A Blueprint for Centralized Research Data Storage and Sharing

By Becky Yeager, Thomas Hauser, Peter Ruprecht, and Dan Milroy, University of Colorado, Boulder

March 3, 2014

The University of Colorado Boulder PetaLibrary storage system was recently deployed by the CU Research Computing (RC) group to address the increasing challenges that researchers face regarding large-scale data storage and data management. The PetaLibrary, in part funded by the National Science Foundation, provides a variety of services to campus researchers including high-performance short-term storage, long-term archive storage, and the ability to share data with collaborators at CU-Boulder and across the country.

The PetaLibrary offers several petabytes of data storage using an expandable and modular hardware design. Currently, more than a dozen research groups are using over 100 TB of data on the PetaLibrary system. Researchers and Data Scientists in disciplines ranging from Humanities to Biology, as well as the University of Colorado Boulder Libraries (CU-Boulder Libraries), are using the PetaLibrary storage services. These researchers all have one thing in common, the need for large-scale and low-cost data storage. Usage of the PetaLibrary is expected to double in the next few months.

The two main categories of service offered to customers of the PetaLibrary are Active storage for data that needs to be accessed frequently and Archive storage for data that is accessed infrequently. Active data is always stored on disk and is accessible to researchers on compute resources managed by RC. Archive storage consists of a two level hierarchical storage management (HSM) solution, with disk storage for data that is more likely to be accessed and tape for data that is less likely to be accessed frequently. The HSM configuration was developed in collaboration between RC and a consultant from Re-Store LLC to produce a cost effective solution for allowing automatic transfer between disk and tape.  For data whose importance warrants multiple copies, options for replication to separate tape cartridges or even to a disk-based storage system in a remote datacenter are available.

Disk storage for the PetaLibrary resides on scalable high-density DDN SFA10K and IBM DCS3700 RAID-6 systems.  These are grouped into GPFS clusters for high performance and reliability.  The tape storage system consists of an IBM TS-3584 library with four LTO-6 drives.  We use Tivoli Storage Manager to move data to and from tape.  TSM’s HSM module, plus a number of custom scripts, enables policy-based migration of files between the GPFS filesystem and the tape storage.

Large scale storage on its own is only useful if the associated network infrastructure is designed with large data transfers in mind. Therefore, RC in collaboration with CU’s Office of Information Technology, has deployed a ScienceDMZ, funded by a NSF CC-NIE grant. The core of this science network can perform at 80 Gbps and data on the PetaLibrary is accessed through secure, high-performance file transfer programs. With a fast science network, data can be easily retrieved and sent directly to each researcher’s desktop.  In order to facilitate web-mediated transfers the PetaLibrary utilizes tools provided by Globus. Globus makes robust file transfer capabilities, traditionally available only on expensive, special-purpose software systems, accessible to any researcher with an Internet connection and a laptop.  It also facilitates sharing data between collaborators both on- and off-campus. The current ScienceDMZ, is a 10 Gbps ethernet dedicated layer-2 network serving as a critical infrastructure for a number of data transfer services provided by RC to the CU-Boulder campus community. The NSF funded improvements of the ScienceDMZ include upgraded border routers with 100 Gbps and OpenFlow capabilities, up to 80 Gbps for the DMZ core, performance monitoring and security monitoring.

Clients of the PetaLibrary have been pleased with the services they have received so far. The CU-Boulder Libraries was one of the early adopters of the PetaLibrary services. As one of the larger users, the CU-Boulder Libraries uses the PetaLibrary to build digital collections in a variety of media types for research and study. According to digital initiatives librarian Holley Long, “The CU-Boulder Libraries digitizes audio, video, images, text and soon 3D objects, according to nationally-accepted archival standards.” Large-scale storage is important to these projects because of the initial size of the uncompressed files, often as large as 120 GB per hour of digitized video. In 2014 the estimated production capacity for the library’s digital collections could exceed 80 TB (https://content.cu.edu/digitallibrary/cuAuraria.html).

The University of Colorado Museum of Natural History is using the services provided by the PetaLibrary to store digitized copies of their entire collection. The collection includes 4.5 million objects, including the oldest documented Navajo textile, the Aiken bird collection, and Colorado’s largest collection of bees, along with the metadata associated with each object. The metadata for each distinct object includes notes on who found it, where it was found, when it was located, what it is, and pictures of what it looks like. Every object in the museum has its own interesting backstory, one that comes to life when an object is viewed in relationship with its complex metadata. Because we now live in a digital age the museum is attempting to democratize their exhibits (http://cumuseum.colorado.edu/research/databases). This means that every visitor to the museum will have the opportunity to view the collection in its entirety in a digital format.

Being able to digitally store their entire collection provides the museum with the best of both worlds. Pat Kociolek, Director of the Museum of Natural History, describes the importance of the PetaLibrary to their archives, “It allows the museum the opportunity to make these digital dreams come to life. Visitors can physically view individual items, and when our work is complete visitors will also be able to access the entire collection online. Digital collections also allow remote visitors such as teachers, scientists, and students the chance to browse the collection even if they are unable to visit the museum in person”.  As the data needs of the museum reached over 100 TB, they could no longer rely on local storage resources. The PetaLibrary became an important resource for the museum staff allowing them to archive, and keep safe, those digital resources that have been developed as a way to serve all of their constituents. As a centralized facility on campus the PetaLibrary can provide the museum with the security they need to store these items and to share them widely.

On the CU-Boulder campus researchers are producing large amounts of data in diverse areas such as digital humanities, simulation studies, to global climate modeling. Researchers on campus need ways to preserve this data and to make the data accessible to others. Transparency and the ability to share data and resources with others are important parts of any research plan. The PetaLibrary provides the campus with a centralized location to consolidate this data, and the means to share this data with others through Globus Connect Server.

The PetaLibrary is an important part of the evolving data management ecosystem on campus. It allows researchers to use a high-speed network to move data in and out of storage across campus, and around the nation. The Globus software suite makes it easy to transfer data sets, and to share securely with collaborators. A common practice has been for researchers to store data sets on PCs in labs or on USB-connected drives.  The PetaLibrary, by contrast, provides the security of enterprise storage systems with redundant disk arrays in data centers with environmental and access controls, at a comparable cost through the subsidies of the NSF Grant.

The future vision for the PetaLibrary is to expand the storage capabilities of the system and to enable tools that will help with metadata management and data discovery, and enhance sharing options on campus and with public facing data portals.  The PetaLibrary is an important new service that is at the forefront of the campus discussion on how to deal with the challenges of research data, and it is helping to address the current research needs of the campus and the growth that is anticipated in these areas. A newly created faculty committee is discussing the how to bring additional services to researchers including data curation, metadata management, and data management planning, at a reasonable and sustainable cost.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

How ‘Knights Mill’ Gets Its Deep Learning Flops

June 22, 2017

Intel, the subject of much speculation regarding the delayed, rewritten or potentially canceled “Aurora” contract (the Argonne Lab part of the CORAL “pre-exascale” award), parsed out additional information ab Read more…

By Tiffany Trader

Tsinghua Crowned Eight-Time Student Cluster Champions at ISC

June 22, 2017

Always a hard-fought competition, the Student Cluster Competition awards were announced Wednesday, June 21, at the ISC High Performance Conference 2017. Amid whoops and hollers from the crowd, Thomas Sterling presented t Read more…

By Kim McMahon

GPUs, Power9, Figure Prominently in IBM’s Bet on Weather Forecasting

June 22, 2017

IBM jumped into the weather forecasting business roughly a year and a half ago by purchasing The Weather Company. This week at ISC 2017, Big Blue rolled out plans to push deeper into climate science and develop more gran Read more…

By John Russell

Intersect 360 at ISC: HPC Industry at $44B by 2021

June 22, 2017

The care, feeding and sustained growth of the HPC industry increasingly is in the hands of the commercial market sector – in particular, it’s the hyperscale companies and their embrace of AI and deep learning – tha Read more…

By Doug Black

HPE Extreme Performance Solutions

Creating a Roadmap for HPC Innovation at ISC 2017

In an era where technological advancements are driving innovation to every sector, and powering major economic and scientific breakthroughs, high performance computing (HPC) is crucial to tackle the challenges of today and tomorrow. Read more…

At ISC – Goh on Go: Humans Can’t Scale, the Data-Centric Learning Machine Can

June 22, 2017

I've seen the future this week at ISC, it’s on display in prototype or Powerpoint form, and it’s going to dumbfound you. The future is an AI neural network designed to emulate and compete with the human brain. In thi Read more…

By Doug Black

Cray Brings AI and HPC Together on Flagship Supers

June 20, 2017

Cray took one more step toward the convergence of big data and high performance computing (HPC) today when it announced that it’s adding a full suite of big data and artificial intelligence software to its top-of-the-l Read more…

By Alex Woodie

AMD Charges Back into the Datacenter and HPC Workflows with EPYC Processor

June 20, 2017

AMD is charging back into the enterprise datacenter and select HPC workflows with its new EPYC 7000 processor line, code-named Naples, announced today at a “global” launch event in Austin TX. In many ways it was a fu Read more…

By John Russell

Hyperion: Deep Learning, AI Helping Drive Healthy HPC Industry Growth

June 20, 2017

To be at the ISC conference in Frankfurt this week is to experience deep immersion in deep learning. Users want to learn about it, vendors want to talk about it, analysts and journalists want to report on it. Deep learni Read more…

By Doug Black

How ‘Knights Mill’ Gets Its Deep Learning Flops

June 22, 2017

Intel, the subject of much speculation regarding the delayed, rewritten or potentially canceled “Aurora” contract (the Argonne Lab part of the CORAL “ Read more…

By Tiffany Trader

Tsinghua Crowned Eight-Time Student Cluster Champions at ISC

June 22, 2017

Always a hard-fought competition, the Student Cluster Competition awards were announced Wednesday, June 21, at the ISC High Performance Conference 2017. Amid wh Read more…

By Kim McMahon

GPUs, Power9, Figure Prominently in IBM’s Bet on Weather Forecasting

June 22, 2017

IBM jumped into the weather forecasting business roughly a year and a half ago by purchasing The Weather Company. This week at ISC 2017, Big Blue rolled out pla Read more…

By John Russell

Intersect 360 at ISC: HPC Industry at $44B by 2021

June 22, 2017

The care, feeding and sustained growth of the HPC industry increasingly is in the hands of the commercial market sector – in particular, it’s the hyperscale Read more…

By Doug Black

At ISC – Goh on Go: Humans Can’t Scale, the Data-Centric Learning Machine Can

June 22, 2017

I've seen the future this week at ISC, it’s on display in prototype or Powerpoint form, and it’s going to dumbfound you. The future is an AI neural network Read more…

By Doug Black

Cray Brings AI and HPC Together on Flagship Supers

June 20, 2017

Cray took one more step toward the convergence of big data and high performance computing (HPC) today when it announced that it’s adding a full suite of big d Read more…

By Alex Woodie

AMD Charges Back into the Datacenter and HPC Workflows with EPYC Processor

June 20, 2017

AMD is charging back into the enterprise datacenter and select HPC workflows with its new EPYC 7000 processor line, code-named Naples, announced today at a “g Read more…

By John Russell

Hyperion: Deep Learning, AI Helping Drive Healthy HPC Industry Growth

June 20, 2017

To be at the ISC conference in Frankfurt this week is to experience deep immersion in deep learning. Users want to learn about it, vendors want to talk about it Read more…

By Doug Black

Quantum Bits: D-Wave and VW; Google Quantum Lab; IBM Expands Access

March 21, 2017

For a technology that’s usually characterized as far off and in a distant galaxy, quantum computing has been steadily picking up steam. Just how close real-wo Read more…

By John Russell

Trump Budget Targets NIH, DOE, and EPA; No Mention of NSF

March 16, 2017

President Trump’s proposed U.S. fiscal 2018 budget issued today sharply cuts science spending while bolstering military spending as he promised during the cam Read more…

By John Russell

HPC Compiler Company PathScale Seeks Life Raft

March 23, 2017

HPCwire has learned that HPC compiler company PathScale has fallen on difficult times and is asking the community for help or actively seeking a buyer for its a Read more…

By Tiffany Trader

Google Pulls Back the Covers on Its First Machine Learning Chip

April 6, 2017

This week Google released a report detailing the design and performance characteristics of the Tensor Processing Unit (TPU), its custom ASIC for the inference Read more…

By Tiffany Trader

CPU-based Visualization Positions for Exascale Supercomputing

March 16, 2017

In this contributed perspective piece, Intel’s Jim Jeffers makes the case that CPU-based visualization is now widely adopted and as such is no longer a contrarian view, but is rather an exascale requirement. Read more…

By Jim Jeffers, Principal Engineer and Engineering Leader, Intel

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Nvidia highlights strengths of its newest GPU silicon in response to Google's report on the performance and energy advantages of its custom tensor processor. Read more…

By Tiffany Trader

Nvidia’s Mammoth Volta GPU Aims High for AI, HPC

May 10, 2017

At Nvidia's GPU Technology Conference (GTC17) in San Jose, Calif., this morning, CEO Jensen Huang announced the company's much-anticipated Volta architecture a Read more…

By Tiffany Trader

Facebook Open Sources Caffe2; Nvidia, Intel Rush to Optimize

April 18, 2017

From its F8 developer conference in San Jose, Calif., today, Facebook announced Caffe2, a new open-source, cross-platform framework for deep learning. Caffe2 is the successor to Caffe, the deep learning framework developed by Berkeley AI Research and community contributors. Read more…

By Tiffany Trader

Leading Solution Providers

MIT Mathematician Spins Up 220,000-Core Google Compute Cluster

April 21, 2017

On Thursday, Google announced that MIT math professor and computational number theorist Andrew V. Sutherland had set a record for the largest Google Compute Engine (GCE) job. Sutherland ran the massive mathematics workload on 220,000 GCE cores using preemptible virtual machine instances. Read more…

By Tiffany Trader

Google Debuts TPU v2 and will Add to Google Cloud

May 25, 2017

Not long after stirring attention in the deep learning/AI community by revealing the details of its Tensor Processing Unit (TPU), Google last week announced the Read more…

By John Russell

US Supercomputing Leaders Tackle the China Question

March 15, 2017

Joint DOE-NSA report responds to the increased global pressures impacting the competitiveness of U.S. supercomputing. Read more…

By Tiffany Trader

Russian Researchers Claim First Quantum-Safe Blockchain

May 25, 2017

The Russian Quantum Center today announced it has overcome the threat of quantum cryptography by creating the first quantum-safe blockchain, securing cryptocurrencies like Bitcoin, along with classified government communications and other sensitive digital transfers. Read more…

By Doug Black

Groq This: New AI Chips to Give GPUs a Run for Deep Learning Money

April 24, 2017

CPUs and GPUs, move over. Thanks to recent revelations surrounding Google’s new Tensor Processing Unit (TPU), the computing world appears to be on the cusp of Read more…

By Alex Woodie

DOE Supercomputer Achieves Record 45-Qubit Quantum Simulation

April 13, 2017

In order to simulate larger and larger quantum systems and usher in an age of “quantum supremacy,” researchers are stretching the limits of today’s most advanced supercomputers. Read more…

By Tiffany Trader

Messina Update: The US Path to Exascale in 16 Slides

April 26, 2017

Paul Messina, director of the U.S. Exascale Computing Project, provided a wide-ranging review of ECP’s evolving plans last week at the HPC User Forum. Read more…

By John Russell

Knights Landing Processor with Omni-Path Makes Cloud Debut

April 18, 2017

HPC cloud specialist Rescale is partnering with Intel and HPC resource provider R Systems to offer first-ever cloud access to Xeon Phi "Knights Landing" processors. The infrastructure is based on the 68-core Intel Knights Landing processor with integrated Omni-Path fabric (the 7250F Xeon Phi). Read more…

By Tiffany Trader

  • arrow
  • Click Here for More Headlines
  • arrow
Share This