The University of Florida speeds up memory intensive gene research with Dell HPC solution

By Nicole Hemsoth

May 23, 2011

The University of Florida speeds up memory intensive gene research with Dell HPC solution

The whirlwind speed of progress in the computer industry happens at an exponential rate that can be predicted. According to Moore’s Law, the processing speed, memory capacity and even the number of pixels in digital cameras doubles every two years. But there is a branch of technology that’s evolving even faster: gene sequencing, the ordering of nucleotides that make up a strand of DNA in an organism. Gene sequencing is the basis of the whole group of life sciences that study the genetic makeup of humans and other organisms in order to extend life.

Compared with capillary-based sequencing technology of just a few years ago, today’s next-generation sequencing is able to produce a million times more data, which drives up the demands for computation and storage.

“We’ve gone from first-generation DNA sequencing instruments in the 1990s that analyzed 384 sequences at one time to instruments deriving 400 million sequences in parallel,” says Bill Farmerie, associate director of the Interdisciplinary Center for Biotechnology Research (ICBR) at the University of Florida. “And as the volume of data is growing exponentially, that cost of data production has come down by a factor of 100,000.”

Speeding up the pace of biotechnology research

The University of Florida is working to satisfy the demand for faster computers in its ICBR. There, scientists are working with Dell and Intel technology to construct the next generation of high performance computing (HPC) clusters that can keep up with the computational needs of the gene sequencing industry.

“We need to attack larger problems, larger genomes, larger samples and just get larger views of the systems we are studying,” says Aaron Gardner, cyber infrastructure director, Interdisciplinary Center for Biotechnology Research, University of Florida.

As the query sets and databases the queries are run against grew over time, the amount of memory that was available on a computer became of paramount importance. For best performance, it was necessary to cache numerous databases in memory and parallelize the algorithms being used so that they could all share memory between the nodes. The concept of symmetric multiprocessing (SMP) in the HPC cluster evolved to become virtual symmetric multiprocessing (VSMP), in which multiple physical systems appear to function as a single logical system.

Achieving very large shared memory

“We found that traditional HPC on a cluster wasn’t working because we had hard limits on how much memory was available on a single node, and often the software was ill equipped to be able to distribute these databases across all the nodes in a cluster,” says Gardner. “The VSMP system allows us to have a very large shared memory space where we can cache in memory all of the sequence databases and all of the queries that we are searching against. This makes them accessible to all the processors at the same time with minimal latency.”

To build the cluster, the ICBR populated a Dell PowerEdge M1000e modular blade enclosure with 16 Dell PowerEdge M610 blade servers with Intel Xeon processors 5560 and DDR3 memory, which provides approximately one terabyte of shared memory. A quad data rate (QDR), 40 Gb per second Mellanox M3601Q InfiniBand blade switch sourced through Dell busses all the memory and CPU calls between blades.

“We specifically waited for the Intel Xeon processors 5500 series to be developed because of the Intel QuickPath technology which enables all the cores on the individual CPUs, as well as the adjacent sockets within a system, to more quickly route data between their caches,” says Gardner. “Using DDR3 memory with Intel Xeon processors 5500 series is a good match because the processor has higher available bandwidth and memory interface. When we paired the Intel processor with DDR3 with QDR InfiniBand, we were able to minimize latency and improve throughput in the VSMP system for memory performance. The Intel Xeon processors 5500 series alone give us a raw performance improvement of 40 percent up from the previous generation of Intel processors, so we’re building our system on a much faster processor.”

ICBR chose the Dell PowerEdge M1000e blade chassis for the VSMP system for multiple reasons. “It was the only system that we considered that could get us the buffered DDR3 DIMMs that we needed within our time constraints,” says Gardner. “Of the systems we considered, it was also the only one available with QDR InfiniBand, and it facilitates the InfiniBand interconnect between the nodes using the backplane, so there are no cables involved. That increases the reliability and uptime of the VSMP system. So the Dell system was the most complete system, feature wise, for deploying the VSMP solution, as opposed to the others we considered.”

Reducing management overhead

The dual Dell Chassis Management Controllers (CMC) in the PowerEdge M1000e modular blade enclosure provide redundant, secure access paths for administrators to manage the blades from a single console as a single system image. Integrated Dell Remote Access Cards for all the blades and enclosure enable remote management, which, along with reduced complexity on the management end, helped to give Gardner’s team more time to work with researchers on how to best utilize the resources.

“Another factor that we like is the power footprint,” says Gardner. “The Dell PowerEdge blade system has only six power supplies, three of which are required to run the system, and those are higher efficiency power supplies. It helps us to save 6U-10U of rack space and also save on the limited resources we have in our server room for power and cooling versus having power supplies in each discrete system.”

The VSMP technology itself is provided by Dell Business Partner ScaleMP. With ScaleMP vSMP Foundation for SMP software, multiple physical systems appear to function as a single logical system. The innovative ScaleMP Versatile SMP (vSMP) architecture aggregates multiple x86 systems into a single virtual x86 system, delivering an industry-standard, high-end SMP computer. ScaleMP uses software to replace custom hardware and components to offer a new, revolutionary computing paradigm.

Fast setup and deployment

Once ICBR received the Dell enclosure and blades, it took Gardner and his team about three hours to get it racked and powered up and do the diagnostics. “We were taking our time,” says Gardner. “We could have done it faster.”

Deploying the VSMP software took about one day with a ScaleMP representative on site facilitating the VSMP technology. “We were able to accomplish that because the Dell hardware functioned without a hitch,” says Gardner. “And also because we had already created a standardized hardened production image that we were able to deploy on the system. We’ve purchased a lot of hardware from Dell in the past, so it was very easy for us to work within the existing relationship and arrive at the VSMP solution quickly.”

Up to 160x faster results

Prior to the VSMP solution, there were several applications that the university was running on a standard SMP cluster of x86 machines with unsatisfactory results. “We were hitting the memory limits on individual nodes, which meant that the jobs took longer and sometimes just failed,” says Gardner. “So having this larger memory system has enabled us both to get jobs done and to see them through to completion. We’ve seen some substantial performance improvements because we’re able to run all of the data in memory, without going to disk. For example, one assembly application had taken 10 days on our old cluster, and it took only an hour and a half to complete on the Dell VSMP cluster.”

In addition, the university is able to allow researchers to run these jobs in an interactive, real-time manner, rather than waiting in a queue. This enables them to experiment more, and even develop new analysis methods with the system. “This really helps to achieve a better answer in terms of the analysis we’re performing,” says Gardner. “For instance, a DeNova assembly application was swapping to disk because all of the sequences and alignments could not fit into memory. Before we had the VSMP system, we would have had to resort to discarding some sequences, or assembling several smaller assemblies together. These approaches can sometimes produce inferior or misleading results, and cause you to lose consistency and depth with the assembly statistics the software captures. By being able to successfully assembly all of a project’s data at once and get the result back quickly, we are empowered to iterate parameters and adapt our analysis methods in near real time. This is preferable to waiting a week and being forced to work with whatever we get due to the time constraints involved in rerunning those types of jobs.”

Completing the circle

In addition to the Dell VSMP solution, ICBR has been purchasing Dell PowerConnect 6248, 6224, 6220, 5224 Gigabit Ethernet switches for networking infrastructure. “We like the stacking capabilities of the Dell switches,” says Gardner. “We’ve also purchased some Dell PowerConnect 8024 10 Gigabit Ethernet switches as a front-end interconnect to replace our existing Gigabit infrastructure.

With recent 10GbE hardware we are starting to see the performance improve to an acceptable level and we can run almost any protocol over 10GbE. We can also pull a larger portion of our computing staff into supporting research computing because the networking and storage protocols and paradigms with 10GbE are familiar to them.”

As ICBR provides its researchers with the faster processing power they demand, the science of gene sequence will speed up and produce faster results for the life sciences. The immediate result will be more research projects and more grants to fund them.

“It’s all in the papers,” says Farmerie. “By publishing papers, our scientists use the data from the Dell VSMP cluster to generate the next round of proposals that will attract funding. So there’s the cycle that has to be completed each time in order to drive the process of science further down the road.”

See how The University of Florida is using their Dell HPC Solutions to Enable Scientific Research

For more information go to: DellHPCSolutions.com

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!

Google Gets First Dibs on New Skylake Chips

February 27, 2017

As part of an ongoing effort to differentiate its public cloud services, Google made good this week on its intention to bring custom Xeon Skylake chips from Intel Corp. Read more…

By George Leopold

Thomas Sterling on CREST and Academia’s Role in HPC Research

February 27, 2017

The US advances in high performance computing over many decades have been a product of the combined engagement of research centers in industry, government labs, and academia. Read more…

By Thomas Sterling, Indiana University

Advancing Modular Supercomputing with DEEP and DEEP-ER Architectures

February 24, 2017

Knowing that the jump to exascale will require novel architectural approaches capable of delivering dramatic efficiency and performance gains, researchers around the world are hard at work on next-generation HPC systems. Read more…

By Sean Thielen

Weekly Twitter Roundup (Feb. 23, 2017)

February 23, 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

HPE Extreme Performance Solutions

Manufacturers Reaping the Benefits of Remote Visualization

Today’s manufacturers are operating in an ever-changing atmosphere, and finding new ways to boost productivity has never been more vital.

This is why manufacturers are ramping up their investments in high performance computing (HPC), a trend which has helped give rise to the “connected factory” and Industrial Internet of Things (IIoT) concepts that are proliferating throughout the industry today. Read more…

HPE Server Shows Low Latency on STAC-N1 Test

February 22, 2017

The performance of trade and match servers can be a critical differentiator for financial trading houses. Read more…

By John Russell

HPC Financial Update (Feb. 2017)

February 22, 2017

In this recurring feature, we’ll provide you with financial highlights from companies in the HPC industry. Check back in regularly for an updated list with the most pertinent fiscal information. Read more…

By Thomas Ayres

Rethinking HPC Platforms for ‘Second Gen’ Applications

February 22, 2017

Just what constitutes HPC and how best to support it is a keen topic currently. Read more…

By John Russell

HPC Technique Propels Deep Learning at Scale

February 21, 2017

Researchers from Baidu’s Silicon Valley AI Lab (SVAIL) have adapted a well-known HPC communication technique to boost the speed and scale of their neural network training and now they are sharing their implementation with the larger deep learning community. Read more…

By Tiffany Trader

Thomas Sterling on CREST and Academia’s Role in HPC Research

February 27, 2017

The US advances in high performance computing over many decades have been a product of the combined engagement of research centers in industry, government labs, and academia. Read more…

By Thomas Sterling, Indiana University

Advancing Modular Supercomputing with DEEP and DEEP-ER Architectures

February 24, 2017

Knowing that the jump to exascale will require novel architectural approaches capable of delivering dramatic efficiency and performance gains, researchers around the world are hard at work on next-generation HPC systems. Read more…

By Sean Thielen

HPC Technique Propels Deep Learning at Scale

February 21, 2017

Researchers from Baidu’s Silicon Valley AI Lab (SVAIL) have adapted a well-known HPC communication technique to boost the speed and scale of their neural network training and now they are sharing their implementation with the larger deep learning community. Read more…

By Tiffany Trader

IDC: Will the Real Exascale Race Please Stand Up?

February 21, 2017

So the exascale race is on. And lots of organizations are in the pack. Government announcements from the US, China, India, Japan, and the EU indicate that they are working hard to make it happen – some sooner, some later. Read more…

By Bob Sorensen, IDC

TSUBAME3.0 Points to Future HPE Pascal-NVLink-OPA Server

February 17, 2017

Since our initial coverage of the TSUBAME3.0 supercomputer yesterday, more details have come to light on this innovative project. Of particular interest is a new board design for NVLink-equipped Pascal P100 GPUs that will create another entrant to the space currently occupied by Nvidia's DGX-1 system, IBM's "Minsky" platform and the Supermicro SuperServer (1028GQ-TXR). Read more…

By Tiffany Trader

Tokyo Tech’s TSUBAME3.0 Will Be First HPE-SGI Super

February 16, 2017

In a press event Friday afternoon local time in Japan, Tokyo Institute of Technology (Tokyo Tech) announced its plans for the TSUBAME3.0 supercomputer, which will be Japan’s “fastest AI supercomputer,” Read more…

By Tiffany Trader

Drug Developers Use Google Cloud HPC in the Fight Against ALS

February 16, 2017

Within the haystack of a lethal disease such as ALS (amyotrophic lateral sclerosis / Lou Gehrig’s Disease) there exists, somewhere, the needle that will pierce this therapy-resistant affliction. Read more…

By Doug Black

Azure Edges AWS in Linpack Benchmark Study

February 15, 2017

The “when will clouds be ready for HPC” question has ebbed and flowed for years. Read more…

By John Russell

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

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

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

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

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

IBM Wants to be “Red Hat” of Deep Learning

January 26, 2017

IBM today announced the addition of TensorFlow and Chainer deep learning frameworks to its PowerAI suite of deep learning tools, which already includes popular offerings such as Caffe, Theano, and Torch. Read more…

By John Russell

Tokyo Tech’s TSUBAME3.0 Will Be First HPE-SGI Super

February 16, 2017

In a press event Friday afternoon local time in Japan, Tokyo Institute of Technology (Tokyo Tech) announced its plans for the TSUBAME3.0 supercomputer, which will be Japan’s “fastest AI supercomputer,” Read more…

By Tiffany Trader

HPC Startup Advances Auto-Parallelization’s Promise

January 23, 2017

The shift from single core to multicore hardware has made finding parallelism in codes more important than ever, but that hasn’t made the task of parallel programming any easier. Read more…

By Tiffany Trader

Leading Solution Providers

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

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

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

TSUBAME3.0 Points to Future HPE Pascal-NVLink-OPA Server

February 17, 2017

Since our initial coverage of the TSUBAME3.0 supercomputer yesterday, more details have come to light on this innovative project. Of particular interest is a new board design for NVLink-equipped Pascal P100 GPUs that will create another entrant to the space currently occupied by Nvidia's DGX-1 system, IBM's "Minsky" platform and the Supermicro SuperServer (1028GQ-TXR). Read more…

By Tiffany Trader

IDG to Be Bought by Chinese Investors; IDC to Spin Out HPC Group

January 19, 2017

US-based publishing and investment firm International Data Group, Inc. (IDG) will be acquired by a pair of Chinese investors, China Oceanwide Holdings Group Co., Ltd. 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

Is Liquid Cooling Ready to Go Mainstream?

February 13, 2017

Lost in the frenzy of SC16 was a substantial rise in the number of vendors showing server oriented liquid cooling technologies. Three decades ago liquid cooling was pretty much the exclusive realm of the Cray-2 and IBM mainframe class products. That’s changing. We are now seeing an emergence of x86 class server products with exotic plumbing technology ranging from Direct-to-Chip to servers and storage completely immersed in a dielectric fluid. Read more…

By Steve Campbell

What Knights Landing Is Not

June 18, 2016

As we get ready to launch the newest member of the Intel Xeon Phi family, code named Knights Landing, it is natural that there be some questions and potentially some confusion. Read more…

By James Reinders, Intel

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