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!

US Exascale Computing Update with Paul Messina

December 8, 2016

Around the world, efforts are ramping up to cross the next major computing threshold with machines that are 50-100x more performant than today’s fastest number crunchers.  Read more…

By Tiffany Trader

Weekly Twitter Roundup (Dec. 8, 2016)

December 8, 2016

Here at HPCwire, we aim to keep the HPC community apprised of the most relevant and interesting news items that get tweeted throughout the week. Read more…

By Thomas Ayres

Qualcomm Targets Intel Datacenter Dominance with 10nm ARM-based Server Chip

December 8, 2016

Claiming no less than a reshaping of the future of Intel-dominated datacenter computing, Qualcomm Technologies, the market leader in smartphone chips, announced the forthcoming availability of what it says is the world’s first 10nm processor for servers, based on ARM Holding’s chip designs. Read more…

By Doug Black

Which Schools Produce the Top Coders in the World?

December 8, 2016

Ever wonder which universities worldwide produce the best coders? The answers may surprise you, at least as judged by the results of a competition posted yesterday on the HackerRank blog. Read more…

By John Russell

Enlisting Deep Learning in the War on Cancer

December 7, 2016

Sometime in Q2 2017 the first ‘results’ of the Joint Design of Advanced Computing Solutions for Cancer (JDACS4C) will become publicly available according to Rick Stevens. He leads one of three JDACS4C pilot projects pressing deep learning (DL) into service in the War on Cancer. The pilots, supported in part by DOE exascale funding, not only seek to do good by advancing cancer research and therapy but also to advance deep learning capabilities and infrastructure with an eye towards eventual use on exascale machines. Read more…

By John Russell

DDN Enables 50TB/Day Trans-Pacific Data Transfer for Yahoo Japan

December 6, 2016

Transferring data from one data center to another in search of lower regional energy costs isn’t a new concept, but Yahoo Japan is putting the idea into transcontinental effect with a system that transfers 50TB of data a day from Japan to the U.S., where electricity costs a quarter of the rates in Japan. Read more…

By Doug Black

Infographic Highlights Career of Admiral Grace Murray Hopper

December 5, 2016

Dr. Grace Murray Hopper (December 9, 1906 – January 1, 1992) was an early pioneer of computer science and one of the most famous women achievers in a field dominated by men. Read more…

By Staff

Ganthier, Turkel on the Dell EMC Road Ahead

December 5, 2016

Who is Dell EMC and why should you care? Glad you asked is Jim Ganthier’s quick response. Ganthier is SVP for validated solutions and high performance computing for the new (even bigger) technology giant Dell EMC following Dell’s acquisition of EMC in September. In this case, says Ganthier, the blending of the two companies is a 1+1 = 5 proposition. Not bad math if you can pull it off. Read more…

By John Russell

US Exascale Computing Update with Paul Messina

December 8, 2016

Around the world, efforts are ramping up to cross the next major computing threshold with machines that are 50-100x more performant than today’s fastest number crunchers.  Read more…

By Tiffany Trader

Enlisting Deep Learning in the War on Cancer

December 7, 2016

Sometime in Q2 2017 the first ‘results’ of the Joint Design of Advanced Computing Solutions for Cancer (JDACS4C) will become publicly available according to Rick Stevens. He leads one of three JDACS4C pilot projects pressing deep learning (DL) into service in the War on Cancer. The pilots, supported in part by DOE exascale funding, not only seek to do good by advancing cancer research and therapy but also to advance deep learning capabilities and infrastructure with an eye towards eventual use on exascale machines. Read more…

By John Russell

Ganthier, Turkel on the Dell EMC Road Ahead

December 5, 2016

Who is Dell EMC and why should you care? Glad you asked is Jim Ganthier’s quick response. Ganthier is SVP for validated solutions and high performance computing for the new (even bigger) technology giant Dell EMC following Dell’s acquisition of EMC in September. In this case, says Ganthier, the blending of the two companies is a 1+1 = 5 proposition. Not bad math if you can pull it off. Read more…

By John Russell

AWS Launches Massive 100 Petabyte ‘Sneakernet’

December 1, 2016

Amazon Web Services now offers a way to move data into its cloud by the truckload. Read more…

By Tiffany Trader

Lighting up Aurora: Behind the Scenes at the Creation of the DOE’s Upcoming 200 Petaflops Supercomputer

December 1, 2016

In April 2015, U.S. Department of Energy Undersecretary Franklin Orr announced that Intel would be the prime contractor for Aurora: Read more…

By Jan Rowell

Seagate-led SAGE Project Delivers Update on Exascale Goals

November 29, 2016

Roughly a year and a half after its launch, the SAGE exascale storage project led by Seagate has delivered a substantive interim report – Data Storage for Extreme Scale. Read more…

By John Russell

Nvidia Sees Bright Future for AI Supercomputing

November 23, 2016

Graphics chipmaker Nvidia made a strong showing at SC16 in Salt Lake City last week. Read more…

By Tiffany Trader

HPE-SGI to Tackle Exascale and Enterprise Targets

November 22, 2016

At first blush, and maybe second blush too, Hewlett Packard Enterprise’s (HPE) purchase of SGI seems like an unambiguous win-win. SGI’s advanced shared memory technology, its popular UV product line (Hanna), deep vertical market expertise, and services-led go-to-market capability all give HPE a leg up in its drive to remake itself. Bear in mind HPE came into existence just a year ago with the split of Hewlett-Packard. The computer landscape, including HPC, is shifting with still unclear consequences. One wonders who’s next on the deal block following Dell’s recent merger with EMC. Read more…

By John Russell

Why 2016 Is the Most Important Year in HPC in Over Two Decades

August 23, 2016

In 1994, two NASA employees connected 16 commodity workstations together using a standard Ethernet LAN and installed open-source message passing software that allowed their number-crunching scientific application to run on the whole “cluster” of machines as if it were a single entity. Read more…

By Vincent Natoli, Stone Ridge Technology

IBM Advances Against x86 with Power9

August 30, 2016

After offering OpenPower Summit attendees a limited preview in April, IBM is unveiling further details of its next-gen CPU, Power9, which the tech mainstay is counting on to regain market share ceded to rival Intel. Read more…

By Tiffany Trader

AWS Beats Azure to K80 General Availability

September 30, 2016

Amazon Web Services has seeded its cloud with Nvidia Tesla K80 GPUs to meet the growing demand for accelerated computing across an increasingly-diverse range of workloads. The P2 instance family is a welcome addition for compute- and data-focused users who were growing frustrated with the performance limitations of Amazon's G2 instances, which are backed by three-year-old Nvidia GRID K520 graphics cards. Read more…

By Tiffany Trader

Think Fast – Is Neuromorphic Computing Set to Leap Forward?

August 15, 2016

Steadily advancing neuromorphic computing technology has created high expectations for this fundamentally different approach to computing. Read more…

By John Russell

The Exascale Computing Project Awards $39.8M to 22 Projects

September 7, 2016

The Department of Energy’s Exascale Computing Project (ECP) hit an important milestone today with the announcement of its first round of funding, moving the nation closer to its goal of reaching capable exascale computing by 2023. Read more…

By Tiffany Trader

ARM Unveils Scalable Vector Extension for HPC at Hot Chips

August 22, 2016

ARM and Fujitsu today announced a scalable vector extension (SVE) to the ARMv8-A architecture intended to enhance ARM capabilities in HPC workloads. Fujitsu is the lead silicon partner in the effort (so far) and will use ARM with SVE technology in its post K computer, Japan’s next flagship supercomputer planned for the 2020 timeframe. This is an important incremental step for ARM, which seeks to push more aggressively into mainstream and HPC server markets. Read more…

By John Russell

IBM Debuts Power8 Chip with NVLink and Three New Systems

September 8, 2016

Not long after revealing more details about its next-gen Power9 chip due in 2017, IBM today rolled out three new Power8-based Linux servers and a new version of its Power8 chip featuring Nvidia’s NVLink interconnect. Read more…

By John Russell

Vectors: How the Old Became New Again in Supercomputing

September 26, 2016

Vector instructions, once a powerful performance innovation of supercomputing in the 1970s and 1980s became an obsolete technology in the 1990s. But like the mythical phoenix bird, vector instructions have arisen from the ashes. Here is the history of a technology that went from new to old then back to new. Read more…

By Lynd Stringer

Leading Solution Providers

US, China Vie for Supercomputing Supremacy

November 14, 2016

The 48th edition of the TOP500 list is fresh off the presses and while there is no new number one system, as previously teased by China, there are a number of notable entrants from the US and around the world and significant trends to report on. Read more…

By Tiffany Trader

HPE Gobbles SGI for Larger Slice of $11B HPC Pie

August 11, 2016

Hewlett Packard Enterprise (HPE) announced today that it will acquire rival HPC server maker SGI for $7.75 per share, or about $275 million, inclusive of cash and debt. The deal ends the seven-year reprieve that kept the SGI banner flying after Rackable Systems purchased the bankrupt Silicon Graphics Inc. for $25 million in 2009 and assumed the SGI brand. Bringing SGI into its fold bolsters HPE's high-performance computing and data analytics capabilities and expands its position... Read more…

By Tiffany Trader

Intel Launches Silicon Photonics Chip, Previews Next-Gen Phi for AI

August 18, 2016

At the Intel Developer Forum, held in San Francisco this week, Intel Senior Vice President and General Manager Diane Bryant announced the launch of Intel's Silicon Photonics product line and teased a brand-new Phi product, codenamed "Knights Mill," aimed at machine learning workloads. Read more…

By Tiffany Trader

CPU Benchmarking: Haswell Versus POWER8

June 2, 2015

With OpenPOWER activity ramping up and IBM’s prominent role in the upcoming DOE machines Summit and Sierra, it’s a good time to look at how the IBM POWER CPU stacks up against the x86 Xeon Haswell CPU from Intel. Read more…

By Tiffany Trader

Beyond von Neumann, Neuromorphic Computing Steadily Advances

March 21, 2016

Neuromorphic computing – brain inspired computing – has long been a tantalizing goal. The human brain does with around 20 watts what supercomputers do with megawatts. And power consumption isn’t the only difference. Fundamentally, brains ‘think differently’ than the von Neumann architecture-based computers. While neuromorphic computing progress has been intriguing, it has still not proven very practical. Read more…

By John Russell

Dell EMC Engineers Strategy to Democratize HPC

September 29, 2016

The freshly minted Dell EMC division of Dell Technologies is on a mission to take HPC mainstream with a strategy that hinges on engineered solutions, beginning with a focus on three industry verticals: manufacturing, research and life sciences. "Unlike traditional HPC where everybody bought parts, assembled parts and ran the workloads and did iterative engineering, we want folks to focus on time to innovation and let us worry about the infrastructure," said Jim Ganthier, senior vice president, validated solutions organization at Dell EMC Converged Platforms Solution Division. Read more…

By Tiffany Trader

Container App ‘Singularity’ Eases Scientific Computing

October 20, 2016

HPC container platform Singularity is just six months out from its 1.0 release but already is making inroads across the HPC research landscape. It's in use at Lawrence Berkeley National Laboratory (LBNL), where Singularity founder Gregory Kurtzer has worked in the High Performance Computing Services (HPCS) group for 16 years. Read more…

By Tiffany Trader

Micron, Intel Prepare to Launch 3D XPoint Memory

August 16, 2016

Micron Technology used last week’s Flash Memory Summit to roll out its new line of 3D XPoint memory technology jointly developed with Intel while demonstrating the technology in solid-state drives. Micron claimed its Quantx line delivers PCI Express (PCIe) SSD performance with read latencies at less than 10 microseconds and writes at less than 20 microseconds. Read more…

By George Leopold

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