Intelligent Application of SSDs to Accelerate HPC Workloads

By Nicole Hemsoth

October 1, 2012

Introduction

In most industries today, (whether it is financial services, manufacturing, academic research, healthcare and life sciences, or energy exploration) data analysis, modeling, and visualization efforts are critical to success.

To gain a competitive edge, most organizations are incorporating ever-large data sets and more variable data formats into these computational workflows to help derive better information upon which to make smarter decisions.

These big data applications are placing new attention on the high performance computing (HPC) solutions used to run the algorithms and process the raw data. Due to the larger volumes and greater variety of data types, as well as the desire to use more robust analysis, modeling, and visualization routines, HPC solutions can be used to provide high sustained I/O and throughput, while being optimized to cost-effectively handle highly variable workflows.

The essential element in all of this work is a need for speed. Organizations need fast time-to-results so that they can make the right decisions (which well to drill, which new drug candidate to develop, which product design to produce, which customer to award a lower rate loan to) before their competitors.

Complications and challenges that can impede HPC workflows

When looking to accelerate HPC workloads, there are several factors that can play a major role in overall performance.

To start, today’s analysis, modeling, and visualization efforts are carried out using much more sophisticated algorithms in order to derive more detailed and realistic results. The output from these routines offers finer spatial or temporal resolution and consequently results in much larger size output data sets. In a typical workflow, those output files might be used as input to another analysis, modeling, or visualization application.

These operations can impact HPC workflows since the great volumes of data produced by the initial run must be written to disk and saved and then the data must be ingested by yet another routine. Both operations can generate high I/O and throughput demands on an infrastructure. And if the infrastructure is not capable of sustaining these data transfers, the computational workflows can slow significantly.

Another factor has to do with the data that is being used in today’s analysis, modeling, and visualization efforts. Nearly every industry is now making use of much larger data sets, richer sets (such as that produced from newer seismic imaging tools or next-generation sequencers), and many more types of data. However, most users, even those who primarily have large data sets, also have large numbers of small files – even if they consume a relatively small percentage of the total capacity.

Big data and HPC solutions must therefore not only be capable of quickly accessing the large volumes of data required for the computations, they also must intelligently stage the different types of data, which comes in varying file formats and sizes, on suitably high performance storage.

Required storage solution characteristics

Organizations continually deploy new servers with more powerful CPUs to improve and speed up their analysis, modeling, and visualization efforts. To make the best use of such computing resources, an HPC solution must have a suitable storage solution to sustain HPC workflows.

A storage solution for today’s big data and HPC environments must be able to easily scale. Some solutions offer help meeting the growing data volume demands, but fall short when trying to keep CPUs satiated. To help accelerate HPC workflows, a storage solution must also scale in performance so that as the data volumes grow, the system supports the higher I/O and throughput required to get faster results.

Finally, a storage solution must be optimized to handle today’s HPC big data workflows consisting of data sets of files of all sizes. If all data used were in the same format – a structured database, for example – or of the same relative file size, a solution could be highly optimized to handle the specific data. Working with the mixed data sets used today requires a storage solution that optimizes workflow performance for each data type.

Panasas introduces an integrated SSD/SATA approach

Panasas ActiveStor storage systems have a modular blade architecture integrated with its PanFS parallel file system. The design eliminates the bottleneck of a single RAID controller to deliver high-performance, scalable storage. Prior generations of ActiveStor have been based solely on SATA drives and were well-tuned for high throughput.

With the fifth-generation ActiveStor 14, Panasas has taken a unique approach, leveraging lightning fast SSDs integrated with high capacity SATA disk to improve storage performance while keeping costs down. Rather than use SSD for caching or for “most recent” file access as many other vendors have done, ActiveStor 14 stores all metadata and small files (less than 60KB) on the SSDs and larger files on SATA drives.

Metadata is accessed frequently so fast metadata access benefits all types of workloads. All file operations, including reads and writes, require access to metadata. In many cases, such as directory listings, access to the metadata is all that is required to satisfy an I/O request. Storing metadata on SSD boosts performance for all storage operations, especially for directory functions (listing, searches, etc.) and RAID rebuilds in the event of a drive error. Rebuild performance has been improved so that the new 4TB drives can be rebuilt in the same amount of time as the 3TB drives in the prior generation ActiveStor 12, maintaining a high level of data integrity and system reliability.

Small file access can be disproportionately slow when read from, or written to, standard hard disk drives. Accesses of less than a full sector are inefficient, particularly for random I/O. Furthermore, reads and writes of small files can conflict with streaming reads or writes of large files to the same disk. By maintaining small files on SSD, such conflicts are eliminated. In addition, ActiveStor 14 stores the first 12KB of all files inside the file system metadata, improving SSD efficiency while increasing small file performance. This efficient storage of small files on SSD, dramatically improves response time and IOPS, as evidenced by very impressive SPEC sfs2008 NFS IOPS results that Panasas has published.

ActiveStor 14 is available in three configurations with varying sizes of SSD, SATA and cache. The amount of SSD for acceleration ranges from 1.5 percent up to 10.7 percent of total storage capacity. The bulk of the storage capacity, however, is on cost-effective SATA drives, keeping the overall cost per terabyte lower than the prior generation, and very competitive in the market today.

The Importance of Ease of Use and Management

Equally important to the performance and reliability of any storage system is the ease of use and management of the product. With ActiveStor, organizations can simply add blade enclosures to non-disruptively increase capacity and performance of the global file system as storage requirements grow. Parallel access to data and automated load balancing ensure that performance is optimized. This makes it easy to linearly scale capacity to over eight petabytes and performance to 150GB/s or 1.4M IOPS.

Conclusion

The end result is a high-performance storage system that delivers high throughput and IOPS, ideal for the most demanding HPC and big data workloads and accelerates time-to-results. ActiveStor delivers unmatched scale-out NAS performance in addition to the manageability, reliability, and value required by demanding computing organizations in the biosciences, energy, finance, government, manufacturing, media, and other research sectors.

To learn more about how the Panasas ActiveStor 14 can help your organization, register for the live webinar: http://www.panasas.com/news/webinars

 

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!

Spurred by Global Ambitions, Inspur in Joint HPC Deal with DDN

January 17, 2017

Inspur, the fast-growth cloud computing and server vendor from China that has several systems on the current Top500 list, and DDN, a leader in high-end storage, have announced a joint sales and marketing agreement to produce solutions based on DDN storage platforms integrated with servers, networking, software and services from Inspur. Read more…

By Doug Black

Weekly Twitter Roundup (Jan. 12, 2017)

January 12, 2017

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

NSF Seeks Input on Cyberinfrastructure Advances Needed

January 12, 2017

In cased you missed it, the National Science Foundation posted a “Dear Colleague Letter” (DCL) late last week seeking input on needs for the next generation of cyberinfrastructure to support science and engineering. Read more…

By John Russell

NSF Approves Bridges Phase 2 Upgrade for Broader Research Use

January 12, 2017

The recently completed phase 2 upgrade of the Bridges supercomputer at the Pittsburgh Supercomputing Center (PSC) has been approved by the National Science Foundation (NSF) making it now available for research allocations to the national scientific community, according to an announcement posted this week on the XSEDE web site. Read more…

By John Russell

HPE Extreme Performance Solutions

Remote Visualization: An Integral Technology for Upstream Oil & Gas

As the exploration and production (E&P) of natural resources evolves into an even more complex and vital task, visualization technology has become integral for the upstream oil and gas industry. Read more…

Clemson Software Optimizes Big Data Transfers

January 11, 2017

Data-intensive science is not a new phenomenon as the high-energy physics and astrophysics communities can certainly attest, but today more and more scientists are facing steep data and throughput challenges fueled by soaring data volumes and the demands of global-scale collaboration. Read more…

By Tiffany Trader

For IBM/OpenPOWER: Success in 2017 = (Volume) Sales

January 11, 2017

To a large degree IBM and the OpenPOWER Foundation have done what they said they would – assembling a substantial and growing ecosystem and bringing Power-based products to market, all in about three years. Read more…

By John Russell

UberCloud Cites Progress in HPC Cloud Computing

January 10, 2017

200 HPC cloud experiments, 80 case studies, and a ton of hands-on experience gained, that’s the harvest of four years of UberCloud HPC Experiments. Read more…

By Wolfgang Gentzsch and Burak Yenier

A Conversation with Women in HPC Director Toni Collis

January 6, 2017

In this SC16 video interview, HPCwire Managing Editor Tiffany Trader sits down with Toni Collis, the director and founder of the Women in HPC (WHPC) network, to discuss the strides made since the organization’s debut in 2014. Read more…

By Tiffany Trader

Spurred by Global Ambitions, Inspur in Joint HPC Deal with DDN

January 17, 2017

Inspur, the fast-growth cloud computing and server vendor from China that has several systems on the current Top500 list, and DDN, a leader in high-end storage, have announced a joint sales and marketing agreement to produce solutions based on DDN storage platforms integrated with servers, networking, software and services from Inspur. Read more…

By Doug Black

For IBM/OpenPOWER: Success in 2017 = (Volume) Sales

January 11, 2017

To a large degree IBM and the OpenPOWER Foundation have done what they said they would – assembling a substantial and growing ecosystem and bringing Power-based products to market, all in about three years. Read more…

By John Russell

UberCloud Cites Progress in HPC Cloud Computing

January 10, 2017

200 HPC cloud experiments, 80 case studies, and a ton of hands-on experience gained, that’s the harvest of four years of UberCloud HPC Experiments. Read more…

By Wolfgang Gentzsch and Burak Yenier

A Conversation with Women in HPC Director Toni Collis

January 6, 2017

In this SC16 video interview, HPCwire Managing Editor Tiffany Trader sits down with Toni Collis, the director and founder of the Women in HPC (WHPC) network, to discuss the strides made since the organization’s debut in 2014. Read more…

By Tiffany Trader

BioTeam’s Berman Charts 2017 HPC Trends in Life Sciences

January 4, 2017

Twenty years ago high performance computing was nearly absent from life sciences. Today it’s used throughout life sciences and biomedical research. Genomics and the data deluge from modern lab instruments are the main drivers, but so is the longer-term desire to perform predictive simulation in support of Precision Medicine (PM). There’s even a specialized life sciences supercomputer, ‘Anton’ from D.E. Shaw Research, and the Pittsburgh Supercomputing Center is standing up its second Anton 2 and actively soliciting project proposals. There’s a lot going on. Read more…

By John Russell

Fast Rewind: 2016 Was a Wild Ride for HPC

December 23, 2016

Some years quietly sneak by – 2016 not so much. It’s safe to say there are always forces reshaping the HPC landscape but this year’s bunch seemed like a noisy lot. Among the noisemakers: TaihuLight, DGX-1/Pascal, Dell EMC & HPE-SGI et al., KNL to market, OPA-IB chest thumping, Fujitsu-ARM, new U.S. President-elect, BREXIT, JR’s Intel Exit, Exascale (whatever that means now), NCSA@30, whither NSCI, Deep Learning mania, HPC identity crisis…You get the picture. Read more…

By John Russell

AWI Uses New Cray Cluster for Earth Sciences and Bioinformatics

December 22, 2016

The Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), headquartered in Bremerhaven, Germany, is one of the country's premier research institutes within the Helmholtz Association of German Research Centres, and is an internationally respected center of expertise for polar and marine research. In November 2015, AWI awarded Cray a contract to install a cluster supercomputer that would help the institute accelerate time to discovery. Now the effort is starting to pay off. Read more…

By Linda Barney

Addison Snell: The ‘Wild West’ of HPC Disaggregation

December 16, 2016

We caught up with Addison Snell, CEO of HPC industry watcher Intersect360, at SC16 last month, and Snell had his expected, extensive list of insights into trends driving advanced-scale technology in both the commercial and research sectors. Read more…

By Doug Black

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

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

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

For IBM/OpenPOWER: Success in 2017 = (Volume) Sales

January 11, 2017

To a large degree IBM and the OpenPOWER Foundation have done what they said they would – assembling a substantial and growing ecosystem and bringing Power-based products to market, all in about three years. Read more…

By John Russell

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

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

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

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. Read more…

By John Russell

Leading Solution Providers

D-Wave SC16 Update: What’s Bo Ewald Saying These Days

November 18, 2016

Tucked in a back section of the SC16 exhibit hall, quantum computing pioneer D-Wave has been talking up its new 2000-qubit processor announced in September. Forget for a moment the criticism sometimes aimed at D-Wave. This small Canadian company has sold several machines including, for example, ones to Lockheed and NASA, and has worked with Google on mapping machine learning problems to quantum computing. In July Los Alamos National Laboratory took possession of a 1000-quibit D-Wave 2X system that LANL ordered a year ago around the time of SC15. Read more…

By John Russell

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

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

New Genomics Pipeline Combines AWS, Local HPC, and Supercomputing

September 22, 2016

Declining DNA sequencing costs and the rush to do whole genome sequencing (WGS) of large cohort populations – think 5000 subjects now, but many more thousands soon – presents a formidable computational challenge to researchers attempting to make sense of large cohort datasets. Read more…

By John Russell

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

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

Dell Knights Landing Machine Sets New STAC Records

November 2, 2016

The Securities Technology Analysis Center, commonly known as STAC, has released a new report characterizing the performance of the Knight Landing-based Dell PowerEdge C6320p server on the STAC-A2 benchmarking suite, widely used by the financial services industry to test and evaluate computing platforms. The Dell machine has set new records for both the baseline Greeks benchmark and the large Greeks benchmark. Read more…

By Tiffany Trader

Deep Learning Paves Way for Better Diagnostics

September 19, 2016

Stanford researchers are leveraging GPU-based machines in the Amazon EC2 cloud to run deep learning workloads with the goal of improving diagnostics for a chronic eye disease, called diabetic retinopathy. The disease is a complication of diabetes that can lead to blindness if blood sugar is poorly controlled. It affects about 45 percent of diabetics and 100 million people worldwide, many in developing nations. Read more…

By Tiffany Trader

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