Automating Topology Aware Mapping for Supercomputers

Petascale machines with hundreds of thousands of cores are being built. These machines have varying interconnect topologies and large network diameters. Computation is cheap and communication on the network is becoming the bottleneck for scaling of parallel applications. Network contention, specifically, is becoming an increasingly important factor affecting overall performance. The broad goal of this dissertation is performance optimization of parallel applications through reduction of network contention. Most parallel applications have a certain communication topology. Mapping of tasks in a parallel application based on their communication graph, to the physical processors on a machine can potentially lead to performance improvements. Mapping of the communication graph for an application on to the interconnect topology of a machine while trying to localize communication is the research problem under consideration. The farther different messages travel on the network, greater is the chance of resource sharing between messages. This can create contention on the network for networks commonly used today. Evaluative studies in this dissertation show that on IBM Blue Gene and Cray XT machines, message latencies can be severely affected under contention. Realizing this fact, application developers have started paying attention to the mapping of tasks to physical processors to minimize contention. Placement of communicating tasks on nearby physical processors can minimize the distance traveled by messages and reduce the chances of contention. Performance improvements through topology aware placement for applications such as NAMD and OpenAtom are used to motivate this work. Building on these ideas, the dissertation proposes algorithms and techniques for automatic mapping of parallel applications to relieve the application developers of this burden. The effect of contention on message latencies is studied in depth to guide the design of mapping algorithms. The hop-bytes metric is proposed for the evaluation of mapping algorithms as a better metric than the previously used maximum dilation metric. The main focus of this dissertation is on developing topology aware mapping algorithms for parallel applications with regular and irregular communication patterns. The automatic mapping framework is a suite of such algorithms with capabilities to choose the best mapping for a problem with a given communication graph. The dissertation also briefly discusses completely distributed mapping techniques which will be imperative for machines of the future.published or submitted for publicationnot peer reviewe

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

Load Balancing Regular Meshes on SMPS with MPI

Domain decomposition for regular meshes on parallel computers has traditionally been performed by attempting to exactly partition the work among the available processors (now cores). However, these strategies often do not consider the inherent system noise which can hinder MPI application scalability to emerging peta-scale machines with 10000+ nodes. In this work, we suggest a solution that uses a tunable hybrid static/dynamic scheduling strategy that can be incorporated into current MPI implementations of mesh codes. By applying this strategy to a 3D jacobi algorithm, we achieve performance gains of at least 16% for 64 SMP nodes

Project Final Report: HPC-Colony II

This report recounts the HPC Colony II Project which was a computer science effort funded by DOE's Advanced Scientific Computing Research office. The project included researchers from ORNL, IBM, and the University of Illinois at Urbana-Champaign. The topic of the effort was adaptive system software for extreme scale parallel machines. A description of findings is included

Enabling and scaling biomolecular simulations of 100 million atoms on petascale machines with a multicore-optimized message-driven runtime

A 100-million-atom biomolecular simulation with NAMD is one of the three benchmarks for the NSF-funded sustainable petascale machine. Simulating this large molecular system on a petascale machine presents great challenges, including handling I/O, large memory footprint and getting good strong-scaling results. In this paper, we present parallel I/O techniques to enable the simula-tion. A new SMP model is designed to efficiently utilize ubiquitous wide multicore clusters by extending the CHARM++ asynchronous message-driven runtime. We exploit node-aware techniques to op-timize both the application and the underlying SMP runtime. Hi-erarchical load balancing is further exploited to scale NAMD to the full Jaguar PF Cray XT5 (224,076 cores) at Oak Ridge Na-tional Laboratory, both with and without PME full electrostatics, achieving 93 % parallel efficiency (vs 6720 cores) at 9 ms per step for a simple cutoff calculation. Excellent scaling is also obtained on 65,536 cores of the Intrepid Blue Gene/P at Argonne National Laboratory. 1

MaxEVA: Maximizing the Efficiency of Matrix Multiplication on Versal AI Engine

The increasing computational and memory requirements of Deep Learning (DL) workloads has led to outstanding innovations in hardware architectures. An archetype of such architectures is the novel Versal AI Engine (AIE) by AMD/Xilinx. The AIE comprises multiple programmable processors optimized for vector-based algorithms. An AIE array consisting of 400 processor cores, operating at 1.25 GHz is able to deliver a peak throughput of 8 TFLOPs for 32-bit floating-point (fp32), and 128 TOPs for 8-bit integer (int8) precision. In this work, we propose MaxEVA: a novel framework to efficiently map Matrix Multiplication (MatMul) workloads on Versal AIE devices. Our framework maximizes the performance and energy efficiency of MatMul applications by efficiently exploiting features of the AIE architecture and resolving performance bottlenecks from multiple angles. When demonstrating on the VC1902 device of the VCK190 board, MaxEVA accomplishes up to 5.44 TFLOPs and 77.01 TOPs throughput for fp32 and int8 precisions, respectively. In terms of energy efficiency, MaxEVA attains up to 124.16 GFLOPs/W for fp32, and 1.16 TOPs/W for int8. Our proposed method substantially outperforms the state-of-the-art approach by exhibiting up to 2.19x throughput gain and 20.4% higher energy efficiency. The MaxEVA framework provides notable insights to fill the knowledge gap in effectively designing MatMul-based DL workloads on the new Versal AIE devices.Comment: Accepted as full paper at FPT 202

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

Doctor of Philosophy

dissertationIn recent years, a number of trends have started to emerge, both in microprocessor and application characteristics. As per Moore's law, the number of cores on chip will keep doubling every 18-24 months. International Technology Roadmap for Semiconductors (ITRS) reports that wires will continue to scale poorly, exacerbating the cost of on-chip communication. Cores will have to navigate an on-chip network to access data that may be scattered across many cache banks. The number of pins on the package, and hence available off-chip bandwidth, will at best increase at sublinear rate and at worst, stagnate. A number of disruptive memory technologies, e.g., phase change memory (PCM) have begun to emerge and will be integrated into the memory hierarchy sooner than later, leading to non-uniform memory access (NUMA) hierarchies. This will make the cost of accessing main memory even higher. In previous years, most of the focus has been on deciding the memory hierarchy level where data must be placed (L1 or L2 caches, main memory, disk, etc.). However, in modern and future generations, each level is getting bigger and its design is being subjected to a number of constraints (wire delays, power budget, etc.). It is becoming very important to make an intelligent decision about where data must be placed within a level. For example, in a large non-uniform access cache (NUCA), we must figure out the optimal bank. Similarly, in a multi-dual inline memory module (DIMM) non uniform memory access (NUMA) main memory, we must figure out the DIMM that is the optimal home for every data page. Studies have indicated that heterogeneous main memory hierarchies that incorporate multiple memory technologies are on the horizon. We must develop solutions for data management that take heterogeneity into account. For these memory organizations, we must again identify the appropriate home for data. In this dissertation, we attempt to verify the following thesis statement: "Can low-complexity hardware and OS mechanisms manage data placement within each memory hierarchy level to optimize metrics such as performance and/or throughput?" In this dissertation we argue for a hardware-software codesign approach to tackle the above mentioned problems at different levels of the memory hierarchy. The proposed methods utilize techniques like page coloring and shadow addresses and are able to handle a large number of problems ranging from managing wire-delays in large, shared NUCA caches to distributing shared capacity among different cores. We then examine data-placement issues in NUMA main memory for a many-core processor with a moderate number of on-chip memory controllers. Using codesign approaches, we achieve efficient data placement by modifying the operating system's (OS) page allocation algorithm for a wide variety of main memory architectures

Chrion: Optimizing Recurrent Neural Network Inference by Collaboratively Utilizing CPUs and GPUs

Deploying deep learning models in cloud clusters provides efficient and prompt inference services to accommodate the widespread application of deep learning. These clusters are usually equipped with host CPUs and accelerators with distinct responsibilities to handle serving requests, i.e. generalpurpose CPUs for input preprocessing and domain-specific GPUs for forward computation. Recurrent neural networks play an essential role in handling temporal inputs and display distinctive computation characteristics because of their high inter-operator parallelism. Hence, we propose Chrion to optimize recurrent neural network inference by collaboratively utilizing CPUs and GPUs. We formulate the model deployment in the CPU-GPU cluster as an NP-hard scheduling problem of directed acyclic graphs on heterogeneous devices. Given an input model in the ONNX format and user-defined SLO requirement, Chrion firstly preprocesses the model by model parsing and profiling, and then partitions the graph to select execution devices for each operator. When an online request arrives, Chrion performs forward computation according to the graph partition by executing the operators on the CPU and GPU in parallel. Our experimental results show that the execution time can be reduced by 19.4% at most in the latency-optimal pattern and GPU memory footprint by 67.5% in the memory-optimal pattern compared with the execution on the GPU