Optimizing Communication for Massively Parallel Processing

The current trends in high performance computing show that large machines with tens of thousands of processors will soon be readily available. The IBM Bluegene-L machine with 128k processors (which is currently being deployed) is an important step in this direction. In this scenario, it is going to be a significant burden for the programmer to manually scale his applications. This task of scaling involves addressing issues like load-imbalance and communication overhead. In this thesis, we explore several communication optimizations to help parallel applications to easily scale on a large number of processors. We also present automatic runtime techniques to relieve the programmer from the burden of optimizing communication in his applications. This thesis explores processor virtualization to improve communication performance in applications. With processor virtualization, the computation is mapped to virtual processors (VPs). After one VP has finished computation and is waiting for responses to its messages, another VP can compute, thus overlapping communication with computation. This overlap is only effective if the processor overhead of the communication operation is a small fraction of the total communication time. Fortunately, with network interfaces having co-processors, this happens to be true and processor virtualization has a natural advantage on such interconnects. The communication optimizations we present in this thesis, are motivated by applications such as NAMD (a classical molecular dynamics application) and CPAIMD (a quantum chemistry application). Applications like NAMD and CPAIMD consume a fair share of the time available on supercomputers. So, improving their performance would be of great value. We have successfully scaled NAMD to 1TF of peak performance on 3000 processors of PSC Lemieux, using the techniques presented in this thesis. We study both point-to-point communication and collective communication (specifically all-to-all communication). On a large number of processors all-to-all communication can take several milli-seconds to finish. With synchronous collectives defined in MPI, the processor idles while the collective messages are in flight. Therefore, we demonstrate an asynchronous collective communication framework, to let the CPU compute while the all-to-all messages are in flight. We also show that the best strategy for all-to-all communication depends on the message size, number of processors and other dynamic parameters. This suggests that these parameters can be observed at runtime and used to choose the optimal strategy for all-to-all communication. In this thesis, we demonstrate adaptive strategy switching for all-to-all communication. The communication optimization framework presented in this thesis, has been designed to optimize communication in the context of processor virtualization and dynamic migrating objects. We present the streaming strategy to optimize fine grained object-to-object communication. In this thesis, we motivate the need for hardware collectives, as processor based collectives can be delayed by intermediate that processors busy with computation. We explore a next generation interconnect that supports collectives in the switching hardware. We show the performance gains of hardware collectives through synthetic benchmarks

Fast Fourier transforms on energy-efficient application-specific processors

Many of the current applications used in battery powered devices are from digital signal processing, telecommunication, and multimedia domains. Traditionally application-specific fixed-function circuits have been used in these designs in form of application-specific integrated circuits (ASIC) to reach the required performance and energy-efficiency. The complexity of these applications has increased over the years, thus the design complexity has increased even faster, which implies increased design time. At the same time, there are more and more standards to be supported, thus using optimised fixed-function implementations for all the functions in all the standards is impractical. The non-recurring engineering costs for integrated circuits have also increased significantly, so manufacturers can only afford fewer chip iterations. Although tailoring the circuit for a specific application provides the best performance and/or energy-efficiency, such approach lacks flexibility. E.g., if an error is found after the manufacturing, an expensive chip iteration is required. In addition, new functionalities cannot be added afterwards to support evolution of standards. Flexibility can be obtained with software based implementation technologies. Unfortunately, general-purpose processors do not provide the energy-efficiency of the fixed-function circuit designs. A useful trade-off between flexibility and performance is implementation based on application-specific processors (ASP) where programmability provides the flexibility and computational resources customised for the given application provide the performance. In this Thesis, application-specific processors are considered by using fast Fourier transform as the representative algorithm. The architectural template used here is transport triggered architecture (TTA) which resembles very long instruction word machines but the operand execution resembles data flow machines rather than traditional operand triggering. The developed TTA processors exploit inherent parallelism of the application. In addition, several characteristics of the application have been identified and those are exploited by developing customised functional units for speeding up the execution. Several customisations are proposed for the data path of the processor but it is also important to match the memory bandwidth to the computation speed. This calls for a memory organisation supporting parallel memory accesses. The proposed optimisations have been used to improve the energy-efficiency of the processor and experiments show that a programmable solution can have energy-efficiency comparable to fixed-function ASIC designs

An In-Depth Analysis of the Slingshot Interconnect

The interconnect is one of the most critical components in large scale computing systems, and its impact on the performance of applications is going to increase with the system size. In this paper, we will describe Slingshot, an interconnection network for large scale computing systems. Slingshot is based on high-radix switches, which allow building exascale and hyperscale datacenters networks with at most three switch-to-switch hops. Moreover, Slingshot provides efficient adaptive routing and congestion control algorithms, and highly tunable traffic classes. Slingshot uses an optimized Ethernet protocol, which allows it to be interoperable with standard Ethernet devices while providing high performance to HPC applications. We analyze the extent to which Slingshot provides these features, evaluating it on microbenchmarks and on several applications from the datacenter and AI worlds, as well as on HPC applications. We find that applications running on Slingshot are less affected by congestion compared to previous generation networks.Comment: To be published in Proceedings of The International Conference for High Performance Computing Networking, Storage, and Analysis (SC '20) (2020

3rd Many-core Applications Research Community (MARC) Symposium. (KIT Scientific Reports ; 7598)

This manuscript includes recent scientific work regarding the Intel Single Chip Cloud computer and describes approaches for novel approaches for programming and run-time organization

Optimization of communication intensive applications on HPC networks

Communication is a necessary but overhead inducing component of parallel programming. Its impact on application design and performance is due to several related aspects of a parallel job execution: network topology, routing protocol, suitability of algorithm being used to the network, job placement, etc. This thesis is aimed at developing an understanding of how communication plays out on networks of high performance computing systems and exploring methods that can be used to improve communication performance of large scale applications. Broadly speaking, three topics have been studied in detail in this thesis. The first of these topics is task mapping and job placement on practical installations of torus and dragonfly networks. Next, use of supervised learning algorithms for conducting diagnostic studies of how communication evolves on networks is explored. Finally, efficacy of packet-level simulations for prediction-based studies of communication performance on different networks using different network parameters is analyzed. The primary contribution of this thesis is development of scalable diagnostic and prediction methods that can assist in the process of network designing, adapting applications to future systems, and optimizing execution of applications on existing systems. These meth- ods include a supervised learning approach, a functional modeling tool (called Damselfly), and a PDES-based packet level simulator (called TraceR), all of which are described in this thesis

Scalability Engineering for Parallel Programs Using Empirical Performance Models

Performance engineering is a fundamental task in high-performance computing (HPC). By definition, HPC applications should strive for maximum performance. As HPC systems grow larger and more complex, the scalability of an application has become of primary concern. Scalability is the ability of an application to show satisfactory performance even when the number of processors or the problems size is increased. Although various analysis techniques for scalability were suggested in past, engineering applications for extreme-scale systems still occurs ad hoc. The challenge is to provide techniques that explicitly target scalability throughout the whole development cycle, thereby allowing developers to uncover bottlenecks earlier in the development process. In this work, we develop a number of fundamental approaches in which we use empirical performance models to gain insights into the code behavior at higher scales. In the first contribution, we propose a new software engineering approach for extreme-scale systems. Specifically, we develop a framework that validates asymptotic scalability expectations of programs against their actual behavior. The most important applications of this method, which is especially well suited for libraries encapsulating well-studied algorithms, include initial validation, regression testing, and benchmarking to compare implementation and platform alternatives. We supply a tool-chain that automates large parts of the framework, thus allowing it to be continuously applied throughout the development cycle with very little effort. We evaluate the framework with MPI collective operations, a data-mining code, and various OpenMP constructs. In addition to revealing unexpected scalability bottlenecks, the results also show that it is a viable approach for systematic validation of performance expectations. As the second contribution, we show how the isoefficiency function of a task-based program can be determined empirically and used in practice to control the efficiency. Isoefficiency, a concept borrowed from theoretical algorithm analysis, binds efficiency, core count, and the input size in one analytical expression, thereby allowing the latter two to be adjusted according to given (realistic) efficiency objectives. Moreover, we analyze resource contention by modeling the efficiency of contention-free execution. This allows poor scaling to be attributed either to excessive resource contention overhead or structural conflicts related to task dependencies or scheduling. Our results, obtained with applications from two benchmark suites, demonstrate that our approach provides insights into fundamental scalability limitations or excessive resource overhead and can help answer critical co-design questions. Our contributions for better scalability engineering can be used not only in the traditional software development cycle, but also in other, related fields, such as algorithm engineering. It is a field that uses the software engineering cycle to produce algorithms that can be utilized in applications more easily. Using our contributions, algorithm engineers can make informed design decisions, get better insights, and save experimentation time

PYDAC: A DISTRIBUTED RUNTIME SYSTEM AND PROGRAMMING MODEL FOR A HETEROGENEOUS MANY-CORE ARCHITECTURE

Heterogeneous many-core architectures that consist of big, fast cores and small, energy-efficient cores are very promising for future high-performance computing (HPC) systems. These architectures offer a good balance between single-threaded perfor- mance and multithreaded throughput. Such systems impose challenges on the design of programming model and runtime system. Specifically, these challenges include (a) how to fully utilize the chip’s performance, (b) how to manage heterogeneous, un- reliable hardware resources, and (c) how to generate and manage a large amount of parallel tasks. This dissertation proposes and evaluates a Python-based programming framework called PyDac. PyDac supports a two-level programming model. At the high level, a programmer creates a very large number of tasks, using the divide-and-conquer strategy. At the low level, tasks are written in imperative programming style. The runtime system seamlessly manages the parallel tasks, system resilience, and inter- task communication with architecture support. PyDac has been implemented on both an field-programmable gate array (FPGA) emulation of an unconventional het- erogeneous architecture and a conventional multicore microprocessor. To evaluate the performance, resilience, and programmability of the proposed system, several micro-benchmarks were developed. We found that (a) the PyDac abstracts away task communication and achieves programmability, (b) the micro-benchmarks are scalable on the hardware prototype, but (predictably) serial operation limits some micro-benchmarks, and (c) the degree of protection versus speed could be varied in redundant threading that is transparent to programmers

Hardware Architectures for Post-Quantum Cryptography

The rapid development of quantum computers poses severe threats to many commonly-used cryptographic algorithms that are embedded in different hardware devices to ensure the security and privacy of data and communication. Seeking for new solutions that are potentially resistant against attacks from quantum computers, a new research field called Post-Quantum Cryptography (PQC) has emerged, that is, cryptosystems deployed in classical computers conjectured to be secure against attacks utilizing large-scale quantum computers. In order to secure data during storage or communication, and many other applications in the future, this dissertation focuses on the design, implementation, and evaluation of efficient PQC schemes in hardware. Four PQC algorithms, each from a different family, are studied in this dissertation. The first hardware architecture presented in this dissertation is focused on the code-based scheme Classic McEliece. The research presented in this dissertation is the first that builds the hardware architecture for the Classic McEliece cryptosystem. This research successfully demonstrated that complex code-based PQC algorithm can be run efficiently on hardware. Furthermore, this dissertation shows that implementation of this scheme on hardware can be easily tuned to different configurations by implementing support for flexible choices of security parameters as well as configurable hardware performance parameters. The successful prototype of the Classic McEliece scheme on hardware increased confidence in this scheme, and helped Classic McEliece to get recognized as one of seven finalists in the third round of the NIST PQC standardization process. While Classic McEliece serves as a ready-to-use candidate for many high-end applications, PQC solutions are also needed for low-end embedded devices. Embedded devices play an important role in our daily life. Despite their typically constrained resources, these devices require strong security measures to protect them against cyber attacks. Towards securing this type of devices, the second research presented in this dissertation focuses on the hash-based digital signature scheme XMSS. This research is the first that explores and presents practical hardware based XMSS solution for low-end embedded devices. In the design of XMSS hardware, a heterogenous software-hardware co-design approach was adopted, which combined the flexibility of the soft core with the acceleration from the hard core. The practicability and efficiency of the XMSS software-hardware co-design is further demonstrated by providing a hardware prototype on an open-source RISC-V based System-on-a-Chip (SoC) platform. The third research direction covered in this dissertation focuses on lattice-based cryptography, which represents one of the most promising and popular alternatives to today\u27s widely adopted public key solutions. Prior research has presented hardware designs targeting the computing blocks that are necessary for the implementation of lattice-based systems. However, a recurrent issue in most existing designs is that these hardware designs are not fully scalable or parameterized, hence limited to specific cryptographic primitives and security parameter sets. The research presented in this dissertation is the first that develops hardware accelerators that are designed to be fully parameterized to support different lattice-based schemes and parameters. Further, these accelerators are utilized to realize the first software-harware co-design of provably-secure instances of qTESLA, which is a lattice-based digital signature scheme. This dissertation demonstrates that even demanding, provably-secure schemes can be realized efficiently with proper use of software-hardware co-design. The final research presented in this dissertation is focused on the isogeny-based scheme SIKE, which recently made it to the final round of the PQC standardization process. This research shows that hardware accelerators can be designed to offload compute-intensive elliptic curve and isogeny computations to hardware in a versatile fashion. These hardware accelerators are designed to be fully parameterized to support different security parameter sets of SIKE as well as flexible hardware configurations targeting different user applications. This research is the first that presents versatile hardware accelerators for SIKE that can be mapped efficiently to both FPGA and ASIC platforms. Based on these accelerators, an efficient software-hardwareco-design is constructed for speeding up SIKE. In the end, this dissertation demonstrates that, despite being embedded with expensive arithmetic, the isogeny-based SIKE scheme can be run efficiently by exploiting specialized hardware. These four research directions combined demonstrate the practicability of building efficient hardware architectures for complex PQC algorithms. The exploration of efficient PQC solutions for different hardware platforms will eventually help migrate high-end servers and low-end embedded devices towards the post-quantum era