Analysis and evaluation of MapReduce solutions on an HPC cluster

HDFS (Hadoop Distributed File System) is the primary storage of Hadoop. Even though data locality offered by HDFS is important for Big Data applications, HDFS suffers from huge I/O bottlenecks due to the tri-replicated data blocks and cannot efficiently utilize the available storage devices in an HPC (High Performance Computing) cluster. Moreover, due to the limitation of local storage space, it is challenging to deploy HDFS in HPC environments. In this paper, we present a hybrid design (Triple-H) that can minimize the I/O bottlenecks in HDFS and ensure efficient utilization of the heterogeneous storage devices (e.g. RAM, SSD, and HDD) available on HPC clusters. We also propose effective data placement policies to speed up Triple-H. Our design integrated with parallel file system (e.g. Lustre) can lead to significant storage space savings and guarantee fault-tolerance. Performance evaluations show that Triple-H can improve the write and read throughputs of HDFS by up to 7x and 2x, respectively. The execution times of data generation benchmarks are reduced by up to 3x. Our design also improves the execution time of the Sort benchmark by up to 40% over default HDFS and 54% over Lustre. The alignment phase of the Cloudburst application is accelerated by 19%. Triple-H also benefits the performance of SequenceCount and Grep in PUMA over both default HDFS and Lustre.

In the UNIX/Linux environment the kernel can log every command process created by every user with process accounting. Thus process accounting logs have many potential uses, particularly the monitoring and forensic investigation of security events. Previous work successfully leveraged the use of process accounting logs to identify a difficult to detect and damaging intrusions within high performance computing (HPC) clusters, masquerade attacks, where intruders pose as legitimate users with purloined authentication credentials. This paper incrementally advances the goal of more accurately identifying masqueraders on HPC clusters by seeking to identify features within command sets that distinguish masqueraders. To accomplish this goal, we created NVision-PA, a software tool which produces text and graphic statistical summaries describing input processing accounting logs. This research is both a promising next step toward creating a real-time masquerade detection sensor for production HPC clusters as well as providing another tool for system administrators to use for statistically monitoring and managing legitimate workloads in HPC environments

There are several popular Big Data processing frameworks including Apache Spark, Dask, and Ray. The Apache Spark software provides an easy-to-use high-level API in different languages including Scala, Java, and Python. Spark supports parallel and distributed execution of user workloads by supporting communication using an event-driven framework called Netty. Some efforts - including RDMA-Spark and SparkUCX - were made in the past to optimize Apache Spark on High-Performance Computing (HPC) systems equipped with high-performance interconnects like InfiniBand. In the HPC community, Message Passing Interface (MPI) libraries are widely adopted for parallelizing science and engineering applications. This paper presents MPI4Spark which uses MPI for communication in a parallel and distributed setting on HPC systems. MPI4Spark can launch the Spark ecosystem using MPI launchers to utilize MPI communication inside the Big Data framework. It also maintains isolation for application execution on worker nodes by forking new processes using Dynamic Process Management (DPM). It bridges semantic differences between the event-driven communication in Spark compared to the application-driven communication engine in MPI. MPI4Spark also provides portability and performance benefits as it is capable of utilizing popular HPC interconnects including InfiniBand, Omni-Path, Slingshot, and others. The performance of MPI4Spark is evaluated against RDMA-Spark and Vanilla Spark using OSU HiBD Benchmarks (OHB) and Intel HiBench that contain a variety of Resilient Distributed Dataset (RDD), Graph Processing, and Machine Learning workloads. This evaluation is done on three HPC systems including TACC Frontera, TACC Stampede2, and an internal cluster. MPI4Spark outperforms Vanilla Spark and RDMA-Spark by 4.23x and 2.04x, respectively, on the TACC Frontera system using 448 processing cores (8 Spark workers) for the GroupByTest benchmark in OHB. The communication performance of MPI4Spark is 13.08x and 5.56x better than Vanilla Spark and RDMA-Spark, respectively.

We benchmarked the performance of the GROMACS 2024 molecular dynamics (MD) code on a modern high-performance computing (HPC) cluster with AMD CPUs on up to 65,536 CPU cores. We used five different MD systems, ranging in size from about 82,000 to 204 million atoms, and evaluated their performance using two different Message Passing Interface (MPI) libraries, Intel-MPI and Open-MPI. The largest system showed near-perfect strong scaling up to 512 nodes or 65,536 cores, maintaining a parallel efficiency above 0.9 even at the highest level of parallelization. Energy efficiency for a given number of nodes was generally equal to or slightly better than parallel efficiency. We achieved peak performances of 687 ns/d for the 82k atom system, 116 ns/d for the 53M atom system, and about 35 ns/d for the largest 204M atom system. These results demonstrate that highly optimized software running on a state-of-the-art HPC cluster provides sufficient computing power to simulate biomolecular systems at the mesoscale of viruses and organelles, and potentially small cells in the near future.

Data-intensive computing has become one of the major workloads on traditional high-performance computing (HPC) clusters. Currently, deploying data-intensive computing software framework on HPC clusters still faces performance and scalability issues. In this paper, we develop a new two-level storage system by integrating Tachyon, an in-memory file system with OrangeFS, a parallel file system. We model the I/O throughputs of four storage structures: HDFS, OrangeFS, Tachyon and two-level storage. We conduct computational experiments to characterize I/O throughput behavior of two-level storage and compare its performance to that of HDFS and OrangeFS, using TeraSort benchmark. Theoretical models and experimental tests both show that the two-level storage system can increase the aggregate I/O throughputs. This work lays a solid foundation for future work in designing and building HPC systems that can provide a better support on I/O intensive workloads with preserving existing computing resources.

Arc4nix: A cross-platform geospatial analytical library for cluster and cloud computing

Scientific collaboration is critical in high performance computational (HPC) environments. Computer security incidents, however, are a constant threat in today's interconnected computational environments. Many sites struggle with finding a balance between the needs of users and the threat from unauthorized usage or access. Understanding the constantly changing battlefield is critical for effective and optimal deployment of computer security resources.This tutorial will provide an underlying knowledge of the current state of computer security, its effects on HPC environments and mitigation strategies. Topics we will address include:1.HPC Security Fundamentals2.HPC Security Protection Fundamentals3.Intrusion Detection Using Bro4.The Changing Computer Protection Environment5.Cross-site Implications of Collaborative Environments6.Keeping One Step Ahead7.Risk Assessment, Mitigation and Compliance8.Components of a Good Protection ProgramWe will also show how described techniques are in use at SC06 to protect SCinet.

Modern High Performance Computing (HPC) applications, such as Earth science simulations, produce large amounts of data due to the surging of computing power, while big data applications have become more compute-intensive due to increasingly sophisticated analysis algorithms. The needs of both HPC and big data technologies for advanced HPC and big data applications create a demand for integrated system support. In this study, we introduce Scientific Data Processing (SciDP) to support both HPC and big data applications via integrated scientific data processing. SciDP can directly process scientific data stored on a Parallel File System (PFS), which is typically deployed in an HPC environment, in a big data programming environment running atop Hadoop Distributed File System (HDFS). SciDP seamlessly integrates PFS, HDFS, and the widely-used R data analysis system to support highly efficient processing of scientific data. It utilizes the merits of both PFS and HDFS for fast data transfer, overlaps computing with data accessing, and integrates R into the data transfer process. Experimental results show that SciDP accelerates analysis and visualization of a production NASA Center for Climate Simulation (NCCS) climate and weather application by 6x to 8x when compared to existing solutions.

This Research to Practice Full Paper presents the experience of implementing micro HPC (μHPC) clusters in the education context. In developing countries, access to and experience of High Performance Computing (HPC) facilities (which are important for the economic development of those countries) has presented challenges to academic institutions due to prohibitive costs of acquisition and maintenance of HPC systems. These challenges affect the delivery of courses, which include HPC and parallel computation in their syllabi. However, due to advancements in integrated circuit technologies, credit-card-sized personal computers (PCs) have emerged with the capabilities of a fully-fledged PC. These credit-card-sized PCs offer an opportunity for system integrators to build micro HPC (μHPC) clusters which, apart from their efficiency, scalability and availability, have a number of attributes which are not shared with conventional data-center based HPC clusters These include their low power consumption, portability, diskless nodes, cost-effectiveness and excellent price to performance ratios. μHPC clusters are, therefore, ideally suited to support curricula in all educational disciplines that demand parallel computation. The purpose of this study is to investigate the implementation of μHPC to find out from students how ease of use of a μHPC system is to acquire skills and knowledge of HPC. We used focus groups and surveys to gather data in the framework of the design science research paradigm. The implementation of μHPC clusters involved a demonstration of the system in the problem context that provided valuable lessons. The results indicate that μHPC is the ease of use HPC artifact for learning about management, integration, deployment, installation, downloading, and running of parallel programs.

Summary form only given. The effect of Intel/spl reg/ hyper-threading (HT) technology on a system's performance varies according to the characteristics of the application running on the system and the configuration of the system. High performance computing (HPC) clusters introduce additional variables, such as the math libraries used in solving linear algebra equations that can affect the performance of scientific and engineering applications in particular. We study the effect of HT on MPI-based applications by varying the math library. We configure an Intel-based HPC cluster and used the High Performance Linpack (HPL) benchmark to study the performance characteristics without changing hardware or communication parameters, but by linking the application with different math libraries. What we have found is that, even though the application or hardware parameters remain the same, HT may help or hinder the overall performance of the cluster depending on the computational efficiency of the mathematical functions.

Various benchmarks exist for assessing performance characteristics of commodity hardware utilized in high performance computing (HPC) cluster environments. An additional assessment of bandwidth for Intel's 44-core processors considers network saturation via message passing focused on indirectly connected cores. The benchmark developed in this work provides a means of measuring bandwidth of two Broadwell nodes when communicating inter-chassis with all cores of each node utilized. This benchmark was developed in three phases using Message Passing Interface (MPI). First, the bandwidth measure was tested for MPI_Send operations in point-to-point communication. Second, the merge sort algorithm was implemented as a means of assessing bandwidth and a tree-structured communication algorithm was developed and implemented to maximize internode communication and minimize intra-node communication. Third, the benchmark was tuned to the configuration of the Distributed Environment for Academic Computing (DEAC) Cluster. A second benchmark removing local computation from the merge sort algorithm effectively performs a gather operation in a tree-structure. These benchmarks were tested and compared with relevant Intel MPI Benchmarks (IMB) tests. In the developed benchmarks, the nodes requested significantly more bandwidth than in the existing MPI_Gather operation and IMB benchmarks due to the large size of the messages simultaneously placed on the network.

Typically, a High Performance Computing (HPC) cluster loosely couples multiple Symmetric Multi-Processor (SMP) platforms into a single processing complex. Each SMP uses shared memory for its processors to communicate, whereas communication across SMPs goes through the intra-cluster interconnect. By analyzing the communication pattern of processes, it is possible to arrive at a mapping of processes to processors to ensure optimal communication paths for critical traffic. This critical traffic refers to the communication pattern of the program, which can be characterized by either frequency or size (or both) of the messages. To find an ideal mapping, it is imperative to understand the communication characteristics of the SMP memory system, intra-cluster interconnection, and the Message Passing Interface (MPI) program running on a cluster.Our approach is to study the ideal mapping for two classes of interconnects: 1) standard, high-volume Ethernet interconnects, and 2) proprietary, low-latency high-bandwidth interconnects. In the first installment of our work presented in this paper, we have focused on the ideal mapping for the first class.We configured a 16-node dual-processor cluster, interconnected with Fast Ethernet, Gigabit Ethernet, Giganet, and Myrinet. We used High Performance Linpack (HPL) benchmark to demonstrate that re-mapping of processes to processors (or changing the order of processors used) can affect the overall performance. The mappings are based on the HPL program analysis obtained from running a MPI profiling tool. Our results suggest that the performance of HPL using Fast Ethernet as the interconnect can be improved from 10% to 50% depending on the process mapping and the problem size. Conversely, an ad hoc mapping can adversely affect the cluster performance.

The lightweight nature, application portability, and deployment flexibility of containers is driving their widespread adoption in cloud solutions. Data analysis and deep learning (DL)/machine learning (ML) applications have especially benefited from containerization. As such data analysis is adopted in high performance computing (HPC), the need for container support in HPC has become paramount. However, containers face crucial performance and I/O challenges in HPC. One obstacle is that while there have been HPC containers, such solutions have not been thoroughly investigated, especially from the aspect of their impact on the crucial HPC I/O throughput. To this end, this paper provides a first-of-its-kind empirical analysis of state-of-the-art representative container solutions (Docker, Podman, Singularity, and Charliecloud) in HPC environments. We also explore how containers interact with an HPC parallel file system like Lustre. We present the design of an analysis framework that is deployed on all nodes in an HPC environment, and captures CPU, memory, network, and file I/O statistics from the nodes and the storage system. We are able to garner key insights from our analysis, e.g., Charliecloud outperforms other container solutions in terms of container start-up time, while Singularity and Charliecloud are equivalent in I/O throughput. But this comes at a cost, as Charliecloud invokes the most metadata and I/O operations on the underlying Lustre file system. By identifying such trade-offs and optimization opportunities, we can enhance HPC containers performance and the ML/DL applications that increasingly rely on them.

Over the past two decades, the Message Passing Interface (MPI) has evolved as the de-facto standard for programming High-Performance Computing (HPC) clusters. Its widespread utilization led to the rapid development of applications and high reusability. Meanwhile, energy- and compute-efficient devices such as Field-Programmable Gate Arrays (FPGAs) are stepping into modern data centers and HPC clusters to address the nearing end of technology scaling. This combination of traditional CPU servers and FPGA nodes leads to Reconfigurable Heterogeneous HPC (ReH 2 PC) systems that are particularly cumbersome to program because of the absence of a standard programming model. This work advocates the use of MPI to program such ReH 2 PC clusters and presents a proof of concept based on a cross-compiler, a High-Level Synthesis library, C++ library, an FPGA- and a CPU-runtime environment. The result is a one-click solution, which compiles a standard MPI application for a ReH 2 PC cluster.

High Performance Computing (HPC) applications commonly use Message Passing Interface (MPI) to scale complex workloads on distributed memory architectures, while Graphical User Interface (GUI) is the primary basis for pre-processing and post-processing. Containerization enables portability and reproducibility for applications. Docker is a widely used containerization platform but cannot be easily adopted in secure HPC environments due to the need for root privileges to run Docker containers and the ensuing security issues, as well as the lack of native support for Message Passing Interface (MPI) and HPC workload managers. In addition to offering portability and reproducibility to scientific computing, Singularity and Sarus are container runtimes that enable containers to run on HPC with user credentials by removing security concerns and allowing reuse of Docker containers without any changes. This work presents approaches to creating and running MPI and GUI applications in an isolated container environment on HPC in the cloud. We provide performance evaluation of application containers transformed from Docker to Singularity and Sarus in the context of native on HPC in the cloud.