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D4M 2.0 Schema: a general purpose high performance schema for the Accumulo database

September 10, 2013
  |
Conference Paper
Author:
Jeremy Kepner
…
Published in:
HPEC 2013: IEEE Conf. on High Performance Extreme Computing, 10-12 September 2013.
Topic:
supercomputing
R&D area:
R&D group:

Summary

Non-traditional, relaxed consistency, triple store databases are the backbone of many web companies (e.g., Google Big Table, Amazon Dynamo, and Facebook Cassandra). The Apache Accumulo database is a high performance open source relaxed consistency database that is widely used for government applications. Obtaining the full benefits of Accumulo requires using novel schemas. The Dynamic Distributed Dimensional Data Model (D4M) [http://www.mit.edu/~kepner/D4M] provides a uniform mathematical framework based on associative arrays that encompasses both traditional (i.e., SQL) and non-traditional databases. For non-traditional databases D4M naturally leads to a general purpose schema that can be used to fully index and rapidly query every unique string in a dataset. The D4M 2.0 Schema has been applied with little or no customization to cyber, bioinformatics, scientific citation, free text, and social media data. The D4M 2.0 Schema is simple, requires minimal parsing, and achieves the highest published Accumulo ingest rates. The benefits of the D4M 2.0 Schema are independent of the D4M interface. Any interface to Accumulo can achieve these benefits by using the D4M 2.0 Schema.
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Summary

Non-traditional, relaxed consistency, triple store databases are the backbone of many web companies (e.g., Google Big Table, Amazon Dynamo, and Facebook Cassandra). The Apache Accumulo database is a high performance open source relaxed consistency database that is widely used for government applications. Obtaining the full benefits of Accumulo requires using...

READ MORE
D4M 2.0 Schema: a general purpose high performance schema for the Accumulo database

LLSuperCloud: sharing HPC systems for diverse rapid prototyping

September 10, 2013
  |
Conference Paper
Author:
Albert I. Reuther
…
Published in:
HPEC 2013: IEEE Conf. on High Performance Extreme Computing, 10-12 September 2013.
Topic:
supercomputing
R&D area:
R&D group:

Summary

The supercomputing and enterprise computing arenas come from very different lineages. However, the advent of commodity computing servers has brought the two arenas closer than they have ever been. Within enterprise computing, commodity computing servers have resulted in the development of a wide range of new cloud capabilities: elastic computing, virtualization, and data hosting. Similarly, the supercomputing community has developed new capabilities in heterogeneous, massively parallel hardware and software. Merging the benefits of enterprise clouds and supercomputing has been a challenging goal. Significant effort has been expended in trying to deploy supercomputing capabilities on cloud computing systems. These efforts have resulted in unreliable, low performance solutions, which requires enormous expertise to maintain. LLSuperCloud provides a novel solution to the problem of merging enterprise cloud and supercomputing technology. More specifically LLSuperCloud reverses the traditional paradigm of attempting to deploy supercomputing capabilities on a cloud and instead deploys cloud capabilities on a supercomputer. The result is a system that can handle heterogeneous, massively parallel workloads while also providing high performance elastic computing, virtualization, and databases. The benefits of LLSuperCloud are highlighted using a mixed workload of C MPI, parallel MATLAB, Java, databases, and virtualized web services.
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Summary

The supercomputing and enterprise computing arenas come from very different lineages. However, the advent of commodity computing servers has brought the two arenas closer than they have ever been. Within enterprise computing, commodity computing servers have resulted in the development of a wide range of new cloud capabilities: elastic computing...

READ MORE
LLSuperCloud: sharing HPC systems for diverse rapid prototyping

D4M 2.0 Schema: a general purpose high performance schema for the Accumulo database

September 10, 2013
  |
Conference Paper
Author:
Jeremy Kepner
…
Published in:
HPEC 2013: IEEE Conf. on High Performance Extreme Computing, 10-12 September 2013.
Topic:
big data
R&D area:
R&D group:

Summary

Non-traditional, relaxed consistency, triple store databases are the backbone of many web companies (e.g., Google Big Table, Amazon Dynamo, and Facebook Cassandra). The Apache Accumulo database is a high performance open source relaxed consistency database that is widely used for government applications. Obtaining the full benefits of Accumulo requires using novel schemas. The Dynamic Distributed Dimensional Data Model (D4M) [http://www.mit.edu/~kepner/D4M] provides a uniform mathematical framework based on associative arrays that encompasses both traditional (i.e., SQL) and non-traditional databases. For non-traditional databases D4M naturally leads to a general purpose schema that can be used to fully index and rapidly query every unique string in a dataset. The D4M 2.0 Schema has been applied with little or no customization to cyber, bioinformatics, scientific citation, free text, and social media data. The D4M 2.0 Schema is simple, requires minimal parsing, and achieves the highest published Accumulo ingest rates. The benefits of the D4M 2.0 Schema are independent of the D4M interface. Any interface to Accumulo can achieve these benefits by using the D4M 2.0 Schema.
READ LESS

Summary

Non-traditional, relaxed consistency, triple store databases are the backbone of many web companies (e.g., Google Big Table, Amazon Dynamo, and Facebook Cassandra). The Apache Accumulo database is a high performance open source relaxed consistency database that is widely used for government applications. Obtaining the full benefits of Accumulo requires using...

READ MORE
D4M 2.0 Schema: a general purpose high performance schema for the Accumulo database

Very large graphs for information extraction (VLG) - summary of first-year proof-of-concept study

August 20, 2013
  |
Project Report
Author:
Benjamin A. Miller
…
Published in:
MIT Lincoln Laboratory Report VLG-1
Topic:
signal processing
R&D area:
R&D group:

Summary

In numerous application domains relevant to the Department of Defense and the Intelligence Community, data of interest take the form of entities and the relationships between them, and these data are commonly represented as graphs. Under the Very Large Graphs for Information Extraction effort--a one-year proof-of-concept study--MIT LL developed novel techniques for anomalous subgraph detection, building on tools in the signal processing research literature. This report documents the technical results of this effort. Two datasets--a snapshot of Thompson Reuters? Web of Science database and a stream of web proxy logs--were parsed, and graphs were constructed from the raw data. From the phenomena in these datasets, several algorithms were developed to model the dynamic graph behavior, including a preferential attachment mechanism with memory, a streaming filter to model a graph as a weighted average of its past connections, and a generalized linear model for graphs where connection probabilities are determined by additional side information or metadata. A set of metrics was also constructed to facilitate comparison of techniques. The study culminated in a demonstration of the algorithms on the datasets of interest, in addition to simulated data. Performance in terms of detection, estimation, and computational burden was measured according to the metrics. Among the highlights of this demonstration were the detection of emerging coauthor clusters in the Web of Science data, detection of botnet activity in the web proxy data after 15 minutes (which took 10 days to detect using state-of-the-practice techniques), and demonstration of the core algorithm on a simulated 1-billion-vertex graph using a commodity computing cluster.
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Summary

In numerous application domains relevant to the Department of Defense and the Intelligence Community, data of interest take the form of entities and the relationships between them, and these data are commonly represented as graphs. Under the Very Large Graphs for Information Extraction effort--a one-year proof-of-concept study--MIT LL developed novel...

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Very large graphs for information extraction (VLG) - summary of first-year proof-of-concept study

LLGrid: supercomputer for sensor processing

April 15, 2013
  |
Book Chapter
Author:
Jeremy Kepner
…
Published in:
Chapter 24 in Contemporary High Performance Computing, April 2013.
Topic:
supercomputing
R&D area:
R&D group:

Summary

MIT Lincoln Laboratory is a federally funded research and development center that applies advanced technology to problems of national interest. Research and development activities focus on long-term technology development as well as rapid system prototyping and demonstration. A key part of this mission is to develop and deploy advanced sensor systems. Developing the algorithms for these systems requires interactive access to large scale computing and data storage. Deploying these systems requires that the computing and storage capabilities are transportable and energy efficient. The LLGrid system of supercomputers allows hundreds of researchers simultaneous interactive access to large amounts of processing and storage for development and testing of their sensor processing algorithms. The requirements of the LLGrid user base are as diverse as the sensors they are developing: sonar, radar, infrared, optical, hyperspectral, video, bio and cyber. However, there are two common elements: delivering large amounts of data interactively to many processors and high level user interfaces that require minimal user training. The LLGrid software stack provides these capabilities on dozens of LLGrid computing clusters across Lincoln Laboratory. LLGrid systems range from very small (a few nodes) to very large (40+ racks).
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Summary

MIT Lincoln Laboratory is a federally funded research and development center that applies advanced technology to problems of national interest. Research and development activities focus on long-term technology development as well as rapid system prototyping and demonstration. A key part of this mission is to develop and deploy advanced sensor...

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LLGrid: supercomputer for sensor processing

Novel graph processor architecture

January 30, 2013
  |
Journal Article
Author:
William S. Song
…
Published in:
Lincoln Laboratory Journal, Vol. 20, No. 1, 2013, pp. 92-104.
Topic:
supercomputing
R&D area:
R&D group:

Summary

Graph algorithms are increasingly used in applications that exploit large databases. However, conventional processor architectures are hard-pressed to handle the throughput and memory requirements of graph computation. Lincoln Laboratory's graph-processor architecture represents a fundamental rethinking of architectures. It utilizes innovations that include high-bandwidth three-dimensional (3D) communication links, a sparse matrix-based graph instruction set, accelerator-based architecture, a systolic sorter, randomized communications, a cacheless memory system, and 3D packaging.
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Summary

Graph algorithms are increasingly used in applications that exploit large databases. However, conventional processor architectures are hard-pressed to handle the throughput and memory requirements of graph computation. Lincoln Laboratory's graph-processor architecture represents a fundamental rethinking of architectures. It utilizes innovations that include high-bandwidth three-dimensional (3D) communication links, a sparse matrix-based...

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Novel graph processor architecture

Taming biological big data with D4M

January 30, 2013
  |
Journal Article
Author:
Jeremy Kepner
…
Published in:
Lincoln Laboratory Journal, Vol. 20, No. 1, 2013, pp. 82-91.
Topic:
supercomputing
R&D area:
R&D group:

Summary

The supercomputing community has taken up the challenge of "taming the beast" spawned by the massive amount of data available in the bioinformatics domain: How can these data be exploited faster and better? MIT Lincoln Laboratory computer scientists demonstrated how a new Laboratory-developed technology, the Dynamic Distributed Dimensional Data Model (D4M), can be used to accelerate DNA sequence comparison, a core operation in bioinformatics.
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Summary

The supercomputing community has taken up the challenge of "taming the beast" spawned by the massive amount of data available in the bioinformatics domain: How can these data be exploited faster and better? MIT Lincoln Laboratory computer scientists demonstrated how a new Laboratory-developed technology, the Dynamic Distributed Dimensional Data Model...

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Taming biological big data with D4M

Driving big data with big compute

September 10, 2012
  |
Conference Paper
Author:
Chansup Byun
…
Published in:
HPEC 2012: IEEE Conf. on High Performance Extreme Computing, 10-12 September 2012.
Topic:
supercomputing
R&D area:
R&D group:

Summary

Big Data (as embodied by Hadoop clusters) and Big Compute (as embodied by MPI clusters) provide unique capabilities for storing and processing large volumes of data. Hadoop clusters make distributed computing readily accessible to the Java community and MPI clusters provide high parallel efficiency for compute intensive workloads. Bringing the big data and big compute communities together is an active area of research. The LLGrid team has developed and deployed a number of technologies that aim to provide the best of both worlds. LLGrid MapReduce allows the map/reduce parallel programming model to be used quickly and efficiently in any language on any compute cluster. D4M (Dynamic Distributed Dimensional Data Model) provided a high level distributed arrays interface to the Apache Accumulo database. The accessibility of these technologies is assessed by measuring the effort to use these tools and is typically a few lines of code. The performance is assessed by measuring the insert rate into the Accumulo database. Using these tools a database insert rate of 4M inserts/second has been achieved on an 8 node cluster.
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Summary

Big Data (as embodied by Hadoop clusters) and Big Compute (as embodied by MPI clusters) provide unique capabilities for storing and processing large volumes of data. Hadoop clusters make distributed computing readily accessible to the Java community and MPI clusters provide high parallel efficiency for compute intensive workloads. Bringing the...

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Driving big data with big compute

HPC-VMs: virtual machines in high performance computing systems

September 10, 2012
  |
Journal Article
Author:
Albert I. Reuther
…
Published in:
HPEC 2012: IEEE Conf. on High Performance Extreme Computing, 10-12 September 2012.
Topic:
supercomputing
R&D area:
R&D group:

Summary

The concept of virtual machines dates back to the 1960s. Both IBM and MIT developed operating system features that enabled user and peripheral time sharing, the underpinnings of which were early virtual machines. Modern virtual machines present a translation layer of system devices between a guest operating system and the host operating system executing on a computer system, while isolating each of the guest operating systems from each other. In the past several years, enterprise computing has embraced virtual machines to deploy a wide variety of capabilities from business management systems to email server farms. Those who have adopted virtual deployment environments have capitalized on a variety of advantages including server consolidation, service migration, and higher service reliability. But they have also ended up with some challenges including a sacrifice in performance and more complex system management. Some of these advantages and challenges also apply to HPC in virtualized environments. In this paper, we analyze the effectiveness of using virtual machines in a high performance computing (HPC) environment. We propose adding some virtual machine capability to already robust HPC environments for specific scenarios where the productivity gained outweighs the performance lost for using virtual machines. Finally, we discuss an implementation of augmenting virtual machines into the software stack of a HPC cluster, and we analyze the affect on job launch time of this implementation.
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Summary

The concept of virtual machines dates back to the 1960s. Both IBM and MIT developed operating system features that enabled user and peripheral time sharing, the underpinnings of which were early virtual machines. Modern virtual machines present a translation layer of system devices between a guest operating system and the...

READ MORE
HPC-VMs: virtual machines in high performance computing systems

Large scale network situational awareness via 3D gaming technology

September 10, 2012
  |
Conference Paper
Author:
Matthew Hubbell
…
Published in:
HPEC 2012: IEEE Conf. on High Performance Extreme Computing, 10-12 September 2012.
Topic:
supercomputing
R&D area:
R&D group:

Summary

Obtaining situational awareness of network activity across an enterprise presents unique visualization challenges. IT analysts are required to quickly gather and correlate large volumes of disparate data to identify the existence of anomalous behavior. This paper will show how the MIT Lincoln Laboratory LLGrid Team has approached obtaining network situational awareness utilizing the Unity 3D video game engine. We have developed a 3D environment of the physical plant in the format of a networked multi player First Person Shooter (FPS) to demonstrate a virtual depiction of the current state of the network and the machines operating on the network. Within the game or virtual world an analyst or player can gather critical information on all network assets as well as perform physical system actions on machines in question. 3D gaming technology provides tools to create an environment that is both visually familiar to the player as well display immense amounts of system data in a meaningful and easy to absorb format. Our prototype system was able to monitor and display 5000 assets in ~10% of the time of our network time window.
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Summary

Obtaining situational awareness of network activity across an enterprise presents unique visualization challenges. IT analysts are required to quickly gather and correlate large volumes of disparate data to identify the existence of anomalous behavior. This paper will show how the MIT Lincoln Laboratory LLGrid Team has approached obtaining network situational...

READ MORE
Large scale network situational awareness via 3D gaming technology
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