The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing

Simulations of Coherent Synchrotron Radiation on Parallel Hybrid GPU/CPU Platform

Coherent synchrotron radiation (CSR) is an effect of self-interaction of an electron bunch as it traverses a curved path. It can cause a significant emittance degradation, as well as fragmentation and microbunching. Numerical simulations of the 2D/3D CSR effects have been extremely challenging due to computational bottlenecks associated with calculating retarded potentials via integrating over the history of the bunch. We present a new high-performance 2D, particle-in-cell code which uses massively parallel multicore GPU/GPU platforms to alleviate computational bottlenecks. The code formulates the CSR problem from first principles by using the retarded scalar and vector potentials to compute the self-interaction fields. The speedup due to the parallel implementation on GPU/CPU platforms exceeds three orders of magnitude, thereby bringing a previously intractable problem within reach. The accuracy of the code is verified against analytic 1D solutions (rigid bunch) and semi-analytic 2D solutions for the chirped bunch. Finally, we use the new code in conjunction with a genetic algorithm to optimize the design of a fiducial chicane

Using message logs and resource use data for cluster failure diagnosis

Failure diagnosis for large compute clusters using only message logs is known to be incomplete. Recent availability of resource use data provides another potentially useful source of data for failure detection and diagnosis. Early work combining message logs and resource use data for failure diagnosis has shown promising results. This paper describes the CRUMEL framework which implements a new approach to combining rationalized message logs and resource use data for failure diagnosis. CRUMEL identifies patterns of errors and resource use and correlates these patterns by time with system failures. Application of CRUMEL to data from the Ranger supercomputer has yielded improved diagnoses over previous research. CRUMEL has: (i) showed that more events correlated with system failures can only be identified by applying different correlation algorithms, (ii) confirmed six groups of errors, (iii) identified Lustre I/O resource use counters which are correlated with occurrence of Lustre faults which are potential flags for online detection of failures, (iv) matched the dates of correlated error events and correlated resource use with the dates of compute node hangups and (v) identified two more error groups associated with compute node hang-ups. The pre-processed data will be put on the public domain in September, 2016

Performance Models for Data Transfers: A Case Study with Molecular Chemistry Kernels

With increasing complexity of hardwares, systems with different memory nodes are ubiquitous in High Performance Computing (HPC). It is paramount to develop strategies to overlap the data transfers between memory nodes with computations in order to exploit the full potential of these systems. In this article, we consider the problem of deciding the order of data transfers between two memory nodes for a set of independent tasks with the objective to minimize the makespan. We prove that with limited memory capacity, obtaining the optimal order of data transfers is a NP-complete problem. We propose several heuristics for this problem and provide details about their favorable situations. We present an analysis of our heuristics on traces, obtained by running 2 molecular chemistry kernels, namely, Hartree-Fock (HF) and Coupled Cluster Single Double (CCSD) on 10 nodes of an HPC system. Our results show that some of our heuristics achieve significant overlap for moderate memory capacities and are very close to the lower bound of makespan

An Unstructured CFD Mini-Application for the Performance Prediction of a Production CFD Code

Maintaining the performance of large scientific codes is a difficult task. To aid in this task, a number of mini-applications have been developed that are more tractable to analyze than large-scale production codes while retaining the performance characteristics of them. These “mini-apps” also enable faster hardware evaluation and, for sensitive commercial codes, allow evaluation of code and system changes outside of access approval processes. In this paper, we develop MG-CFD, a mini-application that represents a geometric multigrid, unstructured computational fluid dynamics (CFD) code, designed to exhibit similar performance characteristics without sharing commercially sensitive code. We detail our experiences of developing this application using guidelines detailed in existing research and contributing further to these. Our application is validated against the inviscid flux routine of HYDRA, a CFD code developed by Rolls-Royce plc for turbomachinery design. This paper (1) documents the development of MG-CFD, (2) introduces an associated performance model with which it is possible to assess the performance of HYDRA on new HPC architectures, and (3) demonstrates that it is possible to use MG-CFD and the performance models to predict the performance of HYDRA with a mean error of 9.2% for strong-scaling studies

Recent Advances in Fully Dynamic Graph Algorithms

In recent years, significant advances have been made in the design and analysis of fully dynamic algorithms. However, these theoretical results have received very little attention from the practical perspective. Few of the algorithms are implemented and tested on real datasets, and their practical potential is far from understood. Here, we present a quick reference guide to recent engineering and theory results in the area of fully dynamic graph algorithms

The Hardness of Optimization Problems on the Weighted Massively Parallel Computation Model

The topology-aware Massively Parallel Computation (MPC) model is proposed and studied recently, which enhances the classical MPC model by the awareness of network topology. The work of Hu et al. on topology-aware MPC model considers only the tree topology. In this paper a more general case is considered, where the underlying network is a weighted complete graph. We then call this model as Weighted Massively Parallel Computation (WMPC) model, and study the problem of minimizing communication cost under it. Two communication cost minimization problems are defined based on different pattern of communication, which are the Data Redistribution Problem and Data Allocation Problem. We also define four kinds of objective functions for communication cost, which consider the total cost, bottleneck cost, maximum of send and receive cost, and summation of send and receive cost, respectively. Combining the two problems in different communication pattern with the four kinds of objective cost functions, 8 problems are obtained. The hardness results of the 8 problems make up the content of this paper. With rigorous proof, we prove that some of the 8 problems are in P, some FPT, some NP-complete, and some W[1]-complete

TweTriS: Twenty trillion-atom simulation

Significant improvements are presented for the molecular dynamics code ls1 mardyn — a linked cell-based code for simulating a large number of small, rigid molecules with application areas in chemical engineering. The changes consist of a redesign of the SIMD vectorization via wrappers, MPI improvements and a software redesign to allow memory-efficient execution with the production trunk to increase portability and extensibility. Two novel, memory-efficient OpenMP schemes for the linked cell-based force calculation are presented, which are able to retain Newton’s third law optimization. Comparisons to well-optimized Verlet list-based codes, such as LAMMPS and GROMACS, demonstrate the viability of the linked cell-based approach. The present version of ls1 mardyn is used to run simulations on entire supercomputers, maximizing the number of sampled atoms. Compared to the preceding version of ls1 mardyn on the entire set of 9216 nodes of SuperMUC, Phase 1, 27% more atoms are simulated. Weak scaling performance is increased by up to 40% and strong scaling performance by up to more than 220%. On Hazel Hen, strong scaling efficiency of up to 81% and 189 billion molecule updates per second is attained, when scaling from 8 to 7168 nodes. Moreover, a total of 20 trillion atoms is simulated at up to 88% weak scaling efficiency running at up to 1.33 PFLOPS. This represents a fivefold increase in terms of the number of atoms simulated to date.BMBF, 01IH16008, Verbundprojekt: TaLPas - Task-basierte Lastverteilung und Auto-Tuning in der Partikelsimulatio

Parallel Working-Set Search Structures

In this paper we present two versions of a parallel working-set map on p processors that supports searches, insertions and deletions. In both versions, the total work of all operations when the map has size at least p is bounded by the working-set bound, i.e., the cost of an item depends on how recently it was accessed (for some linearization): accessing an item in the map with recency r takes O(1+log r) work. In the simpler version each map operation has O((log p)^2+log n) span (where n is the maximum size of the map). In the pipelined version each map operation on an item with recency r has O((log p)^2+log r) span. (Operations in parallel may have overlapping span; span is additive only for operations in sequence.) Both data structures are designed to be used by a dynamic multithreading parallel program that at each step executes a unit-time instruction or makes a data structure call. To achieve the stated bounds, the pipelined data structure requires a weak-priority scheduler, which supports a limited form of 2-level prioritization. At the end we explain how the results translate to practical implementations using work-stealing schedulers. To the best of our knowledge, this is the first parallel implementation of a self-adjusting search structure where the cost of an operation adapts to the access sequence. A corollary of the working-set bound is that it achieves work static optimality: the total work is bounded by the access costs in an optimal static search tree.Comment: Authors' version of a paper accepted to SPAA 201