Design and Implementation of MPICH2 over InfiniBand with RDMA Support

For several years, MPI has been the de facto standard for writing parallel applications. One of the most popular MPI implementations is MPICH. Its successor, MPICH2, features a completely new design that provides more performance and flexibility. To ensure portability, it has a hierarchical structure based on which porting can be done at different levels. In this paper, we present our experiences designing and implementing MPICH2 over InfiniBand. Because of its high performance and open standard, InfiniBand is gaining popularity in the area of high-performance computing. Our study focuses on optimizing the performance of MPI-1 functions in MPICH2. One of our objectives is to exploit Remote Direct Memory Access (RDMA) in Infiniband to achieve high performance. We have based our design on the RDMA Channel interface provided by MPICH2, which encapsulates architecture-dependent communication functionalities into a very small set of functions. Starting with a basic design, we apply different optimizations and also propose a zero-copy-based design. We characterize the impact of our optimizations and designs using microbenchmarks. We have also performed an application-level evaluation using the NAS Parallel Benchmarks. Our optimized MPICH2 implementation achieves 7.6 $\mu$s latency and 857 MB/s bandwidth, which are close to the raw performance of the underlying InfiniBand layer. Our study shows that the RDMA Channel interface in MPICH2 provides a simple, yet powerful, abstraction that enables implementations with high performance by exploiting RDMA operations in InfiniBand. To the best of our knowledge, this is the first high-performance design and implementation of MPICH2 on InfiniBand using RDMA support.Comment: 12 pages, 17 figure

Optimizations of Client's side communications in a Distributed File System within a Myrinet Cluster

International audienceThis paper presents a study of the interaction between high-speed interconnects and a distributed file system client. We use our remote file access protocol and network with the software layer to show how the highly specific programming model of high-speed interconnects may be used in a high performance distributed file system client. We present both a user-level and a kernel-level client implementations with either buffered or non-buffered accesses. These implementations show high performances and may be transparently used by applications. Our improvements focus on pin-down cache techniques and memory registration issues. Our modifications show no impact on its performances while the network usage in the distributed file system client is improved

Adaptive Routing Strategies for Modern High Performance Networks

Today’s scalable high-performance applications heavily depend on the bandwidth characteristics of their commu-nication patterns. Contemporary multi-stage interconnec-tion networks suffer from network contention which might decrease application performance. Our experiments show that the effective bisection bandwidth of a non-blocking 512-node Clos network is as low as 38 % if the network is routed statically. In this paper, we propose and ana-lyze different adaptive routing schemes for those networks. We chose Myrinet/MX to implement our proposed routing schemes. Our best adaptive routing scheme is able to in-crease the effective bisection bandwidth to 77 % for 512 nodes and 100 % for smaller node counts. Thus, we show that our proposed adaptive routing schemes are able to im-prove network throughput significantly.

Performance Evaluation of Supercomputers using HPCC and IMB Benchmarks

The HPC Challenge (HPCC) benchmark suite and the Intel MPI Benchmark (IMB) are used to compare and evaluate the combined performance of processor, memory subsystem and interconnect fabric of five leading supercomputers - SGI Altix BX2, Cray XI, Cray Opteron Cluster, Dell Xeon cluster, and NEC SX-8. These five systems use five different networks (SGI NUMALINK4, Cray network, Myrinet, InfiniBand, and NEC IXS). The complete set of HPCC benchmarks are run on each of these systems. Additionally, we present Intel MPI Benchmarks (IMB) results to study the performance of 11 MPI communication functions on these systems

NewMadeleine: An Efficient Support for High-Performance Networks in MPICH2

International audienceThis paper describes how the NewMadeleine communication library has been integrated within the MPICH2 MPI implementation and the benefits brought. NewMadeleine is integrated as a Nemesis network module but the upper layers and in particular the CH3 layer has been modified. By doing so, we allow NewMadeleine to fully deliver its performance to an MPI application. NewMadeleine features sophisticated strategies for sending messages and natively supports multirail network configurations, even heterogeneous ones. It also uses a software element called PIOMan that uses multithreading in order to enhance reactivity and create more efficient progress engines. We show various results that prove that NewMadeleine is indeed well suited as a low-level communication library for building MPI implementations

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

An Efficient Network API for in-Kernel Applications in Clusters

International audienceRunning parallel applications on clusters with high-speed local networks requires fast communication between computing nodes but also low latency and high bandwidth file access. However, the application programming interfaces of high-speed local networks were designed for MPI communication and do not always meet the requirements of other applications like distributed file systems. In this paper, we explore several solutions to improve the use of high-speed network for in-kernel applications. Distributed file systems implemented on top of the GM interface of Myrinet are first examined to demonstrate how hard it is to get an efficient interaction between such applications and the network. Then, we propose solutions to simplify and improve this interaction and integrate them into the kernel interface of the new Myrinet. Performance comparisons between MX and GM, and their usage in both a distributed file system and a zero-copy protocol show nice improvements. Moreover, we are able to improve the performance of the flexible kernel API we designed in MX that allows to remove some intermediate copy

Comparison and tuning of MPI implementations in a grid context

Today, clusters are often interconnected by long distance networks within grids to offer a huge number of available ressources to a range of users. MPI, the standard communication library used to write parallel applications, has been implemented for clusters. Two main features of grids: long distance networks and technological heterogeneity, raise the question of MPI efficiency in grids. This report presents an evaluation of four recent MPI implementations (MPICH2, MPICH-Madeleine, OpenMPI and GridMPI) in the french research grid: Grid'5000. The comparison is based on the execution of pingpong, NAS Parallel Benchmarks and a real application in geophysics. We show that this implementations present performance differences. Executing MPI applications on the grid can be beneficial if the parameters are well tuned. The paper details the tuning required on each implementation to get the best performances

Efficient Interaction between High-Speed Networks and Distributed Storage in Clusters

Parallel applications running on clusters require both high-performance communications between nodes and efficient access to the storage system. We propose to improve the performance of distributed storage systems in clusters by efficiently using the underlying high-performance network to access distant storage systems. We show that storage requirements are very different from those of parallel computation and that a modification of the network programming interface is required. We detail several propositions for these interfaces which make their utilization easier in the context of distributed storage. Performance evaluations show that their integration makes it easy to use and very efficient in the context of storage