Dell Boxes Up HPC for Life Sciences

By Nicole Hemsoth

June 5, 2013

Dell has its sights set on a duo of trends unfolding around high-end computing. On the one side, the pace, price and practically of genomics is converging to create an exploding market. And on that note, the compute infrastructure required to push it all forward is facing some convergence of its own.

There are a range of figures demonstrating the rapid growth of genomics in the last decade, all of which coincide with the deepening dip in the cost to sequence genes. With more companies sequencing more genetic samples to aid in everything from drug discovery, disease cures and the creation of new materials, the time is ripe for an explosion of purpose-built all-in-one infrastructure approaches.

According to IDC, spending on converged systems is predicted to grow “at a compound annual rate of more than 54 percent over the 2011-2016 forecast period, driven by the cost advantages and efficiency related to operations and management of IT, simplification of vendor engagement and faster time to productivity with IT system updates.”

This week at their Dell Enterprise Forum, the company snapped these trends together with the unveiling of their Active Infrastructure for HPC Life Sciences offering. Set for release in August, the company describes their package as a “modular high performance computing and storage building blocks” which include the required bricks stacked into a single rack housing 32 nodes.

The packaged PowerEdge blades are orchestrated with Bright Cluster Manager and come with Intel inside, namely of the 8-core, dual socket Xeon E5-2400 ilk. On their own, these particular blades offer up 16 cores with 2.5 MB cache per core. With this power, Dell says one cabinet can support the data load of two to four sequencers.

In other words, if you have the practical know-how, a cool million bucks should be able to get you up and running with two sequencers (if they’re at the low end like the “commodity” ones set to be offered by Life Technologies) and a nice fridge from Dell to handle all your genomic data. While that may be a bit of a stretch, power costs and general practicality aside, Dell insists that there’s a hungry market of smaller companies eager to remove the IT hassle and stick to the sequencing.

Dell says that users can tap up to 512 cores, 1.5 terabytes of memory, 540 terabytes of Dell NFS and Lustre file system storage, all strung together with either a 10 GbE or Infiniband network.

The company claims that the impetus and research work behind their converged life science offering was based on their work with the Translational Genomics Research Institute (TGen), where they were able to shave genomic analysis time from one week to one day.

Dell is making a number of other big claims for their genomics-flavored tailoring, the most prominent of which is that users can cut their genomic analysis workflows from days to hours via the ability to optimize analytical software and data across the cluster and file system. The end result is the ability to process a reported 38 genomes per day on a single system.

They note that in addition to cutting down the processing time, acquiring, optimizing and maintaining a custom cluster built from commodity parts can add significant overhead to time and cost. Their $650,000 rack, when compared to what simple server math reveals isn’t stunning, but for users who simply want to shed the datacenter hassle and get back to research, the “plug and play” element could be rather attractive.

What will be interesting to watch over the coming couple of years is how the cost line of sequencing is affected by the IT side of the equation. As noted earlier, the sequencers themselves are becoming more widely available due to price point. If the server side of the genomics business follows suit in a more competitive way, the goals of personalized medicine could be closer than we think–and not just because of the work of a relatively few research institutions that had enough funding…Imagine an average clinician’s ability to tailor treatment based on a quick sequence effort at one-twentieth of the cost it would have been in 2009.

According to Jason Corneveaux, a bioinformatician in the neurogenomics division at the Translational Genomics Research Institute, “With diseases like neuroblastoma, hours matter.” He says that their Dell system allows them to score the needed processing in a “clinically relevant amount of time.”

Subscribe to HPCwire's Weekly Update!

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

Harvard/Google Use AI to Help Produce Astonishing 3D Map of Brain Tissue

May 10, 2024

Although LLMs are getting all the notice lately, AI techniques of many varieties are being infused throughout science. For example, Harvard researchers, Google, and colleagues published a 3D map in Science this week that Read more…

ISC Preview: Focus Will Be on Top500 and HPC Diversity 

May 9, 2024

Last year's Supercomputing 2023 in November had record attendance, but the direction of high-performance computing was a hot topic on the floor. Expect more of that at the upcoming ISC High Performance 2024, which is hap Read more…

Processor Security: Taking the Wong Path

May 9, 2024

More research at UC San Diego revealed yet another side-channel attack on x86_64 processors. The research identified a new vulnerability that allows precise control of conditional branch prediction in modern processors.� Read more…

The Ultimate 2024 Winter Class Round-Up

May 8, 2024

To make navigating easier, we have compiled a collection of all the 2024 Winter Classic News in this single page round-up. Meet The Teams   Introducing Team Lobo This is the other team from University of New Mex Read more…

How the Chip Industry is Helping a Battery Company

May 8, 2024

Chip companies, once seen as engineering pure plays, are now at the center of geopolitical intrigue. Chip manufacturing firms, especially TSMC and Intel, have become the backbone of devices with an on/off switch. Thes Read more…

Illinois Considers $20 Billion Quantum Manhattan Project Says Report

May 7, 2024

There are multiple reports that Illinois governor Jay Robert Pritzker is considering a $20 billion Quantum Manhattan-like project for the Chicago area. According to the reports, photonics quantum computer developer PsiQu Read more…

ISC Preview: Focus Will Be on Top500 and HPC Diversity 

May 9, 2024

Last year's Supercomputing 2023 in November had record attendance, but the direction of high-performance computing was a hot topic on the floor. Expect more of Read more…

Illinois Considers $20 Billion Quantum Manhattan Project Says Report

May 7, 2024

There are multiple reports that Illinois governor Jay Robert Pritzker is considering a $20 billion Quantum Manhattan-like project for the Chicago area. Accordin Read more…

The NASA Black Hole Plunge

May 7, 2024

We have all thought about it. No one has done it, but now, thanks to HPC, we see what it looks like. Hold on to your feet because NASA has released videos of wh Read more…

How Nvidia Could Use $700M Run.ai Acquisition for AI Consumption

May 6, 2024

Nvidia is touching $2 trillion in market cap purely on the brute force of its GPU sales, and there's room for the company to grow with software. The company hop Read more…

Hyperion To Provide a Peek at Storage, File System Usage with Global Site Survey

May 3, 2024

Curious how the market for distributed file systems, interconnects, and high-end storage is playing out in 2024? Then you might be interested in the market anal Read more…

Qubit Watch: Intel Process, IBM’s Heron, APS March Meeting, PsiQuantum Platform, QED-C on Logistics, FS Comparison

May 1, 2024

Intel has long argued that leveraging its semiconductor manufacturing prowess and use of quantum dot qubits will help Intel emerge as a leader in the race to de Read more…

Stanford HAI AI Index Report: Science and Medicine

April 29, 2024

While AI tools are incredibly useful in a variety of industries, they truly shine when applied to solving problems in scientific and medical discovery. Research Read more…

IBM Delivers Qiskit 1.0 and Best Practices for Transitioning to It

April 29, 2024

After spending much of its December Quantum Summit discussing forthcoming quantum software development kit Qiskit 1.0 — the first full version — IBM quietly Read more…

Nvidia H100: Are 550,000 GPUs Enough for This Year?

August 17, 2023

The GPU Squeeze continues to place a premium on Nvidia H100 GPUs. In a recent Financial Times article, Nvidia reports that it expects to ship 550,000 of its lat Read more…

Synopsys Eats Ansys: Does HPC Get Indigestion?

February 8, 2024

Recently, it was announced that Synopsys is buying HPC tool developer Ansys. Started in Pittsburgh, Pa., in 1970 as Swanson Analysis Systems, Inc. (SASI) by John Swanson (and eventually renamed), Ansys serves the CAE (Computer Aided Engineering)/multiphysics engineering simulation market. Read more…

Intel’s Server and PC Chip Development Will Blur After 2025

January 15, 2024

Intel's dealing with much more than chip rivals breathing down its neck; it is simultaneously integrating a bevy of new technologies such as chiplets, artificia Read more…

Comparing NVIDIA A100 and NVIDIA L40S: Which GPU is Ideal for AI and Graphics-Intensive Workloads?

October 30, 2023

With long lead times for the NVIDIA H100 and A100 GPUs, many organizations are looking at the new NVIDIA L40S GPU, which it’s a new GPU optimized for AI and g Read more…

Choosing the Right GPU for LLM Inference and Training

December 11, 2023

Accelerating the training and inference processes of deep learning models is crucial for unleashing their true potential and NVIDIA GPUs have emerged as a game- Read more…

Shutterstock 1606064203

Meta’s Zuckerberg Puts Its AI Future in the Hands of 600,000 GPUs

January 25, 2024

In under two minutes, Meta's CEO, Mark Zuckerberg, laid out the company's AI plans, which included a plan to build an artificial intelligence system with the eq Read more…

AMD MI3000A

How AMD May Get Across the CUDA Moat

October 5, 2023

When discussing GenAI, the term "GPU" almost always enters the conversation and the topic often moves toward performance and access. Interestingly, the word "GPU" is assumed to mean "Nvidia" products. (As an aside, the popular Nvidia hardware used in GenAI are not technically... Read more…

Nvidia’s New Blackwell GPU Can Train AI Models with Trillions of Parameters

March 18, 2024

Nvidia's latest and fastest GPU, codenamed Blackwell, is here and will underpin the company's AI plans this year. The chip offers performance improvements from Read more…

Leading Solution Providers

Contributors

Shutterstock 1285747942

AMD’s Horsepower-packed MI300X GPU Beats Nvidia’s Upcoming H200

December 7, 2023

AMD and Nvidia are locked in an AI performance battle – much like the gaming GPU performance clash the companies have waged for decades. AMD has claimed it Read more…

Eyes on the Quantum Prize – D-Wave Says its Time is Now

January 30, 2024

Early quantum computing pioneer D-Wave again asserted – that at least for D-Wave – the commercial quantum era has begun. Speaking at its first in-person Ana Read more…

The GenAI Datacenter Squeeze Is Here

February 1, 2024

The immediate effect of the GenAI GPU Squeeze was to reduce availability, either direct purchase or cloud access, increase cost, and push demand through the roof. A secondary issue has been developing over the last several years. Even though your organization secured several racks... Read more…

Intel Plans Falcon Shores 2 GPU Supercomputing Chip for 2026  

August 8, 2023

Intel is planning to onboard a new version of the Falcon Shores chip in 2026, which is code-named Falcon Shores 2. The new product was announced by CEO Pat Gel Read more…

The NASA Black Hole Plunge

May 7, 2024

We have all thought about it. No one has done it, but now, thanks to HPC, we see what it looks like. Hold on to your feet because NASA has released videos of wh Read more…

GenAI Having Major Impact on Data Culture, Survey Says

February 21, 2024

While 2023 was the year of GenAI, the adoption rates for GenAI did not match expectations. Most organizations are continuing to invest in GenAI but are yet to Read more…

China Is All In on a RISC-V Future

January 8, 2024

The state of RISC-V in China was discussed in a recent report released by the Jamestown Foundation, a Washington, D.C.-based think tank. The report, entitled "E Read more…

Q&A with Nvidia’s Chief of DGX Systems on the DGX-GB200 Rack-scale System

March 27, 2024

Pictures of Nvidia's new flagship mega-server, the DGX GB200, on the GTC show floor got favorable reactions on social media for the sheer amount of computing po Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire