NVIDIA K80 GPU-System Speeds Up Bioinformatics Tool 12X

By John Russell

January 28, 2015

Not long ago, the high cost and relative slowness of DNA sequencing were the rate-limiting bottlenecks in biomedical research. Today, post-sequencing data analysis is the biggest challenge. The reason, of course, is the prodigious output from modern next-generation sequencing (NGS) instruments (e.g., Illumina and ThermoFisher/Life Technologies) overwhelming analysis pipelines.

Efficiently sifting the data treasure trove is a huge headache for the bioinformatics community. Moreover, there are many different kinds of post-sequencing data analysis, (e.g., assembly, alignment, variant calling, RNAseq) all of which may stress HPC systems in different ways. Recently, HPC blogger Richard Casey reported achieving a 12X analysis speed-up using the new the Tesla K80, NVIDIA’s newest GPU in the Tesla series.

Casey detailed the work on in his blog. He chose to tackle NGS data alignment, a frequent and time-consuming step. Casey is a bioinformaticist at Colorado Statue University Next Generation Sequencing Core. His main role is providing bioinformatics and data analysis support to principal investigators and researchers who use the Core’s NextGen sequencers.

Blog Excerpt: “Typically, the DNA reads coming off the sequencers are aligned to a so-called reference genome.  This step attempts to map sample reads to the reference genome, in which the results are used for SNP analysis and other types of reports. The current human reference genome contains about 3.1 billion nucleotide bases. This is a fairly large genome (although there are considerably larger genomes in other species).

“Sequence alignment of NGS sample reads against the reference human genome can take a few hours to several hours to run on a reasonably high-end server or cluster. Although this is not excessive for a single sample, with the shear number of samples handled by current sequencers, and with multiple sequencers in an NGS Core or lab, the accumulated time spent in the sequence alignment step can be problematic.

“To help alleviate this alignment issue, we have been evaluating parallel sequence alignment algorithms and software alignment tools.  As mentioned in an earlier blog post, we’re testing the NVBIO suite on NVIDIA GPU’s. nvBowtie is a GPU-enabled sequence alignment tool in this software suite. bowtie2 is a popular CPU-only counterpart to nvBowtie.  To compare the performance of these two applications, we performed a DNA sequence alignment benchmark test with human genome datasets.”

It’s best to refer to Casey’s blog for the full details (sample sources, sequencers used, reference genome used, etc.). The tools benchmarked included nvBowtie v.0.9.9.3 from the NVBIO suite and bowtie2 v.2.2.4 sequence alignment tools.  “nvBowtie is designed for highly-parallel GPU-only sequence alignments, whereas bowtie2 is designed for moderately-parallel CPU-only alignments.  In a sense this is a comparison of fine-grained vs. coarse-grained parallelism,” wrote Casey.

Numerical simulations were performed on Microway’s Tesla GPU Test Drive accelerated compute cluster. The performance comparisons were made between a cpu-only and gpu-only system.

The CPU-only Test used bowtie2 with the following system and run configurations:

  • Cray XT6m
  • (2) 12-core AMD Opteron 6100 CPU’s per compute node
  • 32 GB RAM per compute node
  • 12 CPU-threads
  • Ran bowtie2 on a single compute node

Results of the CPU-only sequence alignment runs were 206 min. or 3.4 hrs.

The GPU-only Test used nvBowtie with the following system and run configurations:

  • Intel cluster
  • (2) 12-core Xeon E5-2680v3 CPU’s per compute node
  • 128 GB host CPU RAM per compute node
  • NVIDIA Tesla K80 GPU per compute node
  • Ran nvBowtie on a single compute node

Results of the GPU-only sequence alignment runs were 16 min. or 0.25 hrs.

All netted out, the CPU-only bowtie2 run versus the GPU-only nvBowtie run produced a 12.8X speed-up (206 min/16 min).

Casey wrote: “The 12.8X speedup of nvBowtie on a K80 GPU is encouraging.  For human genome sequence alignments, this reduced the wall-clock run time from several hours to a few minutes.

“The older AMD Opteron series processors used in these tests have been superseded by newer AMD FX series and Intel 5th generation processors, among others. The speedups seen here would undoubtedly be reduced somewhat when compared to newer CPU processor models. However, nvBowtie is currently at version 0.9 (not even version one yet). We would expect continued algorithm development and optimization in nvBowtie to result in performance improvements for the code, thus maintaining speedups somewhere in the 8X – 10X range.  In any event, shaving hours off the sequence alignment runtimes is significant.”

The K80 specifications are:

  • 4,992 GPU cores
  • 24 GB GDDR5 RAM
  • 480 GB/sec. memory bandwidth
  • 300 W power consumption (important spec!)
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!

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

March 18, 2024

Nvidia's latest and fastest GPU, code-named Blackwell, is here and will underpin the company's AI plans this year. The chip offers performance improvements from its predecessors, including the red-hot H100 and A100 GPUs. Read more…

Nvidia Showcases Quantum Cloud, Expanding Quantum Portfolio at GTC24

March 18, 2024

Nvidia’s barrage of quantum news at GTC24 this week includes new products, signature collaborations, and a new Nvidia Quantum Cloud for quantum developers. While Nvidia may not spring to mind when thinking of the quant Read more…

2024 Winter Classic: Meet the HPE Mentors

March 18, 2024

The latest installment of the 2024 Winter Classic Studio Update Show features our interview with the HPE mentor team who introduced our student teams to the joys (and potential sorrows) of the HPL (LINPACK) and accompany Read more…

Houston We Have a Solution: Addressing the HPC and Tech Talent Gap

March 15, 2024

Generations of Houstonian teachers, counselors, and parents have either worked in the aerospace industry or know people who do - the prospect of entering the field was normalized for boys in 1969 when the Apollo 11 missi Read more…

Apple Buys DarwinAI Deepening its AI Push According to Report

March 14, 2024

Apple has purchased Canadian AI startup DarwinAI according to a Bloomberg report today. Apparently the deal was done early this year but still hasn’t been publicly announced according to the report. Apple is preparing Read more…

Survey of Rapid Training Methods for Neural Networks

March 14, 2024

Artificial neural networks are computing systems with interconnected layers that process and learn from data. During training, neural networks utilize optimization algorithms to iteratively refine their parameters until Read more…

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

March 18, 2024

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

Nvidia Showcases Quantum Cloud, Expanding Quantum Portfolio at GTC24

March 18, 2024

Nvidia’s barrage of quantum news at GTC24 this week includes new products, signature collaborations, and a new Nvidia Quantum Cloud for quantum developers. Wh Read more…

Houston We Have a Solution: Addressing the HPC and Tech Talent Gap

March 15, 2024

Generations of Houstonian teachers, counselors, and parents have either worked in the aerospace industry or know people who do - the prospect of entering the fi Read more…

Survey of Rapid Training Methods for Neural Networks

March 14, 2024

Artificial neural networks are computing systems with interconnected layers that process and learn from data. During training, neural networks utilize optimizat Read more…

PASQAL Issues Roadmap to 10,000 Qubits in 2026 and Fault Tolerance in 2028

March 13, 2024

Paris-based PASQAL, a developer of neutral atom-based quantum computers, yesterday issued a roadmap for delivering systems with 10,000 physical qubits in 2026 a Read more…

India Is an AI Powerhouse Waiting to Happen, but Challenges Await

March 12, 2024

The Indian government is pushing full speed ahead to make the country an attractive technology base, especially in the hot fields of AI and semiconductors, but Read more…

Charles Tahan Exits National Quantum Coordination Office

March 12, 2024

(March 1, 2024) My first official day at the White House Office of Science and Technology Policy (OSTP) was June 15, 2020, during the depths of the COVID-19 loc Read more…

AI Bias In the Spotlight On International Women’s Day

March 11, 2024

What impact does AI bias have on women and girls? What can people do to increase female participation in the AI field? These are some of the questions the tech Read more…

Alibaba Shuts Down its Quantum Computing Effort

November 30, 2023

In case you missed it, China’s e-commerce giant Alibaba has shut down its quantum computing research effort. It’s not entirely clear what drove the change. 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…

Analyst Panel Says Take the Quantum Computing Plunge Now…

November 27, 2023

Should you start exploring quantum computing? Yes, said a panel of analysts convened at Tabor Communications HPC and AI on Wall Street conference earlier this y Read more…

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…

DoD Takes a Long View of Quantum Computing

December 19, 2023

Given the large sums tied to expensive weapon systems – think $100-million-plus per F-35 fighter – it’s easy to forget the U.S. Department of Defense is a 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…

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…

Leading Solution Providers

Contributors

Baidu Exits Quantum, Closely Following Alibaba’s Earlier Move

January 5, 2024

Reuters reported this week that Baidu, China’s giant e-commerce and services provider, is exiting the quantum computing development arena. Reuters reported � Read more…

Training of 1-Trillion Parameter Scientific AI Begins

November 13, 2023

A US national lab has started training a massive AI brain that could ultimately become the must-have computing resource for scientific researchers. Argonne N Read more…

Shutterstock 1179408610

Google Addresses the Mysteries of Its Hypercomputer 

December 28, 2023

When Google launched its Hypercomputer earlier this month (December 2023), the first reaction was, "Say what?" It turns out that the Hypercomputer is Google's t 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…

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…

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…

Google Introduces ‘Hypercomputer’ to Its AI Infrastructure

December 11, 2023

Google ran out of monikers to describe its new AI system released on December 7. Supercomputer perhaps wasn't an apt description, so it settled on Hypercomputer 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…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire