With Supercheck21 Symposium, NERSC Opens International Checkpoint/Restart Dialogue

February 25, 2021

Feb. 25, 2021 — Earlier this month, the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory hosted the First International Symposium on Checkpointing for Supercomputing (SuperCheck21). This free virtual event drew more than 250 participants from around the world.

Organized by NERSC HPC Consultant Zhengji Zhao and User Engagement Group Lead Rebecca Hartman-Baker, in collaboration with Devesh Tiwari and Gene Cooperman at Northeastern University, the symposium showcased the latest research on checkpoint/restart (C/R), sought to motivate the development of usable C/R tools, and boost the adoption of those tools in supercomputing workloads.

“Checkpoint/Restart is like saving your place in a video game. But in our case, we want to ‘checkpoint’ or save scientific computing jobs to resume later, for example, so that when the supercomputer unexpectedly needs to be shut down, the job can pick up where it left off when the system comes back online,” said Hartman-Baker.

According to Zhao, the fault-tolerant computing capability that C/R provides greatly benefits both users and computing centers. For supercomputer users, C/R enables long-running applications and improves queue turnaround. For computing centers, C/R improves system utilization, prepares for unexpected system failures, and provides scheduling flexibility to support diverse workloads with different priorities, for instance, making space for high-priority, real-time workloads by preempting low-priority jobs. She adds that these benefits make C/R critical to many of NERSC’s future plans.

While transparently checkpointing and restarting a huge number of applications at NERSC  at the system level remains a daunting task, Zhao notes that it can be broken into incremental steps by prioritizing top applications,  which account for more than 70% of the computing cycles at NERSC. NERSC is looking into the MPI Agnostic and Network Agnostic (MANA) transparent checkpointing tool, implemented in DMTCP (Distributed MultiThreaded Checkpointing), which is a promising C/R tool to be used on front-edge HPC systems.

Despite the promise of MANA and DMTCP, few high performance computing (HPC) users are applying these tools in real-world scenarios, says Zhao. This disconnect between C/R research and real-world applied use is what inspired the duo to host an international symposium.

“I tried DMTCP for myself about two years ago and found it to be unreliable, at least for the SPAdes genome assembly tool at the time,” said Tony Wildish, Cloud Bioinformatics Lead Architect at the European Bioinformatics Institute who attended the event. “When I heard about the talk on checkpointing SPAdes at SuperCheck21, I was very interested. Twinkle Jain gave an excellent presentation and gave me a pointer to her code. I’ve started experimenting with it and am able to make it work, so we’ll be investigating it more thoroughly now.”

“The checkpointing that most of my users, and even myself, do is fairly rudimentary since our jobs usually have shorter runtimes. So, I saw this symposium as an opportunity to attend a few talks and learn what really challenging checkpointing looks like—I learned that and more,” said Albert Reuther, senior technical staff at the MIT Lincoln Laboratory Supercomputing Center. “I have several sets of users who do computational fluid dynamics, structural dynamics, and electromagnetic simulations. After Supercheck21, I now understand the challenges that those users face when they do a checkpoint. If this event were held again, I would definitely recommend it to them.”

After a successful first symposium, Hartman-Baker and Zhao would like to see this become an annual event where different organizations share the responsibility of hosting.

“Our intention is to build a strong and active C/R community, and we hope that this work is carried onto the next generation of computational scientists. That’s why we included a lot of students and early career researchers in our program committee,” said Hartman-Baker. “To protect research, we want checkpointing to become second nature at NERSC.”

Presentation slides and extended abstracts from the event will be available here: https://ckpt-symposium.lbl.gov/resources

About NERSC and Berkeley Lab

The National Energy Research Scientific Computing Center (NERSC) is a U.S. Department of Energy Office of Science User Facility that serves as the primary high-performance computing center for scientific research sponsored by the Office of Science. Located at Lawrence Berkeley National Laboratory, the NERSC Center serves more than 7,000 scientists at national laboratories and universities researching a wide range of problems in combustion, climate modeling, fusion energy, materials science, physics, chemistry, computational biology, and other disciplines. Berkeley Lab is a DOE national laboratory located in Berkeley, California. It conducts unclassified scientific research and is managed by the University of California for the U.S. Department of Energy. »Learn more about computing sciences at Berkeley Lab.


Source: NERSC

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!

Organizations Partner to Rescue Petabytes of Data from the Arecibo Observatory

April 21, 2021

The Arecibo Observatory in Puerto Rico stood as the world’s largest single-aperture telescope for more than half a century, its grandiosity earning it a turn as a major filming location in the James Bond movie GoldenEy Read more…

MLPerf Issues New Inferencing Results, Adds Power Metrics, Nvidia Wins (Again)

April 21, 2021

MLPerf.org, the young ML benchmarking organization, today issued its third round of inferencing results (MLPerf Inference v1.0) intended to compare how well various systems and accelerators perform inferencing on a suite Read more…

Cerebras Doubles AI Performance with Second-Gen 7nm Wafer Scale Engine

April 20, 2021

Nearly two years since its massive 1.2 trillion transistor Wafer Scale Engine chip debuted at Hot Chips, Cerebras Systems is announcing its second-generation technology (WSE-2), which its says packs twice the performance Read more…

The New Scalability

April 20, 2021

HPC is all about scalability. The most powerful systems. The biggest data sets. The most cores, the most bytes, the most flops, the most bandwidth. HPC scales! Notwithstanding a few recurring arguments over the last twenty years about scaling up versus scaling out, the definition of scalability... Read more…

Supercomputer-Powered Climate Model Makes Startling Sea Level Rise Prediction

April 19, 2021

The climate science community is tasked with striking a difficult balance: inspiring precisely the amount of alarm commensurate to the climate crisis. Make estimates that are too conservative, and the public might not re Read more…

AWS Solution Channel

Research computing with RONIN on AWS

To allow more visibility into and management of Amazon Web Services (AWS) resources and expenses and minimize the cloud skills training required to operate these resources, AWS Partner RONIN created the RONIN research computing platform. Read more…

San Diego Supercomputer Center Opens ‘Expanse’ to Industry Users

April 15, 2021

When San Diego Supercomputer Center (SDSC) at the University of California San Diego was getting ready to deploy its flagship Expanse supercomputer for the large research community it supports, it also sought to optimize Read more…

MLPerf Issues New Inferencing Results, Adds Power Metrics, Nvidia Wins (Again)

April 21, 2021

MLPerf.org, the young ML benchmarking organization, today issued its third round of inferencing results (MLPerf Inference v1.0) intended to compare how well var Read more…

Cerebras Doubles AI Performance with Second-Gen 7nm Wafer Scale Engine

April 20, 2021

Nearly two years since its massive 1.2 trillion transistor Wafer Scale Engine chip debuted at Hot Chips, Cerebras Systems is announcing its second-generation te Read more…

The New Scalability

April 20, 2021

HPC is all about scalability. The most powerful systems. The biggest data sets. The most cores, the most bytes, the most flops, the most bandwidth. HPC scales! Notwithstanding a few recurring arguments over the last twenty years about scaling up versus scaling out, the definition of scalability... Read more…

San Diego Supercomputer Center Opens ‘Expanse’ to Industry Users

April 15, 2021

When San Diego Supercomputer Center (SDSC) at the University of California San Diego was getting ready to deploy its flagship Expanse supercomputer for the larg Read more…

GTC21: Dell Building Cloud Native Supercomputers at U Cambridge and Durham

April 14, 2021

In conjunction with GTC21, Dell Technologies today announced new supercomputers at universities across DiRAC (Distributed Research utilizing Advanced Computing) in the UK with plans to explore use of Nvidia BlueField DPU technology. The University of Cambridge will expand... Read more…

The Role and Potential of CPUs in Deep Learning

April 14, 2021

Deep learning (DL) applications have unique architectural characteristics and efficiency requirements. Hence, the choice of computing system has a profound impa Read more…

GTC21: Nvidia Launches cuQuantum; Dips a Toe in Quantum Computing

April 13, 2021

Yesterday Nvidia officially dipped a toe into quantum computing with the launch of cuQuantum SDK, a development platform for simulating quantum circuits on GPU-accelerated systems. As Nvidia CEO Jensen Huang emphasized in his keynote, Nvidia doesn’t plan to build... Read more…

Nvidia Aims Clara Healthcare at Drug Discovery, Imaging via DGX

April 12, 2021

Nvidia Corp. continues to expand its Clara healthcare platform with the addition of computational drug discovery and medical imaging tools based on its DGX A100 platform, related InfiniBand networking and its AGX developer kit. The Clara partnerships announced during... Read more…

Julia Update: Adoption Keeps Climbing; Is It a Python Challenger?

January 13, 2021

The rapid adoption of Julia, the open source, high level programing language with roots at MIT, shows no sign of slowing according to data from Julialang.org. I Read more…

Intel Launches 10nm ‘Ice Lake’ Datacenter CPU with Up to 40 Cores

April 6, 2021

The wait is over. Today Intel officially launched its 10nm datacenter CPU, the third-generation Intel Xeon Scalable processor, codenamed Ice Lake. With up to 40 Read more…

CERN Is Betting Big on Exascale

April 1, 2021

The European Organization for Nuclear Research (CERN) involves 23 countries, 15,000 researchers, billions of dollars a year, and the biggest machine in the worl Read more…

Programming the Soon-to-Be World’s Fastest Supercomputer, Frontier

January 5, 2021

What’s it like designing an app for the world’s fastest supercomputer, set to come online in the United States in 2021? The University of Delaware’s Sunita Chandrasekaran is leading an elite international team in just that task. Chandrasekaran, assistant professor of computer and information sciences, recently was named... Read more…

HPE Launches Storage Line Loaded with IBM’s Spectrum Scale File System

April 6, 2021

HPE today launched a new family of storage solutions bundled with IBM’s Spectrum Scale Erasure Code Edition parallel file system (description below) and featu Read more…

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…

Saudi Aramco Unveils Dammam 7, Its New Top Ten Supercomputer

January 21, 2021

By revenue, oil and gas giant Saudi Aramco is one of the largest companies in the world, and it has historically employed commensurate amounts of supercomputing Read more…

Quantum Computer Start-up IonQ Plans IPO via SPAC

March 8, 2021

IonQ, a Maryland-based quantum computing start-up working with ion trap technology, plans to go public via a Special Purpose Acquisition Company (SPAC) merger a Read more…

Leading Solution Providers

Contributors

Can Deep Learning Replace Numerical Weather Prediction?

March 3, 2021

Numerical weather prediction (NWP) is a mainstay of supercomputing. Some of the first applications of the first supercomputers dealt with climate modeling, and Read more…

Livermore’s El Capitan Supercomputer to Debut HPE ‘Rabbit’ Near Node Local Storage

February 18, 2021

A near node local storage innovation called Rabbit factored heavily into Lawrence Livermore National Laboratory’s decision to select Cray’s proposal for its CORAL-2 machine, the lab’s first exascale-class supercomputer, El Capitan. Details of this new storage technology were revealed... Read more…

New Deep Learning Algorithm Solves Rubik’s Cube

July 25, 2018

Solving (and attempting to solve) Rubik’s Cube has delighted millions of puzzle lovers since 1974 when the cube was invented by Hungarian sculptor and archite Read more…

African Supercomputing Center Inaugurates ‘Toubkal,’ Most Powerful Supercomputer on the Continent

February 25, 2021

Historically, Africa hasn’t exactly been synonymous with supercomputing. There are only a handful of supercomputers on the continent, with few ranking on the Read more…

AMD Launches Epyc ‘Milan’ with 19 SKUs for HPC, Enterprise and Hyperscale

March 15, 2021

At a virtual launch event held today (Monday), AMD revealed its third-generation Epyc “Milan” CPU lineup: a set of 19 SKUs -- including the flagship 64-core, 280-watt 7763 part --  aimed at HPC, enterprise and cloud workloads. Notably, the third-gen Epyc Milan chips achieve 19 percent... Read more…

The History of Supercomputing vs. COVID-19

March 9, 2021

The COVID-19 pandemic poses a greater challenge to the high-performance computing community than any before. HPCwire's coverage of the supercomputing response t Read more…

HPE Names Justin Hotard New HPC Chief as Pete Ungaro Departs

March 2, 2021

HPE CEO Antonio Neri announced today (March 2, 2021) the appointment of Justin Hotard as general manager of HPC, mission critical solutions and labs, effective Read more…

GTC21: Nvidia Launches cuQuantum; Dips a Toe in Quantum Computing

April 13, 2021

Yesterday Nvidia officially dipped a toe into quantum computing with the launch of cuQuantum SDK, a development platform for simulating quantum circuits on GPU-accelerated systems. As Nvidia CEO Jensen Huang emphasized in his keynote, Nvidia doesn’t plan to build... Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire