Fault tolerance for the upcoming exascale generation has long been an area of active research. One of the components of a fault tolerance strategy is checkpointing. Petascale-level checkpointing is demonstrated through a new mechanism for virtualization of the InfiniBand UD (unreliable datagram) mode, and for updating the remote address on each UD-based send, due to lack of a fixed peer. Note that InfiniBand UD is required to support modern MPI implementations. An extrapolation from the current results to future SSD-based storage systems provides evidence that the current approach will remain practical in the exascale generation. This transparent checkpointing approach is evaluated using a framework of the DMTCP checkpointing package. Results are shown for HPCG (linear algebra), NAMD (molecular dynamics), and the NAS NPB benchmarks. In tests up to 32,752 MPI processes on 32,752 CPU cores, checkpointing of a computation with a 38 TB memory footprint in 11 minutes is demonstrated. Runtime overhead is reduced to less than 1%. The approach is also evaluated across three widely used MPI implementations.

A majority of parallel applications executed on HPC clusters use MPI for communication between processes. Most users treat MPI as a black box, executing their programs using the cluster's default settings. While the default settings perform adequately for many cases, it is well known that optimizing the MPI environment can significantly improve application performance. Although the existing optimization tools are effective when used by performance experts, they require deep knowledge of MPI library behavior and the underlying hardware architecture in which the application will be executed. Therefore, an easy-to-use tool that provides recommendations for configuring the MPI environment to optimize application performance is highly desirable. This paper addresses this need by presenting an easy-to-use methodology and tool, named MPI Advisor, that requires just a single execution of the input application to characterize its predominant communication behavior and determine the MPI configuration that may enhance its performance on the target combination of MPI library and hardware architecture. Currently, MPI Advisor provides recommendations that address the four most commonly occurring MPI-related performance bottlenecks, which are related to the choice of: 1) point-to-point protocol (eager vs. rendezvous), 2) collective communication algorithm, 3) MPI tasks-to-cores mapping, and 4) Infiniband transport protocol. The performance gains obtained by implementing the recommended optimizations in the case studies presented in this paper range from a few percent to more than 40%. Specifically, using this tool, we were able to improve the performance of HPCG with MVAPICH2 on four nodes of the Stampede cluster from 6.9 GFLOP/s to 10.1 GFLOP/s. Since the tool provides application-specific recommendations, it also informs the user about correct usage of MPI.

NAS parallel benchmarks (NPB) are a set of applications commonly used to evaluate parallel systems. We use the NPB-OpenMP version to examine the performance of the Intel's new Xeon Phi co-processor and focus in particular on the many core aspect of the Xeon Phi architecture. A first analysis studies the scalability up to 244 threads on 61 cores and the impact of affinity settings on scaling. It also compares performance characteristics of Xeon Phi and traditional Xeon CPUs. The application of several well-established optimization techniques allows us to identify common bottlenecks that can specifically impede performance on the Xeon Phi but are not as severe on multi-core CPUs. We also find that many of the OpenMP-parallel loops are too short (in terms of the number of loop iterations) for a balanced execution by 244 threads. New or redesigned benchmarks will be needed to accommodate the greatly increased number of cores and threads. At the end, we summarize our findings in a set recommendations for performance optimization for Xeon Phi.

Scientists across a wide range of domains increasingly rely on computer simulation for their investigations. Such simulations often spend a majority of their run-times solving large systems of linear equations that require vast amounts of computational power and memory. It is hence critical to design solvers in a highly efficient and scalable manner. Hypre is a high performance, scalable software library that offers several optimized linear solver routines and pre-conditioners. In this paper, we study the characteristics of Hypre's Preconditioned Conjugate Gradient (PCG) solver algorithm. The PCG routine is known to spend a majority of its communication time in the MPI All reduce operation to compute a global summation during the inner product operation. The MPI All reduce is a blocking operation, whose latency is often a limiting factor to the overall efficiency of the PCG solver routine, and correspondingly the performance of simulations that rely on this solver. Hence, hiding the latency of the MPI All reduce operation is critical towards scaling the PCG solver routine and improving the performance of many simulations. The upcoming revision of MPI, MPI-3, will provide support for non-blocking collective communication to enable latency-hiding. The latest Infini Band adapter from Mellanox, ConnectX-2, enables offloading of generalized lists of communication operations to the network interface. Such an interface can be leveraged to design non-blocking collective operations. In this paper, we design fully functional, scalable algorithms for the MPI Iall reduce operation, based on the network offload technology. To the best of our knowledge, these network offload-based algorithms are the first to be presented for the MPI Iall reduce operation. Our designs scale beyond 512 processes and we achieve near perfect communication/computation overlap. We also re-design the PCG solver routine to leverage our proposed MPI Iall reduce operation to hide the latency of the global reduction operations. We observe up to 21% improvements in the run-times of the PCG routine, when compared to the default PCG implementation in Hypre. We also note that about 16% of the overall benefits are due to overlapping the All reduce operations.

Over the last decade, InfiniBand has become an increasingly popular interconnect for deploying modern supercomputing systems. However, there exists no detection service that can discover the underlying network topology in a scalable manner and expose this information to runtime libraries and users of the high performance computing systems in a convenient way. In this paper, we design a novel and scalable method to detect the InfiniBand network topology by using Neighbor-Joining techniques (NJ). To the best of our knowledge, this is the first instance where the neighbor joining algorithm has been applied to solve the problem of detecting InfiniBand network topology. We also design a network-topology-aware MPI library that takes advantage of the network topology service. The library places processes taking part in the MPI job in a network-topology-aware manner with the dual aim of increasing intra-node communication and reducing the long distance inter-node communication across the InfiniBand fabric.

It is an established fact that the network topology can have an impact on the performance of scientific parallel applications. However, little work has been done to design an easy to use solution inside a communication library supporting a parallel programming model where the complexities of making the application performance network topology agnostic is hidden from the end user. Similarly, the rapid improvements in networking technology and speed are resulting in many commodity clusters becoming heterogeneous, with respect to networking speed. For example, switches and adapters belonging to different generations (SDR - 8 Gbps, DDR - 16 Gbps and QDR - 36 Gbps speeds in InfiniBand) are integrated into a single system. This leads to an additional challenge to make the communication library aware of the performance implications of heterogeneous link speeds. Accordingly, the communication library can perform optimizations taking link speed into account. In this paper, we propose a framework to automatically detect the topology and speed of an InfiniBand network and make it available to users through an easy to use interface. We also make design changes inside the MPI library to dynamically query this topology detection service and to form a topology model of the underlying network. We have redesigned the broadcast algorithm to take into account this network topology information and dynamically adapt the communication pattern to best fit the characteristics of the underlying network. To the best of our knowledge, this is the first such work for InfiniBand clusters. Our experimental results show that, for large homogeneous systems and large message sizes, we get up to 14% improvement in the latency of the broadcast operation using our proposed network topology-aware scheme over the default scheme at the micro-benchmark level. At the application level, the proposed framework delivers up to 8% improvement in total application run-time especially as job size scales up. The proposed network speed-aware algorithms are able to attain micro-benchmark performance on the heterogeneous SDR-DDR InfiniBand cluster to perform on par with runs on the DDR only portion of the cluster for small to medium sized messages. We also demonstrate that the network speed aware algorithms perform 70% to 100% better than the naive algorithms when both are run on the heterogeneous SDR-DDR InfiniBand cluster.

Using MPI as communication interface, one or several applications may introduce complex communication behaviors over the network cluster. This effect is increased when nodes of the cluster are multi-processors, and where communications can income or outgo from the same node with a common interval time. Our goal is to understand those behaviors to build a class of predictive models of bandwidth sharing, knowing, on the one hand the flow control mechanisms and, on the other hand, a set of experimental results. This paper present experiences that show how is shared the bandwidth on gigabit Ethernet, Myrinet 2000 and Infiniband network before to introduce the models for Gigabit Ethernet and Myrinet 2000 networks.