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Graph analytics are arguably one of the most demanding workloads for high-performance systems and interconnection networks. Graph applications often display all-to-all, fine-grained, high-rate communication patterns that expose the limits of the network protocol stacks. Load and communication imbalance generate hard-to-predict network hot-spots, and may require computational steering due to unpredictable...
Suffix arrays and trees are fundamental string data structures of importance to many applications in computational biology. Consequently, their parallel construction is an actively studied problem. To date, algorithms with best practical performance lack efficient worst-case run-time guarantees, and vice versa. In addition, much of the recent work targeted low core count, shared memory parallelization...
The job management system is the HPC middleware responsible for distributing computing power to applications. While such systems generate an ever increasing amount of data, they are characterized by uncertainties on some parameters like the job running times. The question raised in this work is: To what extent is it possible/useful to take into account predictions on the job running times for improving the global scheduling?...
Large-scale simulations can produce hundreds of terabytes to petabytes of data, complicating and limiting the efficiency of workflows. Traditionally, outputs are stored on the file system and analyzed in post-processing. With the rapidly increasing size and complexity of simulations, this approach faces an uncertain future. Trending techniques consist of performing the analysis in-situ, utilizing...
The potential impact of blood flow simulations on the diagnosis and treatment of patients suffering from vascular disease is tremendous. Empowering models of the full arterial tree can provide insight into diseases such as arterial hypertension and enables the study of the influence of local factors on global hemodynamics. We present a new, highly scalable implementation of the lattice Boltzmann method...
Engineered proteins are synthetic novel proteins (not found in nature) that are designed to fulfill a predetermined biological function. Such proteins can be used as molecular markers, inhibitory agents, or drugs. For example, a synthetic protein could bind to a critical protein of a pathogen, thereby inhibiting the function of the target protein and potentially reducing the impact of the pathogen...
In this paper, we propose C2-Bound, a data-driven analytical model, that incorporates both memory capacity and data access concurrency factors to optimize many-core design. C2-Bound is characterized by combining the newly proposed latency model, concurrent average memory access time (C-AMAT), with the well-known memory-bounded speedup model (Sun-Ni's law) to facilitate computing tasks. Compared to...
In this paper, we describe our experiences and lessons learned from building a general-purpose in-memory key-value middleware, called HydraDB. HydraDB synthesizes a collection of state-of-the-art techniques, including continuous fault-tolerance, Remote Direct Memory Access (RDMA), as well as awareness for multicore systems, etc, to deliver a high-throughput, low-latency access service in a reliable...
HPC network topology design is currently shifting from high-performance, higher-cost Fat-Trees to more cost-effective architectures. Three diameter-two designs, the Slim Fly, Multi-Layer Full-Mesh, and Two-Level Orthogonal Fat-Tree excel in this, exhibiting a cost per endpoint of only 2 links and 3 router ports with lower end-to-end latency and higher scalability than traditional networks of the same...
Overprovisioning hardware devices and coordinating their power budgets are proposed to improve the application performance of future power-constrained HPC systems. This coordination process is called power shifting. Meanwhile, recent studies have revealed that on/off links can save network power in HPC systems. Future HPC systems will thus adopt on/off links in addition to power shifting. This paper...
We investigate an efficient parallelization of the most common iterative sparse tensor decomposition algorithms on distributed memory systems. A key operation in each iteration of these algorithms is the matricized tensor times Khatri-Rao product (MTTKRP). This operation amounts to element-wise vector multiplication and reduction depending on the sparsity of the tensor. We investigate a fine and a...
Dramatic advances in DNA sequencing technology have made it possible to study microbial environments by direct sequencing of environmental DNA samples. Yet, due to the huge volume and high data complexity, current de novo assemblers cannot handle large metagenomic datasets or fail to perform assembly with acceptable quality. This paper presents the first parallel solution for decomposing the metagenomic...
Today's leadership computing facilities have enabled the execution of transformative simulations at unprecedented scales. However, analyzing the huge amount of output from these simulations remains a challenge. Most analyses of this output is performed in post-processing mode at the end of the simulation. The time to read the output for the analysis can be significantly high due to poor I/O bandwidth,...
A low-rank approximation of a dense matrix plays an important role in many applications. To compute such an approximation, a common approach uses the QR factorization with column pivoting (QRCP). Though the reliability and efficiency of QRCP have been demonstrated, this deterministic approach requires costly communication at each step of the factorization. Since such communication is becoming increasingly...
We consider techniques to improve the performance of parallel sparse triangular solution on non-uniform memory architecture multicores by extending earlier coloring and level set schemes for single-core multiprocessors. We develop STS-k, where k represents a small number of transformations for latency reduction from increased spatial and temporal locality of data accesses. We propose a graph model...
Particle tracking along streamlines and pathlines is a common scientific analysis technique, which has demanding data, computation and communication requirements. It has been studied in the context of high-performance computing due to the difficulty in its efficient parallelization and its high demands on communication and computational load. In this paper, we study efficient evaluation methods for...
The last decade has seen power consumption move from an afterthought to the foremost design constraint of new supercomputers. Measuring the power of a supercomputer can be a daunting proposition, and as a result, many published measurements are extrapolated. This paper explores the validity of these extrapolations in the context of inter-node power variability and power variations over time within...
Current trends for high-performance systems are leading towards hardware overprovisioning where it is no longer possible to run all components at peak power without exceeding a system- or facility-wide power bound. The standard practice of static power scheduling is likely to lead to inefficiencies with over- and under-provisioning of power to components at runtime. In this paper we investigate the...
De novo whole genome assembly reconstructs genomic sequences from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMer, the first high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code. First, we significantly improve scalability...
The amount of data moved over the Internet per year has already exceeded the Exabyte scale and soon will hit the Zettabyte range. To support this massive amount of data movement across the globe, the networking infrastructure as well as the source and destination nodes consume immense amount of electric power, with an estimated cost measured in billions of dollars. Although considerable amount of...
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