Kernel-assisted and Topology-aware MPI Collective Communication among Multicore or Many-core Clusters

Multicore or many-core clusters have become the most prominent form of High Performance Computing (HPC) systems. Hardware complexity and hierarchies not only exist in the inter-node layer, i.e., hierarchical networks, but also exist in internals of multicore compute nodes, e.g., Non Uniform Memory Accesses (NUMA), network-style interconnect, and memory and shared cache hierarchies. Message Passing Interface (MPI), the most widely adopted in the HPC communities, suffers from decreased performance and portability due to increased hardware complexity of multiple levels. We identified three critical issues specific to collective communication: The first problem arises from the gap between logical collective topologies and underlying hardware topologies; Second, current MPI communications lack efficient shared memory message delivering approaches; Last, on distributed memory machines, like multicore clusters, a single approach cannot encompass the extreme variations not only in the bandwidth and latency capabilities, but also in features such as the aptitude to operate multiple concurrent copies simultaneously. To bridge the gap between logical collective topologies and hardware topologies, we developed a distance-aware framework to integrate the knowledge of hardware distance into collective algorithms in order to dynamically reshape the communication patterns to suit the hardware capabilities. Based on process distance information, we used graph partitioning techniques to organize the MPI processes in a multi-level hierarchy, mapping on the hardware characteristics. Meanwhile, we took advantage of the kernel-assisted one-sided single-copy approach (KNEM) as the default shared memory delivering method. Via kernel-assisted memory copy, the collective algorithms offload copy tasks onto non-leader/not-root processes to evenly distribute copy workloads among available cores. Finally, on distributed memory machines, we developed a technique to compose multi-layered collective algorithms together to express a multi-level algorithm with tight interoperability between the levels. This tight collaboration results in more overlaps between inter- and intra-node communication. Experimental results have confirmed that, by leveraging several technologies together, such as kernel-assisted memory copy, the distance-aware framework, and collective algorithm composition, not only do MPI collectives reach the potential maximum performance on a wide variation of platforms, but they also deliver a level of performance immune to modifications of the underlying process-core binding

KNEM: a Generic and Scalable Kernel-Assisted Intra-node MPI Communication Framework

International audienceThe multiplication of cores in today's architectures raises the importance of intra-node communication in modern clusters and their impact on the overall parallel application performance. Although several proposals focused on this issue in the past, there is still a need for a portable and hardware-independent solution that addresses the requirements of both point-to-point and collective MPI operations inside shared-memory computing nodes. This paper presents the KNEM module for the Linux kernel that provides MPI implementations with a flexible and scalable interface for performing kernel-assisted single-copy data transfers between local processes. It enables high-performance communication within most existing MPI implementations and brings significant application performance improvements thanks to more efficient point-to-point and collective operations

Improving the Performance of the MPI_Allreduce Collective Operation through Rank Renaming

Proceedings of: First International Workshop on Sustainable Ultrascale Computing Systems (NESUS 2014). Porto (Portugal), August 27-28, 2014.Collective operations, a key issue in the global efficiency of HPC applications, are optimized in current MPI libraries by choosing at runtime between a set of algorithms, based on platform-dependent beforehand established parameters, as the message size or the number of processes. However, with progressively more cores per node, the cost of a collective algorithm must be mainly imputed to process-to-processor mapping, because its decisive influence over the network traffic. Hierarchical design of collective algorithms pursuits to minimize the data movement through the slowest communication channels of the multi-core cluster. Nevertheless, the hierarchical implementation of some collectives becomes inefficient, and even impracticable, due to the operation definition itself. This paper proposes a new approach that departs from a frequently found regular mapping, either sequential or round-robin. While keeping the mapping, the rank assignation to the processes is temporarily changed prior to the execution of the collective algorithm. The new assignation makes the communication pattern to adapt to the communication channels hierarchy. We explore this technique for the Ring algorithm when used in the well-known MPI_Allreduce collective, and discuss the obtained performance results. Extensions to other algorithms and collective operations are proposed.The work presented in this paper has been partially supported by EU under the COST programme Action IC1305, ’Network for Sustainable Ultrascale Computing (NESUS)’, and by the computing facilities of Extremadura Research Centre for Advanced Technologies (CETACIEMAT), funded by the European Regional Development Fund (ERDF). CETA-CIEMAT belongs to CIEMAT and the Government of Spain

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

Programming Models\u27 Support for Heterogeneous Architecture

Accelerator-enhanced computing platforms have drawn a lot of attention due to their massive peak computational capacity. Heterogeneous systems equipped with accelerators such as GPUs have become the most prominent components of High Performance Computing (HPC) systems. Even at the node level the significant heterogeneity of CPU and GPU, i.e. hardware and memory space differences, leads to challenges for fully exploiting such complex architectures. Extending outside the node scope, only escalate such challenges. Conventional programming models such as data- ow and message passing have been widely adopted in HPC communities. When moving towards heterogeneous systems, the lack of GPU integration causes such programming models to struggle in handling the heterogeneity of different computing units, leading to sub-optimal performance and drastic decrease in developer productivity. To bridge the gap between underlying heterogeneous architectures and current programming paradigms, we propose to extend such programming paradigms with architecture awareness optimization. Two programming models are used to demonstrate the impact of heterogeneous architecture awareness. The PaRSEC task-based runtime, an adopter of the data- ow model, provides opportunities for overlapping communications with computations and minimizing data movements, as well as dynamically adapting the work granularity to the capability of the hardware. To fulfill the demand of an efficient and portable Message Passing Interface (MPI) implementation to communicate GPU data, a GPU-aware design is presented based on the Open MPI infrastructure supporting efficient point-to-point and collective communications of GPU-residential data, for both contiguous and non-contiguous memory layouts, by leveraging GPU network topology and hardware capabilities such as GPUDirect. The tight integration of GPU support in a widely used programming environment, free the developers from manually move data into/out of host memory before/after relying on MPI routines for communications, allowing them to focus instead on algorithmic optimizations. Experimental results have confirmed that supported by such a tight and transparent integration, conventional programming models can once again take advantage of the state-of-the-art hardware and exhibit performance at the levels expected by the underlying hardware capabilities

High-Performance Communication Primitives and Data Structures on Message-Passing Manycores:Broadcast and Map

The constant increase in single core frequency reached a plateau during recent years since the produced heat inside the chip cannot be cooled down by existing technologies anymore. An alternative to harvest more computational power per die is to fabricate more number of cores into a single chip. Therefore manycore chips with more than thousand cores are expected by the end of the decade. These environments provide a high level of parallel processing power while their energy consumption is considerably lower than their multi-chip counterparts. Although shared-memory programming is the classical paradigm to program these environments, there are numerous claims that taking into account the full life cycle of software, the message-passing programming model have numerous advantages. The direct architectural consequence of applying a message-passing programming model is to support message passing between the processing entities directly in the hardware. Therefore manycore architectures with hardware support for message passing are becoming more and more visible. These platforms can be seen in two ways: (i) as a High Performance Computing (HPC) cluster programmed by highly trained scientists using Message Passing Interface (MPI) libraries; or (ii) as a mainstream computing platform requiring a global operating system to abstract away the architectural complexities from the ordinary programmer. In the first view, performance of communication primitives is an important bottleneck for MPI applications. In the second view, kernel data structures have been shown to be a limiting factor. In this thesis (i) we overview existing state-of-the-art techniques to circumvent the mentioned bottlenecks; and (ii) we study high-performance broadcast communication primitive and map data structure on modern manycore architectures, with message-passing support in hardware, in two different chapters respectively. In one chapter, we study how to make use of the hardware features to implement an efficient broadcast primitive. We consider the Intel Single-chip Cloud Computer (SCC) as our target platform which offers the ability to move data between on-chip Message Passing Buffers (MPB) using Remote Memory Access (RMA). We propose OC-Bcast (On-Chip Broadcast), a pipelined k-ary tree algorithm tailored to exploit the parallelism provided by on-chip RMA. Experimental results show that OC-Bcast attains considerably better performance in terms of latency and throughput compared to state-of-the-art solutions. This performance improvement highlights the benefits of exploiting hardware features of the target platform: Our broadcast algorithm takes direct advantage of RMA, unlike the other broadcast solutions which are based on a higher-level send/receive interface. In the other chapter, we study the implementation of high-throughput concurrent maps in message-passing manycores. Partitioning and replication are the two approaches to achieve high throughput in a message-passing system. This chapter presents and compares different strongly-consistent map algorithms based on partitioning and replication. To assess the performance of these algorithms independently of architecture-specific features, we propose a communication model of message-passing manycores to express the throughput of each algorithm. The model is validated through experiments on a 36-core TILE-Gx8036 processor. Evaluations show that replication outperforms partitioning only in a narrow domain

Architecting a One-to-many Traffic-Aware and Secure Millimeter-Wave Wireless Network-in-Package Interconnect for Multichip Systems

With the aggressive scaling of device geometries, the yield of complex Multi Core Single Chip(MCSC) systems with many cores will decrease due to the higher probability of manufacturing defects especially, in dies with a large area. Disintegration of large System-on-Chips(SoCs) into smaller chips called chiplets has shown to improve the yield and cost of complex systems. Therefore, platform-based computing modules such as embedded systems and micro-servers have already adopted Multi Core Multi Chip (MCMC) architectures overMCSC architectures. Due to the scaling of memory intensive parallel applications in such systems, data is more likely to be shared among various cores residing in different chips resulting in a significant increase in chip-to-chip traffic, especially one-to-many traffic. This one-to-many traffic is originated mainly to maintain cache-coherence between many cores residing in multiple chips. Besides, one-to-many traffics are also exploited by many parallel programming models, system-level synchronization mechanisms, and control signals. How-ever, state-of-the-art Network-on-Chip (NoC)-based wired interconnection architectures do not provide enough support as they handle such one-to-many traffic as multiple unicast trafficusing a multi-hop MCMC communication fabric. As a result, even a small portion of such one-to-many traffic can significantly reduce system performance as traditional NoC-basedinterconnect cannot mask the high latency and energy consumption caused by chip-to-chipwired I/Os. Moreover, with the increase in memory intensive applications and scaling of MCMC systems, traditional NoC-based wired interconnects fail to provide a scalable inter-connection solution required to support the increased cache-coherence and synchronization generated one-to-many traffic in future MCMC-based High-Performance Computing (HPC) nodes. Therefore, these computation and memory intensive MCMC systems need an energy-efficient, low latency, and scalable one-to-many (broadcast/multicast) traffic-aware interconnection infrastructure to ensure high-performance. Research in recent years has shown that Wireless Network-in-Package (WiNiP) architectures with CMOS compatible Millimeter-Wave (mm-wave) transceivers can provide a scalable, low latency, and energy-efficient interconnect solution for on and off-chip communication. In this dissertation, a one-to-many traffic-aware WiNiP interconnection architecture with a starvation-free hybrid Medium Access Control (MAC), an asymmetric topology, and a novel flow control has been proposed. The different components of the proposed architecture are individually one-to-many traffic-aware and as a system, they collaborate with each other to provide required support for one-to-many traffic communication in a MCMC environment. It has been shown that such interconnection architecture can reduce energy consumption and average packet latency by 46.96% and 47.08% respectively for MCMC systems. Despite providing performance enhancements, wireless channel, being an unguided medium, is vulnerable to various security attacks such as jamming induced Denial-of-Service (DoS), eavesdropping, and spoofing. Further, to minimize the time-to-market and design costs, modern SoCs often use Third Party IPs (3PIPs) from untrusted organizations. An adversary either at the foundry or at the 3PIP design house can introduce a malicious circuitry, to jeopardize an SoC. Such malicious circuitry is known as a Hardware Trojan (HT). An HTplanted in the WiNiP from a vulnerable design or manufacturing process can compromise a Wireless Interface (WI) to enable illegitimate transmission through the infected WI resulting in a potential DoS attack for other WIs in the MCMC system. Moreover, HTs can be used for various other malicious purposes, including battery exhaustion, functionality subversion, and information leakage. This information when leaked to a malicious external attackercan reveals important information regarding the application suites running on the system, thereby compromising the user profile. To address persistent jamming-based DoS attack in WiNiP, in this dissertation, a secure WiNiP interconnection architecture for MCMC systems has been proposed that re-uses the one-to-many traffic-aware MAC and existing Design for Testability (DFT) hardware along with Machine Learning (ML) approach. Furthermore, a novel Simulated Annealing (SA)-based routing obfuscation mechanism was also proposed toprotect against an HT-assisted novel traffic analysis attack. Simulation results show that,the ML classifiers can achieve an accuracy of 99.87% for DoS attack detection while SA-basedrouting obfuscation could reduce application detection accuracy to only 15% for HT-assistedtraffic analysis attack and hence, secure the WiNiP fabric from age-old and emerging attacks

Parallel Programming with Global Asynchronous Memory: Models, C++ APIs and Implementations

In the realm of High Performance Computing (HPC), message passing has been the programming paradigm of choice for over twenty years. The durable MPI (Message Passing Interface) standard, with send/receive communication, broadcast, gather/scatter, and reduction collectives is still used to construct parallel programs where each communication is orchestrated by the developer-based precise knowledge of data distribution and overheads; collective communications simplify the orchestration but might induce excessive synchronization. Early attempts to bring shared-memory programming model—with its programming advantages—to distributed computing, referred as the Distributed Shared Memory (DSM) model, faded away; one of the main issue was to combine performance and programmability with the memory consistency model. The recently proposed Partitioned Global Address Space (PGAS) model is a modern revamp of DSM that exposes data placement to enable optimizations based on locality, but it still addresses (simple) data- parallelism only and it relies on expensive sharing protocols. We advocate an alternative programming model for distributed computing based on a Global Asynchronous Memory (GAM), aiming to avoid coherency and consistency problems rather than solving them. We materialize GAM by designing and implementing a distributed smart pointers library, inspired by C++ smart pointers. In this model, public and pri- vate pointers (resembling C++ shared and unique pointers, respectively) are moved around instead of messages (i.e., data), thus alleviating the user from the burden of minimizing transfers. On top of smart pointers, we propose a high-level C++ template library for writing applications in terms of dataflow-like networks, namely GAM nets, consisting of stateful processors exchanging pointers in fully asynchronous fashion. We demonstrate the validity of the proposed approach, from the expressiveness perspective, by showing how GAM nets can be exploited to implement both standalone applications and higher-level parallel program- ming models, such as data and task parallelism. As for the performance perspective, preliminary experiments show both close-to-ideal scalability and negligible overhead with respect to state-of-the-art benchmark implementations. For instance, the GAM implementation of a high-quality video restoration filter sustains a 100 fps throughput over 70%-noisy high-quality video streams on a 4-node cluster of Graphics Processing Units (GPUs), with minimal programming effort