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At least 127 records · Page 7

Small file aggregation in a parallel computing system

Techniques are provided for small file aggregation in a parallel computing system. An exemplary method for storing a plurality of files generated by a plurality of processes in a parallel computing system comprises aggregating the plurality of files into a single aggregated file; and generating metadata for the single aggregated file. The metadata comprises an offset and a length of each of the plurality of files in the single aggregated file. The metadata can be used to unpack one or more of the files from the single aggregated file.

97 MATHEMATICS AND COMPUTING↗

Storing files in a parallel computing system based on user-specified parser function

Techniques are provided for storing files in a parallel computing system based on a user-specified parser function. A plurality of files generated by a distributed application in a parallel computing system are stored by obtaining a parser from the distributed application for processing the plurality of files prior to storage; and storing one or more of the plurality of files in one or more storage nodes of the parallel computing system based on the processing by the parser. The plurality of files comprise one or more of a plurality of complete files and a plurality of sub-files. The parser can optionally store only those files that satisfy one or more semantic requirements of the parser. The parser can also extract metadata from one or more of the files and the extracted metadata can be stored with one or more of the plurality of files and used for searching for files.

97 MATHEMATICS AND COMPUTING↗

Optimizing Input/Output Using Adaptive File System Policies

Parallel input/output characterization studies and experiments with flexible resource management algorithms indicate that adaptivity is crucial to file system performance. In this paper we propose an automatic technique for selecting and refining file system policies based on application access patterns and execution environment. An automatic classification framework allows the file system to select appropriate caching and pre-fetching policies, while performance sensors provide feedback used to tune policy parameters for specific system environments. To illustrate the potential performance improvements possible using adaptive file system policies, we present results from experiments involving classification-based and performance-based steering.

Madhyastha, Tara M.↗

Storing files in a parallel computing system based on user or application specification

Techniques are provided for storing files in a parallel computing system based on a user-specification. A plurality of files generated by a distributed application in a parallel computing system are stored by obtaining a specification from the distributed application indicating how the plurality of files should be stored; and storing one or more of the plurality of files in one or more storage nodes of a multi-tier storage system based on the specification. The plurality of files comprise a plurality of complete files and/or a plurality of sub-files. The specification can optionally be processed by a daemon executing on one or more nodes in a multi-tier storage system. The specification indicates how the plurality of files should be stored, for example, identifying one or more storage nodes where the plurality of files should be stored.

97 MATHEMATICS AND COMPUTING↗

Pattern-aware prefetching using parallel log-structured file system

Techniques are provided for pattern-aware prefetching using a parallel log-structured file system. At least a portion of one or more files is accessed by detecting at least one pattern in a non-sequential access of the one or more files; and obtaining at least a portion of the one or more files based on the detected at least one pattern. The obtaining step comprises, for example, a prefetching or pre-allocation of the at least the portion of the one or more files. A prefetch cache can store the portion of the one or more obtained files. The cached portion of the one or more files can be provided from the prefetch cache to an application requesting the at least a portion of the one or more files.

Bent, John M.↗

Request queues for interactive clients in a shared file system of a parallel computing system

Interactive requests are processed from users of log-in nodes. A metadata server node is provided for use in a file system shared by one or more interactive nodes and one or more batch nodes. The interactive nodes comprise interactive clients to execute interactive tasks and the batch nodes execute batch jobs for one or more batch clients. The metadata server node comprises a virtual machine monitor; an interactive client proxy to store metadata requests from the interactive clients in an interactive client queue; a batch client proxy to store metadata requests from the batch clients in a batch client queue; and a metadata server to store the metadata requests from the interactive client queue and the batch client queue in a metadata queue based on an allocation of resources by the virtual machine monitor. The metadata requests can be prioritized, for example, based on one or more of a predefined policy and predefined rules.

97 MATHEMATICS AND COMPUTING↗

Parallel log structured file system collective buffering to achieve a compact representation of scientific and/or dimensional data

Collective buffering and data pattern solutions are provided for storage, retrieval, and/or analysis of data in a collective parallel processing environment. For example, a method can be provided for data storage in a collective parallel processing environment. The method comprises receiving data to be written for a plurality of collective processes within a collective parallel processing environment, extracting a data pattern for the data to be written for the plurality of collective processes, generating a representation describing the data pattern, and saving the data and the representation.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Cloud object store for checkpoints of high performance computing applications using decoupling middleware

Cloud object storage is enabled for checkpoints of high performance computing applications using a middleware process. A plurality of files, such as checkpoint files, generated by a plurality of processes in a parallel computing system are stored by obtaining said plurality of files from said parallel computing system; converting said plurality of files to objects using a log structured file system middleware process; and providing said objects for storage in a cloud object storage system. The plurality of processes may run, for example, on a plurality of compute nodes. The log structured file system middleware process may be embodied, for example, as a Parallel Log-Structured File System (PLFS). The log structured file system middleware process optionally executes on a burst buffer node.

97 MATHEMATICS AND COMPUTING↗

Low-level interfaces for high-level parallel I/O

As the I/O needs of parallel scientific applications increase, file systems for multiprocessors are being designed to provide applications with parallel access to multiple disks. Many parallel file systems present applications with a conventional Unix-like interface that allows the application to access multiple disks transparently. By tracing all the activity of a parallel file system in a production, scientific computing environment, we show that many applications exhibit highly regular, but nonconsecutive I/O access patterns. Since the conventional interface does not provide an efficient method of describing these patterns, we present three extensions to the interface that support strided, nested-strided, and nested-batched I/O requests. We show how these extensions can be used to express common access patterns.

Nieuwejaar, Nils↗

Cloud object store for archive storage of high performance computing data using decoupling middleware

Cloud object storage is enabled for archived data, such as checkpoints and results, of high performance computing applications using a middleware process. A plurality of archived files, such as checkpoint files and results, generated by a plurality of processes in a parallel computing system are stored by obtaining the plurality of archived files from the parallel computing system; converting the plurality of archived files to objects using a log structured file system middleware process; and providing the objects for storage in a cloud object storage system. The plurality of processes may run, for example, on a plurality of compute nodes. The log structured file system middleware process may be embodied, for example, as a Parallel Log-Structured File System (PLFS). The log structured file system middleware process optionally executes on a burst buffer node.

97 MATHEMATICS AND COMPUTING↗

Storage of sparse files using parallel log-structured file system

A sparse file is stored without holes by storing a data portion of the sparse file using a parallel log-structured file system; and generating an index entry for the data portion, the index entry comprising a logical offset, physical offset and length of the data portion. The holes can be restored to the sparse file upon a reading of the sparse file. The data portion can be stored at a logical end of the sparse file. Additional storage efficiency can optionally be achieved by (i) detecting a write pattern for a plurality of the data portions and generating a single patterned index entry for the plurality of the patterned data portions; and/or (ii) storing the patterned index entries for a plurality of the sparse files in a single directory, wherein each entry in the single directory comprises an identifier of a corresponding sparse file.

97 MATHEMATICS AND COMPUTING↗

Global distributed file append using log-structured file system

Techniques are provided for globally appending data from a group of distributed processes to a shared file using a log-structured file system. Data generated by a plurality of processes in a parallel computing system are appended to a shared file by storing the data to the shared file using a log-structured file system (such as a Parallel Log-Structured File System (PLFS)); and generating an index entry for the data, the index entry comprising a logical offset entry and a timestamp entry indicating a time of the storage, wherein the logical offset entry is resolved at read time. The logical offset entry can be populated with an append placeholder that is resolved when the shared file is read. At read time, a plurality of the index entries associated with the shared file can be sorted using the timestamp entry to deliver the requested shared file to a requesting application.

97 MATHEMATICS AND COMPUTING↗

Metadata compression

A computer-executable method, system, and computer program product for managing a Parallel-Logged File System (PLFS) on a data storage system, wherein the data storage system is in communication with an application that updates the data storage system with checkpoint data, the computer-executable method, system, and computer program product comprising receiving a first checkpoint including data from the application; analyzing the data in the first checkpoint to determine whether a pattern exists in the checkpoint data; and upon a positive determination, adding the pattern into PLFS.

97 MATHEMATICS AND COMPUTING↗

High Performance Input/Output for Parallel Computer Systems

The goal of our project is to study the I/O characteristics of parallel applications used in Earth Science data processing systems such as Regional Data Centers (RDCs) or EOSDIS. Our approach is to study the runtime behavior of typical programs and the effect of key parameters of the I/O subsystem both under simulation and with direct experimentation on parallel systems. Our three year activity has focused on two items: developing a test bed that facilitates experimentation with parallel I/O, and studying representative programs from the Earth science data processing application domain. The Parallel Virtual File System (PVFS) has been developed for use on a number of platforms including the Tiger Parallel Architecture Workbench (TPAW) simulator, The Intel Paragon, a cluster of DEC Alpha workstations, and the Beowulf system (at CESDIS). PVFS provides considerable flexibility in configuring I/O in a UNIX- like environment. Access to key performance parameters facilitates experimentation. We have studied several key applications fiom levels 1,2 and 3 of the typical RDC processing scenario including instrument calibration and navigation, image classification, and numerical modeling codes. We have also considered large-scale scientific database codes used to organize image data.

Ligon, W. B.↗

I/O load balancing for big data HPC applications

High Performance Computing (HPC) big data problems require efficient distributed storage systems. However, at scale, such storage systems often experience load imbalance and resource contention due to two factors: the bursty nature of scientific application I/O; and the complex I/O path that is without centralized arbitration and control. For example, the extant Lustre parallel file system-that supports many HPC centers-comprises numerous components connected via custom network topologies, and serves varying demands of a large number of users and applications. Consequently, some storage servers can be more loaded than others, which creates bottlenecks and reduces overall application I/O performance. Existing solutions typically focus on per application load balancing, and thus are not as effective given their lack of a global view of the system. In this paper, we propose a data-driven approach to load balance the I/O servers at scale, targeted at Lustre deployments. To this end, we design a global mapper on Lustre Metadata Server, which gathers runtime statistics from key storage components on the I/O path, and applies Markov chain modeling and a minimum-cost maximum-flow algorithm to decide where data should be placed. Evaluation using a realistic system simulator and a real setup shows that our approach yields better load balancing, which in turn can improve end-to-end performance.

Paul, Arnab K.↗

Parallel compression of data chunks of a shared data object using a log-structured file system

Techniques are provided for parallel compression of data chunks being written to a shared object. A client executing on a compute node or a burst buffer node in a parallel computing system stores a data chunk generated by the parallel computing system to a shared data object on a storage node by compressing the data chunk; and providing the data compressed data chunk to the storage node that stores the shared object. The client and storage node may employ Log-Structured File techniques. The compressed data chunk can be de-compressed by the client when the data chunk is read. A storage node stores a data chunk as part of a shared object by receiving a compressed version of the data chunk from a compute node; and storing the compressed version of the data chunk to the shared data object on the storage node.

97 MATHEMATICS AND COMPUTING↗

Uncovering I/O demands on HPC platforms: Peeking under the hood of Santos Dumont

High-Performance Computing (HPC) platforms are required to solve the most diverse large-scale scientific problems in various research areas, such as biology, chemistry, physics, and health sciences. Researchers use a multitude of scientific softwares, which have different requirements. These include input and output operations, which directly impact performance due to the existing difference in processing and data access speeds. Thus, supercomputers must efficiently handle mixed workload when storing data from the applications. Understanding the set of applications and their performance running in a supercomputer is paramount to understanding the storage system's usage, pinpointing possible bottlenecks, and guiding optimization techniques. This research proposes a methodology and visualization tool to evaluate a supercomputer's data storage infrastructure's performance, taking into account the diverse workload and demands of the system over a long period of operation. As a study case, we focus on the Santos Dumont supercomputer, identifying inefficient usage, problematic performance factors, and providing guidelines on how to tackle those issues.

97 MATHEMATICS AND COMPUTING↗