12,466 research outputs found
Toward More Scalable Off-Line Simulations of MPI Applications
International audienceThe off-line (or post-mortem) analysis of execution event traces is a popular approach to understand the performance of HPC applications that use the message passing paradigm. Combining this analysis with simulation makes it possible to " replay " the application execution to explore " what if? " scenarios, e.g., assessing application performance in a range of (hypothetical) execution environments. However, such off-line analysis faces scalability issues for acquiring, storing, or replaying large event traces. We first present two previously proposed and complementary frameworks for off-line replaying of MPI application event traces, each with its own objectives and limitations. We then describe how these frameworks can be combined so as to capitalize on their respective strengths while alleviating several of their limitations. We claim that the combined framework affords levels of scalability that are beyond that achievable by either one of the two individual frameworks. We evaluate this framework to illustrate the benefits of the proposed combination for a more scalable off-line analysis of MPI applications
ScALPEL: A Scalable Adaptive Lightweight Performance Evaluation Library for application performance monitoring
As supercomputers continue to grow in scale and capabilities, it is becoming
increasingly difficult to isolate processor and system level causes of
performance degradation. Over the last several years, a significant number of
performance analysis and monitoring tools have been built/proposed. However,
these tools suffer from several important shortcomings, particularly in
distributed environments. In this paper we present ScALPEL, a Scalable Adaptive
Lightweight Performance Evaluation Library for application performance
monitoring at the functional level. Our approach provides several distinct
advantages. First, ScALPEL is portable across a wide variety of architectures,
and its ability to selectively monitor functions presents low run-time
overhead, enabling its use for large-scale production applications. Second, it
is run-time configurable, enabling both dynamic selection of functions to
profile as well as events of interest on a per function basis. Third, our
approach is transparent in that it requires no source code modifications.
Finally, ScALPEL is implemented as a pluggable unit by reusing existing
performance monitoring frameworks such as Perfmon and PAPI and extending them
to support both sequential and MPI applications.Comment: 10 pages, 4 figures, 2 table
rDLB: A Novel Approach for Robust Dynamic Load Balancing of Scientific Applications with Parallel Independent Tasks
Scientific applications often contain large and computationally intensive
parallel loops. Dynamic loop self scheduling (DLS) is used to achieve a
balanced load execution of such applications on high performance computing
(HPC) systems. Large HPC systems are vulnerable to processors or node failures
and perturbations in the availability of resources. Most self-scheduling
approaches do not consider fault-tolerant scheduling or depend on failure or
perturbation detection and react by rescheduling failed tasks. In this work, a
robust dynamic load balancing (rDLB) approach is proposed for the robust self
scheduling of independent tasks. The proposed approach is proactive and does
not depend on failure or perturbation detection. The theoretical analysis of
the proposed approach shows that it is linearly scalable and its cost decrease
quadratically by increasing the system size. rDLB is integrated into an MPI DLS
library to evaluate its performance experimentally with two computationally
intensive scientific applications. Results show that rDLB enables the tolerance
of up to (P minus one) processor failures, where P is the number of processors
executing an application. In the presence of perturbations, rDLB boosted the
robustness of DLS techniques up to 30 times and decreased application execution
time up to 7 times compared to their counterparts without rDLB
Performance Evaluation of High Performance Parallel I/O
Performance of the I/O subsystem plays a significant role in parallel applications that need to access large amounts of data. I/O performance in such applications is expected to be scalable and balanced with respect to the communication and CPU performance. MPIIO, a part of the MPI-2 standard has many implementations. Each of the available clientside parallel architectures differ widely in their approach to achieving high performance. This thesis hypothesizes that the effectiveness of each available client-side parallel architecture differs in delivering overall parallel application performance for a given underlying file system and that increasing the performance for different workload characteristics requires different designs. This hypothesis is validated by the development of appropriate metrics and the analysis of the results, obtained from running the experiments
Accelerating Large-Scale Data Analysis by Offloading to High-Performance Computing Libraries using Alchemist
Apache Spark is a popular system aimed at the analysis of large data sets,
but recent studies have shown that certain computations---in particular, many
linear algebra computations that are the basis for solving common machine
learning problems---are significantly slower in Spark than when done using
libraries written in a high-performance computing framework such as the
Message-Passing Interface (MPI).
To remedy this, we introduce Alchemist, a system designed to call MPI-based
libraries from Apache Spark. Using Alchemist with Spark helps accelerate linear
algebra, machine learning, and related computations, while still retaining the
benefits of working within the Spark environment. We discuss the motivation
behind the development of Alchemist, and we provide a brief overview of its
design and implementation.
We also compare the performances of pure Spark implementations with those of
Spark implementations that leverage MPI-based codes via Alchemist. To do so, we
use data science case studies: a large-scale application of the conjugate
gradient method to solve very large linear systems arising in a speech
classification problem, where we see an improvement of an order of magnitude;
and the truncated singular value decomposition (SVD) of a 400GB
three-dimensional ocean temperature data set, where we see a speedup of up to
7.9x. We also illustrate that the truncated SVD computation is easily scalable
to terabyte-sized data by applying it to data sets of sizes up to 17.6TB.Comment: Accepted for publication in Proceedings of the 24th ACM SIGKDD
International Conference on Knowledge Discovery and Data Mining, London, UK,
201
Building Near-Real-Time Processing Pipelines with the Spark-MPI Platform
Advances in detectors and computational technologies provide new
opportunities for applied research and the fundamental sciences. Concurrently,
dramatic increases in the three Vs (Volume, Velocity, and Variety) of
experimental data and the scale of computational tasks produced the demand for
new real-time processing systems at experimental facilities. Recently, this
demand was addressed by the Spark-MPI approach connecting the Spark
data-intensive platform with the MPI high-performance framework. In contrast
with existing data management and analytics systems, Spark introduced a new
middleware based on resilient distributed datasets (RDDs), which decoupled
various data sources from high-level processing algorithms. The RDD middleware
significantly advanced the scope of data-intensive applications, spreading from
SQL queries to machine learning to graph processing. Spark-MPI further extended
the Spark ecosystem with the MPI applications using the Process Management
Interface. The paper explores this integrated platform within the context of
online ptychographic and tomographic reconstruction pipelines.Comment: New York Scientific Data Summit, August 6-9, 201
Algorithmic Based Fault Tolerance Applied to High Performance Computing
We present a new approach to fault tolerance for High Performance Computing
system. Our approach is based on a careful adaptation of the Algorithmic Based
Fault Tolerance technique (Huang and Abraham, 1984) to the need of parallel
distributed computation. We obtain a strongly scalable mechanism for fault
tolerance. We can also detect and correct errors (bit-flip) on the fly of a
computation. To assess the viability of our approach, we have developed a fault
tolerant matrix-matrix multiplication subroutine and we propose some models to
predict its running time. Our parallel fault-tolerant matrix-matrix
multiplication scores 1.4 TFLOPS on 484 processors (cluster jacquard.nersc.gov)
and returns a correct result while one process failure has happened. This
represents 65% of the machine peak efficiency and less than 12% overhead with
respect to the fastest failure-free implementation. We predict (and have
observed) that, as we increase the processor count, the overhead of the fault
tolerance drops significantly
On the conditions for efficient interoperability with threads: An experience with PGAS languages using Cray communication domains
Today's high performance systems are typically built from shared memory nodes connected by a high speed network. That architecture, combined with the trend towards less memory per core, encourages programmers to use a mixture of message passing and multithreaded programming. Unfortunately, the advantages of using threads for in-node programming are hindered by their inability to efficiently communicate between nodes. In this work, we identify some of the performance problems that arise in such hybrid programming environments and characterize conditions needed to achieve high communication performance for multiple threads: addressability of targets, separability of communication paths, and full direct reachability to targets. Using the GASNet communication layer on the Cray XC30 as our experimental platform, we show how to satisfy these conditions. We also discuss how satisfying these conditions is influenced by the communication abstraction, implementation constraints, and the interconnect messaging capabilities. To evaluate these ideas, we compare the communication performance of a thread-based node runtime to a process-based runtime. Without our GASNet extensions, thread communication is significantly slower than processes - up to 21x slower. Once the implementation is modified to address each of our conditions, the two runtimes have comparable communication performance. This allows programmers to more easily mix models like OpenMP, CILK, or pthreads with a GASNet-based model like UPC, with the associated performance, convenience and interoperability advantages that come from using threads within a node. © 2014 ACM
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