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Computational Strategies for Scalable Genomics Analysis.
The revolution in next-generation DNA sequencing technologies is leading to explosive data growth in genomics, posing a significant challenge to the computing infrastructure and software algorithms for genomics analysis. Various big data technologies have been explored to scale up/out current bioinformatics solutions to mine the big genomics data. In this review, we survey some of these exciting developments in the applications of parallel distributed computing and special hardware to genomics. We comment on the pros and cons of each strategy in the context of ease of development, robustness, scalability, and efficiency. Although this review is written for an audience from the genomics and bioinformatics fields, it may also be informative for the audience of computer science with interests in genomics applications
Optimizing the MapReduce Framework on Intel Xeon Phi Coprocessor
With the ease-of-programming, flexibility and yet efficiency, MapReduce has
become one of the most popular frameworks for building big-data applications.
MapReduce was originally designed for distributed-computing, and has been
extended to various architectures, e,g, multi-core CPUs, GPUs and FPGAs. In
this work, we focus on optimizing the MapReduce framework on Xeon Phi, which is
the latest product released by Intel based on the Many Integrated Core
Architecture. To the best of our knowledge, this is the first work to optimize
the MapReduce framework on the Xeon Phi.
In our work, we utilize advanced features of the Xeon Phi to achieve high
performance. In order to take advantage of the SIMD vector processing units, we
propose a vectorization friendly technique for the map phase to assist the
auto-vectorization as well as develop SIMD hash computation algorithms.
Furthermore, we utilize MIMD hyper-threading to pipeline the map and reduce to
improve the resource utilization. We also eliminate multiple local arrays but
use low cost atomic operations on the global array for some applications, which
can improve the thread scalability and data locality due to the coherent L2
caches. Finally, for a given application, our framework can either
automatically detect suitable techniques to apply or provide guideline for
users at compilation time. We conduct comprehensive experiments to benchmark
the Xeon Phi and compare our optimized MapReduce framework with a
state-of-the-art multi-core based MapReduce framework (Phoenix++). By
evaluating six real-world applications, the experimental results show that our
optimized framework is 1.2X to 38X faster than Phoenix++ for various
applications on the Xeon Phi
Towards co-designed optimizations in parallel frameworks: A MapReduce case study
The explosion of Big Data was followed by the proliferation of numerous
complex parallel software stacks whose aim is to tackle the challenges of data
deluge. A drawback of a such multi-layered hierarchical deployment is the
inability to maintain and delegate vital semantic information between layers in
the stack. Software abstractions increase the semantic distance between an
application and its generated code. However, parallel software frameworks
contain inherent semantic information that general purpose compilers are not
designed to exploit.
This paper presents a case study demonstrating how the specific semantic
information of the MapReduce paradigm can be exploited on multicore
architectures. MR4J has been implemented in Java and evaluated against
hand-optimized C and C++ equivalents. The initial observed results led to the
design of a semantically aware optimizer that runs automatically without
requiring modification to application code.
The optimizer is able to speedup the execution time of MR4J by up to 2.0x.
The introduced optimization not only improves the performance of the generated
code, during the map phase, but also reduces the pressure on the garbage
collector. This demonstrates how semantic information can be harnessed without
sacrificing sound software engineering practices when using parallel software
frameworks.Comment: 8 page
Parallel Discrete Event Simulation with Erlang
Discrete Event Simulation (DES) is a widely used technique in which the state
of the simulator is updated by events happening at discrete points in time
(hence the name). DES is used to model and analyze many kinds of systems,
including computer architectures, communication networks, street traffic, and
others. Parallel and Distributed Simulation (PADS) aims at improving the
efficiency of DES by partitioning the simulation model across multiple
processing elements, in order to enabling larger and/or more detailed studies
to be carried out. The interest on PADS is increasing since the widespread
availability of multicore processors and affordable high performance computing
clusters. However, designing parallel simulation models requires considerable
expertise, the result being that PADS techniques are not as widespread as they
could be. In this paper we describe ErlangTW, a parallel simulation middleware
based on the Time Warp synchronization protocol. ErlangTW is entirely written
in Erlang, a concurrent, functional programming language specifically targeted
at building distributed systems. We argue that writing parallel simulation
models in Erlang is considerably easier than using conventional programming
languages. Moreover, ErlangTW allows simulation models to be executed either on
single-core, multicore and distributed computing architectures. We describe the
design and prototype implementation of ErlangTW, and report some preliminary
performance results on multicore and distributed architectures using the well
known PHOLD benchmark.Comment: Proceedings of ACM SIGPLAN Workshop on Functional High-Performance
Computing (FHPC 2012) in conjunction with ICFP 2012. ISBN: 978-1-4503-1577-
Parallel Sort-Based Matching for Data Distribution Management on Shared-Memory Multiprocessors
In this paper we consider the problem of identifying intersections between
two sets of d-dimensional axis-parallel rectangles. This is a common problem
that arises in many agent-based simulation studies, and is of central
importance in the context of High Level Architecture (HLA), where it is at the
core of the Data Distribution Management (DDM) service. Several realizations of
the DDM service have been proposed; however, many of them are either
inefficient or inherently sequential. These are serious limitations since
multicore processors are now ubiquitous, and DDM algorithms -- being
CPU-intensive -- could benefit from additional computing power. We propose a
parallel version of the Sort-Based Matching algorithm for shared-memory
multiprocessors. Sort-Based Matching is one of the most efficient serial
algorithms for the DDM problem, but is quite difficult to parallelize due to
data dependencies. We describe the algorithm and compute its asymptotic running
time; we complete the analysis by assessing its performance and scalability
through extensive experiments on two commodity multicore systems based on a
dual socket Intel Xeon processor, and a single socket Intel Core i7 processor.Comment: Proceedings of the 21-th ACM/IEEE International Symposium on
Distributed Simulation and Real Time Applications (DS-RT 2017). Best Paper
Award @DS-RT 201
High-level programming of stencil computations on multi-GPU systems using the SkelCL library
The implementation of stencil computations on modern, massively parallel systems with GPUs and other accelerators currently relies on manually-tuned coding using low-level approaches like OpenCL and CUDA. This makes development of stencil applications a complex, time-consuming, and error-prone task. We describe how stencil computations can be programmed in our SkelCL approach that combines high-level programming abstractions with competitive performance on multi-GPU systems. SkelCL extends the OpenCL standard by three high-level features: 1) pre-implemented parallel patterns (a.k.a. skeletons); 2) container data types for vectors and matrices; 3) automatic data (re)distribution mechanism. We introduce two new SkelCL skeletons which specifically target stencil computations – MapOverlap and Stencil – and we describe their use for particular application examples, discuss their efficient parallel implementation, and report experimental results on systems with multiple GPUs. Our evaluation of three real-world applications shows that stencil code written with SkelCL is considerably shorter and offers competitive performance to hand-tuned OpenCL code
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