAbx-enteritis/Abx-UTI (0.5 g/L and 1 g/L) administered via gavage did not alter the microbial community and bacterial diversity in the urine of rats (FDR > 0.05); however, Abx-UTI (1 g/L) administered via UC for 1 and 2 weeks altered the urinary microbial community (FDR < 0.05). Rats administered Abx-UTI (1 g/L) via UC for 1 week demonstrated a distinct urinary microbiota in culture. Abx-enteritis/Abx-UTI administered via gavage disrupted the microbial community and reduced bacterial diversity in the faeces of rats (FDR < 0.05), and Abx-UTI administered via UC for 2 weeks (FDR < 0.05) altered the fecal microbiota. Abx-UTI (1 g/L) administered via UC did not alter safety considerations. In addition, we noticed that UC did not induce infections and injuries to the bladder and kidney tissues.ConclusionsAdministration of Abx-UTI via UC for 1 week can be considered a pre-treatment option while investigating the urinary microbiota

The complete mitochondrial genome of Monochamus alternatus alternatus (Coleoptera: Cerambycidae)

Monochamus alternatus alternatus is the major vector of pinewood nematode, Bursaphelenchus xylophilus, in Asia. The length of the complete mitochondria genome of M. alternatus alternatus was 15,880 bp with 21% GC content, including 39.7% A, 12.3% C, 8.7% G and 39.3% T. There were 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and one AT-rich region. This study provides a useful genetic information for subsequent study of the differences between M. alternatus subspecies