With the development of on-chip manufacturing technologies and the requirements of high-performance computing, the core count is growing quickly in Chip Multi/Many-core Processors (CMPs) and Multiprocessor System-on-Chip (MPSoC) to support larger scale parallel execution. Network-on-Chip (NoC) has become the de facto solution for CMPs and MPSoCs in addressing the communication challenge. In the thesis, we tackle a few key problems facing high-performance NoC designs. For general-purpose CMPs, we encompass a full system perspective to design high-performance NoC for multi-threaded programs. By exploring the cache coherence under the whole system scenario, we present a smart communication service called Advance Virtual Channel Reservation (AVCR) to provide a highway to target packets, which can greatly reduce their contention delay in NoC. AVCR takes advantage of the fact that we can know or predict the destination of some packets ahead of their arrival at the Network Interface (NI). Exploiting the time interval before a packet is ready, AVCR establishes an end-to-end highway from the source NI to the destination NI. This highway is built up by reserving the Virtual Channel (VC) resources ahead of the target packet transmission and offering priority service to flits in the reserved VC in the wormhole router, which can avoid the target packets’ VC allocation and switch arbitration delay. Besides, we also propose an admission control method in NoC with a centralized Artificial Neural Network (ANN) admission controller, which can improve system performance by predicting the most appropriate injection rate of each node using the network performance information. In the online control process, a data preprocessing unit is applied to simplify the ANN architecture and make the prediction results more accurate. Based on the preprocessed information, the ANN predictor determines the control strategy and broadcasts it to each node where the admission control will be applied. For application-specific MPSoCs, we focus on developing high-performance NoC and NI compatible with the common AMBA AXI4 interconnect protocol. To offer the possibility of utilizing the AXI4 based processors and peripherals in the on-chip network based system, we propose a whole system architecture solution to make the AXI4 protocol compatible with the NoC based communication interconnect in the many-core system. Due to possible out-of-order transmission in the NoC interconnect, which conflicts with the ordering requirements specified by the AXI4 protocol, in the first place, we especially focus on the design of the transaction ordering units, realizing a high-performance and low cost solution to the ordering requirements. The microarchitectures and the functionalities of the transaction ordering units are also described and explained in detail for ease of implementation. Then, we focus on the NI and the Quality of Service (QoS) support in NoC. In our design, the NI is proposed to make the NoC architecture independent from the AXI4 protocol via message format conversion between the AXI4 signal format and the packet format, offering high flexibility to the NoC design. The NoC based communication architecture is designed to support high-performance multiple QoS schemes. The NoC system contains Time Division Multiplexing (TDM) and VC subnetworks to apply multiple QoS schemes to AXI4 signals with different QoS tags and the NI is responsible for traffic distribution between two subnetworks. Besides, a QoS inheritance mechanism is applied in the slave-side NI to support QoS during packets’ round-trip transfer in NoC. / Med utvecklingen av tillverkningsteknologi av on-chip och kraven på högpresterande da-toranläggning växer kärnantalet snabbt i Chip Multi/Many-core Processors (CMPs) ochMultiprocessor Systems-on-Chip (MPSoCs) för att stödja större parallellkörning. Network-on-Chip (NoC) har blivit den de facto lösningen för CMP:er och MPSoC:er för att mötakommunikationsutmaningen. I uppsatsen tar vi upp några viktiga problem med hög-presterande NoC-konstruktioner.Allmänna CMP:er omfattas ett fullständigt systemperspektiv för att design högprester-ande NoC för flertrådad program. Genom att utforska cachekoherensen under hela system-scenariot presenterar vi en smart kommunikationstjänst, AVCR (Advance Virtual ChannelReservation) för att tillhandahålla en motorväg till målpaket, vilket i hög grad kan min-ska deras förseningar i NoC. AVCR utnyttjar det faktum att vi kan veta eller förutsägadestinationen för vissa paket före deras ankomst till nätverksgränssnittet (Network inter-face, NI). Genom att utnyttja tidsintervallet innan ett paket är klart, etablerar AVCRen ände till ände motorväg från källan NI till destinationen NI. Denna motorväg byggsupp genom att reservera virtuell kanal (Virtual Channel, VC) resurser före målpaket-söverföringen och erbjuda prioriterade tjänster till flisar i den reserverade VC i wormholerouter. Dessutom föreslår vi också en tillträdeskontrollmetod i NoC med en centraliseradartificiellt neuronät (Artificial Neural Network, ANN) tillträdeskontroll, som kan förbättrasystemets prestanda genom att förutsäga den mest lämpliga injektionshastigheten för varjenod via nätverksprestationsinformationen. I onlinekontrollprocessen används en förbehan-dlingsenhet på data för att förenkla ANN-arkitekturen och göra förutsägningsresultatenmer korrekta. Baserat på den förbehandlade informationen bestämmer ANN-prediktornkontrollstrategin och sänder den till varje nod där tillträdeskontrollen kommer att tilläm-pas.För applikationsspecifika MPSoC:er fokuserar vi på att utveckla högpresterande NoCoch NI kompatibla med det gemensamma AMBA AXI4 protokoll. För att erbjuda möj-ligheten att använda AXI4-baserade processorer och kringutrustning i det on-chip baseradenätverkssystemet föreslår vi en hel systemarkitekturlösning för att göra AXI4 protokolletkompatibelt med den NoC-baserade kommunikation i det multikärnsystemet. På grundav den out-of-order överföring i NoC, som strider mot ordningskraven som anges i AXI4-protokollet, fokuserar vi i första hand på utformningen av transaktionsordningsenheterna,för att förverkliga en hög prestanda och låg kostnad-lösning på ordningskraven. Sedanfokuserar vi på NI och Quality of Service (QoS)-stödet i NoC. I vår design föreslås NI attgöra NoC-arkitekturen oberoende av AXI4-protokollet via meddelandeformatkonverteringmellan AXI4 signalformatet och paketformatet, vilket erbjuder NoC-designen hög flexi-bilitet. Den NoC-baserade kommunikationsarkitekturen är utformad för att stödja fleraQoS-schema med hög prestanda. NoC-systemet innehåller Time-Division Multiplexing(TDM) och VC-subnät för att tillämpa flera QoS-scheman på AXI4-signaler med olikaQoS-taggar och NI ansvarar för trafikdistribution mellan två subnät. Dessutom tillämpasen QoS-arvsmekanism i slav-sidan NI för att stödja QoS under paketets tur-returöverföringiNoC / <p>QC 20201008</p>

<p>High-performance computing (HPC) and machine learning (ML) have been widely adopted by both academia and industries to address enormous data problems at extreme scales. While research has reported on the interactions of HPC and ML, achieving high performance and scalability for parallel and distributed ML algorithms is still a challenging task. This dissertation first summarizes the major challenges for applying HPC to ML applications: 1) poor performance and scalability, 2) loss of the convergence rate, 3) lower quality of the trained model, and 4) a lack of performance optimization techniques designed for specific applications. Researchers can address the four challenges in new ML applications. This dissertation shows how to solve them for two specific applications: 1) a clustering algorithm and 2) graph optimization algorithms that use reinforcement learning (RL).</p> <p>As to the clustering algorithm, we first propose an algorithm called the simulated-annealing clustering algorithm. By combining a blocked data layout and asynchronous local optimization within each thread, the simulated-annealing enhanced clustering algorithm has a convergence rate that is comparable to the K-means algorithm but with much higher performance. Experiments with synthetic and real-world datasets show that the simulated-annealing enhanced clustering algorithm is significantly faster than the MPI K-means library using up to 1024 cores. However, the optimization costs (Sum of Square Error (SSE)) of the simulated-annealing enhanced clustering algorithm became higher than the original costs. To tackle this problem, we devise a new algorithm called the full-step feel-the-way clustering algorithm. In the full-step feel-the-way algorithm, there are L local steps within each block of data points. We use the first local step’s results to compute accurate global optimization costs. Our results show that the full-step algorithm can significantly reduce the global number of iterations needed to converge while obtaining low SSE costs. However, the time spent on the local steps is greater than the benefits of the saved iterations. To improve this performance, we next optimize the local step time by incorporating a sampling-based method called reassignment-history-aware sampling. Extensive experiments with various synthetic and real world datasets (e.g., MNIST, CIFAR-10, ENRON, and PLACES-2) show that our parallel algorithms can outperform the fastest open-source MPI K-means implementation by up to 110% on 4,096 CPU cores with comparable SSE costs.</p> <p>Our evaluations of the sampling-based feel-the-way algorithm establish the effectiveness of the local optimization strategy, the blocked data layout, and the sampling methods for addressing the challenges of applying HPC to ML applications. To explore more parallel strategies and optimization techniques, we focus on a more complex application: graph optimization problems using reinforcement learning (RL). RL has proved successful for automatically learning good heuristics to solve graph optimization problems. However, the existing RL systems either do not support graph RL environments or do not support multiple or many GPUs in a distributed setting. This has compromised RL’s ability to solve large scale graph optimization problems due to the lack of parallelization and high scalability. To address the challenges of parallelization and scalability, we develop OpenGraphGym-MG, a high performance distributed-GPU RL framework for solving graph optimization problems. OpenGraphGym-MG focuses on a class of computationally demanding RL problems in which both the RL environment and the policy model are highly computation intensive. In this work, we distribute large-scale graphs across distributed GPUs and use spatial parallelism and data parallelism to achieve scalable performance. We compare and analyze the performance of spatial and data parallelism and highlight their differences. To support graph neural network (GNN) layers that take data samples partitioned across distributed GPUs as input, we design new parallel mathematical kernels to perform operations on distributed 3D sparse and 3D dense tensors. To handle costly RL environments, we design new parallel graph environments to scale up all RL-environment-related operations. By combining the scalable GNN layers with the scalable RL environment, we are able to develop high performance OpenGraphGym-MG training and inference algorithms in parallel.</p> <p>To summarize, after proposing the major challenges for applying HPC to ML applications, this thesis explores several parallel strategies and performance optimization techniques using two ML applications. Specifically, we propose a local optimization strategy, a blocked data layout, and sampling methods for accelerating the clustering algorithm, and we create a spatial parallelism strategy, a parallel graph environment, agent, and policy model, and an optimized replay buffer, and multi-node selection strategy for solving large optimization problems over graphs. Our evaluations prove the effectiveness of these strategies and demonstrate that our accelerations can significantly outperform the state-of-the-art ML libraries and frameworks without loss of quality in trained models.</p>

Advances in the knowledge of chemical structure of coal and development of high performance computational techniques led to more than hundred and thirty four proposed molecular level representations (models) of coal between 1942 and 2010. These models were virtually on the carboniferous coals from the northern hemisphere. There are only two molecular models based on the inertinite- and vitrinite-rich coals from the southern hemisphere. The current investigation is based on the chars derived from the Permian-aged coals in two major South African coalfields, Witbank #4 seam and Waterberg Upper Ecca. The two coals were upgraded to 85 and 93% inertinite- and vitrinite-rich concentrates, on visible mineral matter free basis. The coals were slow heated in inert atmosphere at 20 ℃ min-1 to 450, 700 and 1000 ℃ and held at that temperature for an hour. After the HCl-HF treatment technique at ambient temperatures, the characteristics of the coals and chars were examined with proximate, ultimate, helium density, porosity, surface area, petrographic, solid-state 13C NMR, XRD and HRTEM analytical techniques. The results largely showed that substantial transitions occurred at 700-1000 ℃, where the chars became physically different but chemically similar. Consequently, the chars at the highest temperature (1000 ℃) drew attention to the detailed study of the atomistic properties that may give rise to different reactivity behaviours with CO2 gas. The H/C atomic ratios for the inertinite- and vitrinite-rich chars were respectively 0.31 and 0.49 at 450 ℃ and 0.10 and 0.12 at 1000 ℃. The true density was respectively 1.48 and 1.38 g.cm-3 at 450 ℃ and 1.87 and 1.81 g.cm-3 at 1000 ℃. The char form results from the petrographic analysis technique indicated that the 700-1000 ℃ inertinite-rich chars have lower proportions of thick-walled isotropic coke derived from pure vitrinites (5-8%) compared with the vitrinite-rich chars (91-95%). This property leads to the creation of pores and increases of volume and surface area as the softening walls expand. It was found that the average crystallite diameter, La, and the mean length of the aromatic carbon fringes from the XRD and HRTEM techniques, respectively, were in good agreement and made a definite distinction between the 1000 ℃ inertinite- and vitrinite-rich chars. The crystallite diameter on peak (10) approximations, La(10), of 37.6Å for the 1000 ℃ inertinite-rich chars fell within the HRTEM’s range of minimummaximum length boundary of 11x11 aromatic fringes (27-45Å). The La (10) of 30.7Å for the vitrinite-rich chars fell nearly on the minimum-maximum length range of 7x7 aromatic fringes (17-28Å.) The HRTEM results showed that the 1000 ℃ inertinite-rich chars comprised a higher distribution of larger aromatic fringes (11x11 parallelogram catenations) compared with a higher distribution of smaller aromatic fringes (7x7 parallelogram catenations). The mechanism for the similarity between the 700-1000 ℃ inertinite- and vitrinite-rich chars was the greater transition occurring in the vitrinite-rich coal to match the more resistant inertinite-rich coal. This emphasised that the transitions in the properties of vitrinite-rich coals were more thermally accelerated than those of the inertinite-rich coals. The similarity between the inertinite- and vitrinite-rich chars was shown by the total maceral reflectance, proximate, ultimate, skeletal density and aromaticity results. Evidence for this was the carbon content by mass for the inertinite- and vitrinite-rich chars of respectively 90.5 and 85.3% at 450 ℃ and 95.9 and 94.1% at 1000 ℃. The aromaticity from the XRD technique was respectively 87 and 77% at 450 ℃ and 98 and 96% at 1000 ℃. A similar pattern was found in the hydrogen and oxygen contents, the atomic O/C ratios and the aromaticity from the NMR technique. The subsequent construction of large-scale molecular structures for the 1000 ℃ inertinite-rich chars comprised 106 molecules constructed from a total of 42929 atoms, while the vitrinite-rich char model was made up of 185 molecules consisting of a total of 44315 atoms. The difference between the number of molecules was due to the inertinite-rich char model comprising a higher distribution of larger molecules compared with the vitrinite-rich char model, in agreement with the XRD and HRTEM results. These char structures were used to examine the behaviour on the basis of gasification reactivity with CO2. The density functional theory (DFT) was used to evaluate the interactions between CO2 and the atomistic representations of coal char derived from the inertinite- and vitrinite rich South African coals. The construction of char models used the modal aromatic fringes (fringes of highest frequencies in size distributions) from the HRTEM, for the inertinite- and vitrinite-rich chars, respectively (11x11 and 7x7 parallelogram-shaped aromatic carbon rings). The structures were DFT geometrically optimized and used to measure reactivity with the Fukui function, f+(r) and to depict a representative reactive carbon edge for the simulations of coal gasification reaction mechanism with CO2 gas. The f+(r) reactivity indices of the reactive edge follows the sequence: zigzag C remote from the tip C (Czi = 0.266) > first armchair C (Cr1 = 0.087) > tip C (Ct = 0.075) > second armchair C (Cr2 = 0.029) > zigzag C proximate to the tip C (Cz = 0.027). The DFT simulated mean activation energy, ΔEb, for the gasification reaction mechanism (formation of second CO gas molecule) was 233 kJ mol-1. The reaction for the formation of second CO molecule is defines gasification in essence. The experimental activation energy determined with the TGA and random pore model to account essentially for the pore variation in addition to the gasification chemical reaction were found to be very similar: 191 ± 25 kJ mol-1 and 210 ± 8 kJ mol-1; and in good agreement with the atomistic results. The investigation gave promise towards the utility of molecular representations of coal char within the context of fundamental coal gasification reaction mechanism with CO2. / PhD (Chemical Engineering), North-West University, Potchefstroom Campus, 2015

Advances in the knowledge of chemical structure of coal and development of high performance computational techniques led to more than hundred and thirty four proposed molecular level representations (models) of coal between 1942 and 2010. These models were virtually on the carboniferous coals from the northern hemisphere. There are only two molecular models based on the inertinite- and vitrinite-rich coals from the southern hemisphere. The current investigation is based on the chars derived from the Permian-aged coals in two major South African coalfields, Witbank #4 seam and Waterberg Upper Ecca. The two coals were upgraded to 85 and 93% inertinite- and vitrinite-rich concentrates, on visible mineral matter free basis. The coals were slow heated in inert atmosphere at 20 ℃ min-1 to 450, 700 and 1000 ℃ and held at that temperature for an hour. After the HCl-HF treatment technique at ambient temperatures, the characteristics of the coals and chars were examined with proximate, ultimate, helium density, porosity, surface area, petrographic, solid-state 13C NMR, XRD and HRTEM analytical techniques. The results largely showed that substantial transitions occurred at 700-1000 ℃, where the chars became physically different but chemically similar. Consequently, the chars at the highest temperature (1000 ℃) drew attention to the detailed study of the atomistic properties that may give rise to different reactivity behaviours with CO2 gas. The H/C atomic ratios for the inertinite- and vitrinite-rich chars were respectively 0.31 and 0.49 at 450 ℃ and 0.10 and 0.12 at 1000 ℃. The true density was respectively 1.48 and 1.38 g.cm-3 at 450 ℃ and 1.87 and 1.81 g.cm-3 at 1000 ℃. The char form results from the petrographic analysis technique indicated that the 700-1000 ℃ inertinite-rich chars have lower proportions of thick-walled isotropic coke derived from pure vitrinites (5-8%) compared with the vitrinite-rich chars (91-95%). This property leads to the creation of pores and increases of volume and surface area as the softening walls expand. It was found that the average crystallite diameter, La, and the mean length of the aromatic carbon fringes from the XRD and HRTEM techniques, respectively, were in good agreement and made a definite distinction between the 1000 ℃ inertinite- and vitrinite-rich chars. The crystallite diameter on peak (10) approximations, La(10), of 37.6Å for the 1000 ℃ inertinite-rich chars fell within the HRTEM’s range of minimummaximum length boundary of 11x11 aromatic fringes (27-45Å). The La (10) of 30.7Å for the vitrinite-rich chars fell nearly on the minimum-maximum length range of 7x7 aromatic fringes (17-28Å.) The HRTEM results showed that the 1000 ℃ inertinite-rich chars comprised a higher distribution of larger aromatic fringes (11x11 parallelogram catenations) compared with a higher distribution of smaller aromatic fringes (7x7 parallelogram catenations). The mechanism for the similarity between the 700-1000 ℃ inertinite- and vitrinite-rich chars was the greater transition occurring in the vitrinite-rich coal to match the more resistant inertinite-rich coal. This emphasised that the transitions in the properties of vitrinite-rich coals were more thermally accelerated than those of the inertinite-rich coals. The similarity between the inertinite- and vitrinite-rich chars was shown by the total maceral reflectance, proximate, ultimate, skeletal density and aromaticity results. Evidence for this was the carbon content by mass for the inertinite- and vitrinite-rich chars of respectively 90.5 and 85.3% at 450 ℃ and 95.9 and 94.1% at 1000 ℃. The aromaticity from the XRD technique was respectively 87 and 77% at 450 ℃ and 98 and 96% at 1000 ℃. A similar pattern was found in the hydrogen and oxygen contents, the atomic O/C ratios and the aromaticity from the NMR technique. The subsequent construction of large-scale molecular structures for the 1000 ℃ inertinite-rich chars comprised 106 molecules constructed from a total of 42929 atoms, while the vitrinite-rich char model was made up of 185 molecules consisting of a total of 44315 atoms. The difference between the number of molecules was due to the inertinite-rich char model comprising a higher distribution of larger molecules compared with the vitrinite-rich char model, in agreement with the XRD and HRTEM results. These char structures were used to examine the behaviour on the basis of gasification reactivity with CO2. The density functional theory (DFT) was used to evaluate the interactions between CO2 and the atomistic representations of coal char derived from the inertinite- and vitrinite rich South African coals. The construction of char models used the modal aromatic fringes (fringes of highest frequencies in size distributions) from the HRTEM, for the inertinite- and vitrinite-rich chars, respectively (11x11 and 7x7 parallelogram-shaped aromatic carbon rings). The structures were DFT geometrically optimized and used to measure reactivity with the Fukui function, f+(r) and to depict a representative reactive carbon edge for the simulations of coal gasification reaction mechanism with CO2 gas. The f+(r) reactivity indices of the reactive edge follows the sequence: zigzag C remote from the tip C (Czi = 0.266) > first armchair C (Cr1 = 0.087) > tip C (Ct = 0.075) > second armchair C (Cr2 = 0.029) > zigzag C proximate to the tip C (Cz = 0.027). The DFT simulated mean activation energy, ΔEb, for the gasification reaction mechanism (formation of second CO gas molecule) was 233 kJ mol-1. The reaction for the formation of second CO molecule is defines gasification in essence. The experimental activation energy determined with the TGA and random pore model to account essentially for the pore variation in addition to the gasification chemical reaction were found to be very similar: 191 ± 25 kJ mol-1 and 210 ± 8 kJ mol-1; and in good agreement with the atomistic results. The investigation gave promise towards the utility of molecular representations of coal char within the context of fundamental coal gasification reaction mechanism with CO2. / PhD (Chemical Engineering), North-West University, Potchefstroom Campus, 2015

Proper metazoan development requires that genes are expressed in a spatiotemporally controlled manner, with tightly regulated levels. Altering the expression of genes that govern development leads mostly to aberrations. However, alterations can also be beneficial, leading to the formation of new phenotypes, which contributes to the astounding diversity of animal forms. In the past the expression of developmental genes has been studied mostly in fixed tissues, which is unable to visualize these highly dynamic processes. We combine genomic fosmid transgenes, expressing genes of interest close to endogenous conditions, with Selective Plane Illumination Microscopy (SPIM) to image the expression of genes live with high temporal resolution and at single cell level in the entire embryo. In an effort to expand the toolkit for studying Drosophila development we have characterized the global expression patterns of various developmentally important genes in the whole embryo. To process the large datasets generated by SPIM, we have developed an automated workflow for processing on a High Performance Computing (HPC) cluster. In a parallel project, we wanted to understand how spatiotemporally regulated gene expression patterns and levels lead to different morphologies across Drosophila species. To this end we have compared by SPIM the expression of transcription factors (TFs) encoded by Drosophila melanogaster fosmids to their orthologous Drosophila pseudoobscura counterparts by expressing both fosmids in D. melanogaster. Here, we present an analysis of divergence of expression of orthologous genes compared A) directly by expressing the fosmids, tagged with different fluorophore, in the same D. melanogaster embryo or B) indirectly by expressing the fosmids, tagged with the same fluorophore, in separate D. melanogaster embryos. Our workflow provides powerful methodology for the study of gene expression patterns and levels during development, such knowledge is a basis for understanding both their evolutionary relevance and developmental function.

- HRSK-II-Wartung - Zentrale Firewall an der TU Dresden - Einsatz von Windows 10 an der TU Dresden - Probleme mit Office 2016 und SharePoint 2013 - I/O-Engpässe im HPC überwinden - Workshop zum Thema „Big Data in Business” - ZIH präsentiert sich auf der SC15 in Austin/Texas - ZIH-Publikationen - Veranstaltungen

- IT-Service-Katalog der TU Dresden - Konferenzzugänge für eduroam - Adobe ETLA-Desktop-Rahmenvertrag für Sachsen - Workshop „Videokonferenzen im Wissenschaftsnetz“ - Das ZIH läuft Mitteilung aus dem Dezernat 8 - Eröffnung Frontdesk des ServiceCenterStudium - ZIH-Publikationen - Veranstaltungen

- Aktualisierung Ticketsystem - Umgang mit Spam-Mails - Verbesserung der Cloudstore-Performance - Mitteilung aus dem Medienzentrum - Mitteilung aus dem Dezernat 6 - ZIH-Publikationen - Veranstaltungen

- Neues Virtualisierungs-Cluster - Änderungen am Mailrelay der TU Dresden - Windows Enterprise Upgrades über Campus Sachsen - ZIH-Konzept für umfangreiche Big-Data-Analysen - Algorithmische Differentation in OpenModelica - Deutsche Krebshilfe fördert neues Projekt - Big-Data-Sommerschule 2016 - ZIH-Kolloquium

- Umstellung des ZIH-Login-Bereitstellungsprozesses - Exchange als Standardpostfach für Beschäftigte - DYNAFLOW: Modellierung des Gallenflusses - Lange Nacht der Wissenschaften 2016 - ZIH auf der ISC\'16 - ZIH-Kolloquium Mitteilung aus dem Dezernat 6 - Schulungsangebote Mitteilung aus dem Medienzentrum - Schulungsangebote - ZIH-Publikationen - Veranstaltungen