ORNL Researchers Bridge the Gap Between R, HPC Communities

April 20, 2017

OAK RIDGE, Tenn., April 20, 2017 — The ability to realistically simulate a range of scientific phenomena, such as supernova explosions and the behavior of materials at the nanoscale, has proven a boon to researchers across the scientific spectrum.

Many now consider simulation the third pillar of scientific inquiry, alongside the centuries-old pillars of theory and experiment.

Yet for some areas of science, parallel computing’s promise remains untapped—specifically, fields such as statistics, genomics, finance, economics, sociology, and the environmental sciences, all of which rely strongly on the R programming language. That’s a shame, says Oak Ridge National Laboratory’s George Ostrouchov, who is heading up the Programming with Big Data in R (pbdR) project to bring these untapped domains into the high-performance computing fold.

These “untapped domains” represent an enormous potential user base for world-class computers such as those owned by the Department of Energy and an enormous opportunity for the power of HPC to accelerate research breakthroughs across the statistical sciences.

Ostrouchov and his colleagues have started the ball rolling with a paper in the journal Big Data Research that serves as a tutorial on how to achieve scalable performance with R on leadership computing resources such as ORNL’s Titan, currently the fastest computer in the country for open science. “70-80 percent of statisticians use R,” said Ostrouchov, “and we want to make HPC tools usable for the statistics community.”

The goal of pbdR is to make the tools familiar to R-based communities compatible with HPC, as opposed to the much more taxing option of having these communities change the way in which they do research. Whereas traditional simulation science produces data, R-based research areas seek to use and understand data.

“These communities don’t know HPC, so by providing these tools at least part of their workflow is in a familiar environment,” said Ostrouchov. “We want to make it easier for these communities to accelerate their science.”

Ostrouchov is a statistician by training, but his work at ORNL has brought him into contact with the most powerful machines and some of the brightest minds in the HPC community. His previous experience with R, and his more recent experience with HPC, gave him some ideas on what might work and what wouldn’t, and which pieces were most likely to fit together.

After exploring the potential of R on world-class resources such as Titan for the Department of Energy’s Office of Science and the now retired Kraken for the National Science Foundation, Ostrouchov and his colleagues Wei-Chen Chen, Drew Schmidt and Pragneshkumar Patel have made great strides in merging the two seemingly disparate platforms, and by extension two very different cultures.

The evolution of R

R’s real strength lies in data exploration and the creation of graphics to explain complex datasets, supported by an unmatched variety of transparent and understandable machine learning tools. “It’s probably the gold standard for graphics in data exploration,” said Ostrouchov. Much like other popular languages such as Python and MATLAB it’s scripted – as opposed to compiled as in the case of C and Fortran.

This presents a unique set of challenges for running effectively on HPC platforms, particularly given that all scripted languages load libraries dynamically during runtime, a process which can bog down file systems when thousands of parallel library requests are made.

Fortunately, Ostrouchov’s BDR co-author Mike Matheson has developed a set of partial solutions that enable libraries to load almost seamlessly up to 10,000 cores thus far on Titan. These solutions are still being optimized, meaning that the 10,000-core metric will almost certainly increase in the future.

Thus far the overhead of using a scripted language to drive the libraries has proven remarkably small, approaching the performance of the underlying linear algebra code known as ScaLAPACK used by other codes to perform matrix calculations. “In theory,” said Ostrouchov, “there’s no reason that R couldn’t match the performance of the leading science codes on Titan.”

Equally important is the fact that the pbdR team has made it possible to run R on HPC systems without changes to the serial code in matrix computations, meaning much less work for programmers looking to make the jump; the same code will do the same thing on a single-processor matrix or a multi-processor matrix such as those employed across Titan, or any other world-class HPC resource for that matter.

Portability was always a top priority, said Ostrouchov, adding that the same code will work on nearly any HPC resource, no matter the architecture; one need only swap out the libraries.

The pbdR team’s achievements bode well for the future of R and HPC, but bringing together these two very different communities will take time, and a few pioneers such as ORNL computational biologist Dan Jacobson who, along with a team including graduate research assistant and PhD student at the University of Tennessee’s Bredesen Center Piet Jones, is using R on Titan to advance the state of the art in genomics and bioenergy.

The team has used the pbdR team’s streamlined R bindings for MPI, a messaging framework that enables the many compute nodes in a parallel machine such as Titan to communicate, to distribute gene expression data to multiple nodes for rapid analyses. This technique will enable a better understanding of the biological functions assigned to individual genes and help discover what metabolites are driving certain observations.

“We need to know what is influencing a biological function, whether this be a gene, regulatory element, metabolite or something else,” said Jones, adding that these analyses help researchers better understand pleiotropy, or the idea that genes have multiple functions, and epistasis, in which the interactions of multiple genes results in a certain characteristic.

Their various projects allow for multiple comparisons using different techniques, and by extension allow them to tackle ever bigger problems in genomics.

Jacobson is also now collaborating with other institutions to use R to study plant microbial interfaces for bioenergy applications, work that he can later apply to clinical datasets for a scientific win-win across very different domains.

It will no doubt be the first of many as the R programming community becomes more comfortable with this whole new world of massive computing capability.

Titan is part of the Oak Ridge Leadership Computing Facility, a DOE Office of Science User Facility located at ORNL.

About Oak Ridge National Laboratory

Oak Ridge National Laboratory is supported by the DOE’s Office of Science. The single largest supporter of basic research in the physical sciences in the United States, the Office of Science is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.


Source: Scott Jones, ORNL Communications

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!

NASA Uses Supercomputing to Measure Carbon in the World’s Trees

October 22, 2020

Trees constitute one of the world’s most important carbon sinks, pulling enormous amounts of carbon dioxide from the atmosphere and storing the carbon in their trunks and the surrounding soil. Measuring this carbon sto Read more…

By Oliver Peckham

Nvidia Dominates (Again) Latest MLPerf Inference Results

October 22, 2020

The two-year-old AI benchmarking group MLPerf.org released its second set of inferencing results yesterday and again, as in the most recent MLPerf training results (July 2020), it was almost entirely The Nvidia Show, a p Read more…

By John Russell

With Optane Gaining, Intel Exits NAND Flash

October 21, 2020

In a sign that its 3D XPoint memory technology is gaining traction, Intel Corp. is departing the NAND flash memory and storage market with the sale of its manufacturing base in China to SK Hynix of South Korea. The $9 Read more…

By George Leopold

HPE, AMD and EuroHPC Partner for Pre-Exascale LUMI Supercomputer

October 21, 2020

Not even a week after Nvidia announced that it would be providing hardware for the first four of the eight planned EuroHPC systems, HPE and AMD are announcing another major EuroHPC design win. Finnish supercomputing cent Read more…

By Oliver Peckham

HPE to Build Australia’s Most Powerful Supercomputer for Pawsey

October 20, 2020

The Pawsey Supercomputing Centre in Perth, Western Australia, has had a busy year. Pawsey typically spends much of its time looking to the stars, working with a variety of observatories and astronomers – but when COVID Read more…

By Oliver Peckham

AWS Solution Channel

Live Webinar: AWS & Intel Research Webinar Series – Fast scaling research workloads on the cloud

Date: 27 Oct – 5 Nov

Join us for the AWS and Intel Research Webinar series.

You will learn how we help researchers process complex workloads, quickly analyze massive data pipelines, store petabytes of data, and advance research using transformative technologies. Read more…

Intel® HPC + AI Pavilion

Berlin Institute of Health: Putting HPC to Work for the World

Researchers from the Center for Digital Health at the Berlin Institute of Health (BIH) are using science to understand the pathophysiology of COVID-19, which can help to inform the development of targeted treatments. Read more…

DDN-Tintri Showcases Technology Integration with Two New Products

October 20, 2020

DDN, a long-time leader in HPC storage, announced two new products today and provided more detail around its strategy for integrating DDN HPC technologies with the enterprise strengths of its recent acquisitions, notably Read more…

By John Russell

Nvidia Dominates (Again) Latest MLPerf Inference Results

October 22, 2020

The two-year-old AI benchmarking group MLPerf.org released its second set of inferencing results yesterday and again, as in the most recent MLPerf training resu Read more…

By John Russell

HPE, AMD and EuroHPC Partner for Pre-Exascale LUMI Supercomputer

October 21, 2020

Not even a week after Nvidia announced that it would be providing hardware for the first four of the eight planned EuroHPC systems, HPE and AMD are announcing a Read more…

By Oliver Peckham

HPE to Build Australia’s Most Powerful Supercomputer for Pawsey

October 20, 2020

The Pawsey Supercomputing Centre in Perth, Western Australia, has had a busy year. Pawsey typically spends much of its time looking to the stars, working with a Read more…

By Oliver Peckham

DDN-Tintri Showcases Technology Integration with Two New Products

October 20, 2020

DDN, a long-time leader in HPC storage, announced two new products today and provided more detail around its strategy for integrating DDN HPC technologies with Read more…

By John Russell

Is the Nvidia A100 GPU Performance Worth a Hardware Upgrade?

October 16, 2020

Over the last decade, accelerators have seen an increasing rate of adoption in high-performance computing (HPC) platforms, and in the June 2020 Top500 list, eig Read more…

By Hartwig Anzt, Ahmad Abdelfattah and Jack Dongarra

Nvidia and EuroHPC Team for Four Supercomputers, Including Massive ‘Leonardo’ System

October 15, 2020

The EuroHPC Joint Undertaking (JU) serves as Europe’s concerted supercomputing play, currently comprising 32 member states and billions of euros in funding. I Read more…

By Oliver Peckham

ROI: Is HPC Worth It? What Can We Actually Measure?

October 15, 2020

HPC enables innovation and discovery. We all seem to agree on that. Is there a good way to quantify how much that’s worth? Thanks to a sponsored white pape Read more…

By Addison Snell, Intersect360 Research

Preparing for Exascale Science on Day 1

October 14, 2020

Science simulation, visualization, data, and learning applications will greatly benefit from the massive computational resources available with future exascal Read more…

By Linda Barney

Supercomputer-Powered Research Uncovers Signs of ‘Bradykinin Storm’ That May Explain COVID-19 Symptoms

July 28, 2020

Doctors and medical researchers have struggled to pinpoint – let alone explain – the deluge of symptoms induced by COVID-19 infections in patients, and what Read more…

By Oliver Peckham

Nvidia Said to Be Close on Arm Deal

August 3, 2020

GPU leader Nvidia Corp. is in talks to buy U.K. chip designer Arm from parent company Softbank, according to several reports over the weekend. If consummated Read more…

By George Leopold

Intel’s 7nm Slip Raises Questions About Ponte Vecchio GPU, Aurora Supercomputer

July 30, 2020

During its second-quarter earnings call, Intel announced a one-year delay of its 7nm process technology, which it says it will create an approximate six-month shift for its CPU product timing relative to prior expectations. The primary issue is a defect mode in the 7nm process that resulted in yield degradation... Read more…

By Tiffany Trader

Google Hires Longtime Intel Exec Bill Magro to Lead HPC Strategy

September 18, 2020

In a sign of the times, another prominent HPCer has made a move to a hyperscaler. Longtime Intel executive Bill Magro joined Google as chief technologist for hi Read more…

By Tiffany Trader

HPE Keeps Cray Brand Promise, Reveals HPE Cray Supercomputing Line

August 4, 2020

The HPC community, ever-affectionate toward Cray and its eponymous founder, can breathe a (virtual) sigh of relief. The Cray brand will live on, encompassing th Read more…

By Tiffany Trader

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

By Doug Black

Aurora’s Troubles Move Frontier into Pole Exascale Position

October 1, 2020

Intel’s 7nm node delay has raised questions about the status of the Aurora supercomputer that was scheduled to be stood up at Argonne National Laboratory next year. Aurora was in the running to be the United States’ first exascale supercomputer although it was on a contemporaneous timeline with... Read more…

By Tiffany Trader

European Commission Declares €8 Billion Investment in Supercomputing

September 18, 2020

Just under two years ago, the European Commission formalized the EuroHPC Joint Undertaking (JU): a concerted HPC effort (comprising 32 participating states at c Read more…

By Oliver Peckham

Leading Solution Providers

Contributors

Is the Nvidia A100 GPU Performance Worth a Hardware Upgrade?

October 16, 2020

Over the last decade, accelerators have seen an increasing rate of adoption in high-performance computing (HPC) platforms, and in the June 2020 Top500 list, eig Read more…

By Hartwig Anzt, Ahmad Abdelfattah and Jack Dongarra

Nvidia and EuroHPC Team for Four Supercomputers, Including Massive ‘Leonardo’ System

October 15, 2020

The EuroHPC Joint Undertaking (JU) serves as Europe’s concerted supercomputing play, currently comprising 32 member states and billions of euros in funding. I Read more…

By Oliver Peckham

Google Cloud Debuts 16-GPU Ampere A100 Instances

July 7, 2020

On the heels of the Nvidia’s Ampere A100 GPU launch in May, Google Cloud is announcing alpha availability of the A100 “Accelerator Optimized” VM A2 instance family on Google Compute Engine. The instances are powered by the HGX A100 16-GPU platform, which combines two HGX A100 8-GPU baseboards using... Read more…

By Tiffany Trader

Microsoft Azure Adds A100 GPU Instances for ‘Supercomputer-Class AI’ in the Cloud

August 19, 2020

Microsoft Azure continues to infuse its cloud platform with HPC- and AI-directed technologies. Today the cloud services purveyor announced a new virtual machine Read more…

By Tiffany Trader

Oracle Cloud Infrastructure Powers Fugaku’s Storage, Scores IO500 Win

August 28, 2020

In June, RIKEN shook the supercomputing world with its Arm-based, Fujitsu-built juggernaut: Fugaku. The system, which weighs in at 415.5 Linpack petaflops, topp Read more…

By Oliver Peckham

DOD Orders Two AI-Focused Supercomputers from Liqid

August 24, 2020

The U.S. Department of Defense is making a big investment in data analytics and AI computing with the procurement of two HPC systems that will provide the High Read more…

By Tiffany Trader

Oracle Cloud Deepens HPC Embrace with Launch of A100 Instances, Plans for Arm, More 

September 22, 2020

Oracle Cloud Infrastructure (OCI) continued its steady ramp-up of HPC capabilities today with a flurry of announcements. Topping the list is general availabilit Read more…

By John Russell

Joliot-Curie Supercomputer Used to Build First Full, High-Fidelity Aircraft Engine Simulation

July 14, 2020

When industrial designers plan the design of a new element of a vehicle’s propulsion or exterior, they typically use fluid dynamics to optimize airflow and in Read more…

By Oliver Peckham

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This