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!

Talk to Me: Nvidia Claims NLP Inference, Training Records

August 15, 2019

Nvidia says it’s achieved significant advances in conversation natural language processing (NLP) training and inference, enabling more complex, immediate-response interchanges between customers and chatbots. And the co Read more…

By Doug Black

Trump Administration and NIST Issue AI Standards Development Plan

August 14, 2019

Efforts to develop AI are gathering steam fast. On Monday, the White House issued a federal plan to help develop technical standards for AI following up on a mandate contained in the Administration’s AI Executive Order Read more…

By John Russell

Scientists to Tap Exascale Computing to Unlock the Mystery of our Accelerating Universe

August 14, 2019

The universe and everything in it roared to life with the Big Bang approximately 13.8 billion years ago. It has continued expanding ever since. While we have a good understanding of the early universe, its fate billions Read more…

By Rob Johnson

AWS Solution Channel

Efficiency and Cost-Optimization for HPC Workloads – AWS Batch and Amazon EC2 Spot Instances

High Performance Computing on AWS leverages the power of cloud computing and the extreme scale it offers to achieve optimal HPC price/performance. With AWS you can right size your services to meet exactly the capacity requirements you need without having to overprovision or compromise capacity. Read more…

HPE Extreme Performance Solutions

Bring the combined power of HPC and AI to your business transformation

FPGA (Field Programmable Gate Array) acceleration cards are not new, as they’ve been commercially available since 1984. Typically, the emphasis around FPGAs has centered on the fact that they’re programmable accelerators, and that they can truly offer workload specific hardware acceleration solutions without requiring custom silicon. Read more…

IBM Accelerated Insights

Cloudy with a Chance of Mainframes

[Connect with HPC users and learn new skills in the IBM Spectrum LSF User Community.]

Rapid rates of change sometimes result in unexpected bedfellows. Read more…

Argonne Supercomputer Accelerates Cancer Prediction Research

August 13, 2019

In the fight against cancer, early prediction, which drastically improves prognoses, is critical. Now, new research by a team from Northwestern University – and accelerated by supercomputing resources at Argonne Nation Read more…

By Oliver Peckham

Scientists to Tap Exascale Computing to Unlock the Mystery of our Accelerating Universe

August 14, 2019

The universe and everything in it roared to life with the Big Bang approximately 13.8 billion years ago. It has continued expanding ever since. While we have a Read more…

By Rob Johnson

AI is the Next Exascale – Rick Stevens on What that Means and Why It’s Important

August 13, 2019

Twelve years ago the Department of Energy (DOE) was just beginning to explore what an exascale computing program might look like and what it might accomplish. Today, DOE is repeating that process for AI, once again starting with science community town halls to gather input and stimulate conversation. The town hall program... Read more…

By Tiffany Trader and John Russell

Cray Wins NNSA-Livermore ‘El Capitan’ Exascale Contract

August 13, 2019

Cray has won the bid to build the first exascale supercomputer for the National Nuclear Security Administration (NNSA) and Lawrence Livermore National Laborator Read more…

By Tiffany Trader

AMD Launches Epyc Rome, First 7nm CPU

August 8, 2019

From a gala event at the Palace of Fine Arts in San Francisco yesterday (Aug. 7), AMD launched its second-generation Epyc Rome x86 chips, based on its 7nm proce Read more…

By Tiffany Trader

Lenovo Drives Single-Socket Servers with AMD Epyc Rome CPUs

August 7, 2019

No summer doldrums here. As part of the AMD Epyc Rome launch event in San Francisco today, Lenovo announced two new single-socket servers, the ThinkSystem SR635 Read more…

By Doug Black

Building Diversity and Broader Engagement in the HPC Community

August 7, 2019

Increasing diversity and inclusion in HPC is a community-building effort. Representation of both issues and individuals matters - the more people see HPC in a w Read more…

By AJ Lauer

Xilinx vs. Intel: FPGA Market Leaders Launch Server Accelerator Cards

August 6, 2019

The two FPGA market leaders, Intel and Xilinx, both announced new accelerator cards this week designed to handle specialized, compute-intensive workloads and un Read more…

By Doug Black

Upcoming NSF Cyberinfrastructure Projects to Support ‘Long-Tail’ Users, AI and Big Data

August 5, 2019

The National Science Foundation is well positioned to support national priorities, as new NSF-funded HPC systems to come online in the upcoming year promise to Read more…

By Ken Chiacchia, Pittsburgh Supercomputing Center/XSEDE

High Performance (Potato) Chips

May 5, 2006

In this article, we focus on how Procter & Gamble is using high performance computing to create some common, everyday supermarket products. Tom Lange, a 27-year veteran of the company, tells us how P&G models products, processes and production systems for the betterment of consumer package goods. Read more…

By Michael Feldman

Supercomputer-Powered AI Tackles a Key Fusion Energy Challenge

August 7, 2019

Fusion energy is the Holy Grail of the energy world: low-radioactivity, low-waste, zero-carbon, high-output nuclear power that can run on hydrogen or lithium. T Read more…

By Oliver Peckham

Cray, AMD to Extend DOE’s Exascale Frontier

May 7, 2019

Cray and AMD are coming back to Oak Ridge National Laboratory to partner on the world’s largest and most expensive supercomputer. The Department of Energy’s Read more…

By Tiffany Trader

Graphene Surprises Again, This Time for Quantum Computing

May 8, 2019

Graphene is fascinating stuff with promise for use in a seeming endless number of applications. This month researchers from the University of Vienna and Institu Read more…

By John Russell

AMD Verifies Its Largest 7nm Chip Design in Ten Hours

June 5, 2019

AMD announced last week that its engineers had successfully executed the first physical verification of its largest 7nm chip design – in just ten hours. The AMD Radeon Instinct Vega20 – which boasts 13.2 billion transistors – was tested using a TSMC-certified Calibre nmDRC software platform from Mentor. Read more…

By Oliver Peckham

TSMC and Samsung Moving to 5nm; Whither Moore’s Law?

June 12, 2019

With reports that Taiwan Semiconductor Manufacturing Co. (TMSC) and Samsung are moving quickly to 5nm manufacturing, it’s a good time to again ponder whither goes the venerable Moore’s law. Shrinking feature size has of course been the primary hallmark of achieving Moore’s law... Read more…

By John Russell

Deep Learning Competitors Stalk Nvidia

May 14, 2019

There is no shortage of processing architectures emerging to accelerate deep learning workloads, with two more options emerging this week to challenge GPU leader Nvidia. First, Intel researchers claimed a new deep learning record for image classification on the ResNet-50 convolutional neural network. Separately, Israeli AI chip startup Hailo.ai... Read more…

By George Leopold

Nvidia Embraces Arm, Declares Intent to Accelerate All CPU Architectures

June 17, 2019

As the Top500 list was being announced at ISC in Frankfurt today with an upgraded petascale Arm supercomputer in the top third of the list, Nvidia announced its Read more…

By Tiffany Trader

Leading Solution Providers

ISC 2019 Virtual Booth Video Tour

CRAY
CRAY
DDN
DDN
DELL EMC
DELL EMC
GOOGLE
GOOGLE
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
VERNE GLOBAL
VERNE GLOBAL

Cray Wins NNSA-Livermore ‘El Capitan’ Exascale Contract

August 13, 2019

Cray has won the bid to build the first exascale supercomputer for the National Nuclear Security Administration (NNSA) and Lawrence Livermore National Laborator Read more…

By Tiffany Trader

Top500 Purely Petaflops; US Maintains Performance Lead

June 17, 2019

With the kick-off of the International Supercomputing Conference (ISC) in Frankfurt this morning, the 53rd Top500 list made its debut, and this one's for petafl Read more…

By Tiffany Trader

A Behind-the-Scenes Look at the Hardware That Powered the Black Hole Image

June 24, 2019

Two months ago, the first-ever image of a black hole took the internet by storm. A team of scientists took years to produce and verify the striking image – an Read more…

By Oliver Peckham

Cray – and the Cray Brand – to Be Positioned at Tip of HPE’s HPC Spear

May 22, 2019

More so than with most acquisitions of this kind, HPE’s purchase of Cray for $1.3 billion, announced last week, seems to have elements of that overused, often Read more…

By Doug Black and Tiffany Trader

AMD Launches Epyc Rome, First 7nm CPU

August 8, 2019

From a gala event at the Palace of Fine Arts in San Francisco yesterday (Aug. 7), AMD launched its second-generation Epyc Rome x86 chips, based on its 7nm proce Read more…

By Tiffany Trader

Chinese Company Sugon Placed on US ‘Entity List’ After Strong Showing at International Supercomputing Conference

June 26, 2019

After more than a decade of advancing its supercomputing prowess, operating the world’s most powerful supercomputer from June 2013 to June 2018, China is keep Read more…

By Tiffany Trader

In Wake of Nvidia-Mellanox: Xilinx to Acquire Solarflare

April 25, 2019

With echoes of Nvidia’s recent acquisition of Mellanox, FPGA maker Xilinx has announced a definitive agreement to acquire Solarflare Communications, provider Read more…

By Doug Black

Qualcomm Invests in RISC-V Startup SiFive

June 7, 2019

Investors are zeroing in on the open standard RISC-V instruction set architecture and the processor intellectual property being developed by a batch of high-flying chip startups. Last fall, Esperanto Technologies announced a $58 million funding round. Read more…

By George Leopold

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