On the Spack Track @SC19

By Elizabeth Leake

December 5, 2019

At the annual supercomputing conference, SC19 in Denver, Colorado, there were Spack events each day of the conference. As a reflection of its grassroots heritage, nine sessions were planned by more than a dozen thought leaders from seven organizations, including three U.S. national Department of Energy (DOE) laboratories and Sylabs, the company behind Singularity. Thirteen thousand six hundred conference attendees had the chance to learn about Spack from two meet-and-greets, three birds-of-a-feather (BoF) meetings, three papers, and more.

What is Spack?

Spack is an open-source scientific software package manager for high-performance computing (HPC) environments, MacOS and Linux platforms. It simplifies an otherwise tedious and time-consuming task. There are currently more than 3,600 packages in the Spack library; with 2,300 active users and over 480 contributors from national labs, academia and industry, the number of packages is constantly growing and being improved with community input.

From the Spack website, spack.io, “Packages can be built with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine. It isn’t tied to a particular language; a software stack can be built in Python or R, link to libraries written in C, C++, or Fortran, easily swap compilers, and target specific microarchitectures. Spack can be used to install without root in a home directory, to manage shared installations and modules, or to build combinatorial versions of software for testing.” Packages are templated so users can easily tune for the host environment.

Ninety attended the November 21 BoF led by Todd Gamblin (Senior Principal Member of Technical Staff at Lawrence Livermore National Laboratory (LLNL), middle); Adam Stewart (UIUC); Massimiliano Culpo (Sylabs, Inc.); Greg Becker (LLNL, right); and Peter Scheibel (LLNL, left).

Gamblin leads the Spack development team at LLNL with fellow computer scientists Becker, Scheibel, Tamara Dahlgren, Gregory Lee, and Matt Legendre. Co-developers are from Argonne National Laboratory; Columbia University; École polytechnique fédérale de Lausanne; Fermi National Accelerator Laboratory, Iowa State University; Kitware, Inc.; NASA Goddard Institute for Space Studies, the Center for Climate Systems Research; the National Energy Research Scientific Computing Center; Perimeter Institute; the University of Hamburg, the University of Illinois at Urbana-Champaign; and the University of Iowa.

With widespread adoption among DOE labs, it’s not surprising that the high-energy physics community based at Fermilab in the U.S. and at CERN (European Organization for Nuclear Research) in Switzerland is replacing a longstanding solution with end-to-end tooling built around Spack.

The BoF incorporated a real-time audience polling tool called Glisser. Participant questions and answers populated pie charts and word clouds, which helped to identify development priorities for the future.

When asked what people loved about Spack, most cited convenience in dealing with dependencies. DOE shared the following victories:

  • At LLNL, Spack was used to automate the radiation hydrodynamics code, ARES, with 40 dependency libraries on a dozen compilers running on Blue Gene/Q and commodity Linux clusters. Porting time on a new platform was reduced from two weeks to three hours.
  • At Oak Ridge National Laboratory, Spack reduced deployment time on Summit, the world’s fastest publicly-ranked supercomputer, from two weeks to twelve hours. Summit’s stack of 1,300 packages can be built overnight.
  • DOE’s Exascale Computing Project (ECP) is tasked with ensuring exascale-readiness for the U.S. lab complex. Its software stack is large and complex; a brand-new class of 90 applications is managed with Spack so that users will be able to easily incorporate them in many different environments. Security features were added to the open-source GitLab product that integrate with each center’s identity management and schedulers, such as SLURM and LSF.
  • The Spack development team is in the process of democratizing a pipeline of software management across six DOE labs; automated package builds with both public and private repositories will work with dozens of systems.

Spack is used with Germany’s SuperMUC-NG at the Leibniz Supercomputing Centre of the Bavarian Academy of Sciences (LRZ). Gerald Mathias, Deputy Leader of the LRZ Application Group, explained that their interest in Spack emerged about two years ago when they were undergoing the procurement process for SuperMUC-NG, LRZ’s new 26.9 petaflops HPC system. On the predecessor system, SuperMUC, they managed the HPC software stack for users individually for each packet. Over the years, the stack had grown so large that they realized it wouldn’t be feasible to continue the practice with the larger system. That’s when they began to port their stack into Spack.

In late 2018, LRZ deployed their beta release of a Spack stack on their heterogeneous Linux cluster which serves local Munich universities. At the same time, they were working on the deployment and acceptance phase of SuperMUC-NG where it was the primary software stack at the start of user operations in August 2019. “Currently, our Spack-managed stack yields about 110 packages which supply some 220 modules to our users,” said Mathias. “Step-by-step, we continue to include more packages, particularly custom software, commercial software and core software-like compilers and MPI libraries,” he added.

Gerald Mathias, LRZ

For the future, they intend to push hard to keep pace with Spack’s rapid development. A key target is to provide a preconfigured Spack instance in user spaces. This will allow users to configure and install their own software, individually, but based on the common software stack provided by LRZ. “Furthermore, the definition of ‘environments’ seems very promising to compose easy-to-use software stacks for different scientific tasks and domains,” Mathias added.

While the majority of use cases represent X86 CPU/GPU environments, the Japanese Flagship Supercomputer Project being conducted by RIKEN, uses Spack to develop packages for their Arm (A64FX) system, Fugaku (formerly Post-K).

“Fugaku is optimized for large scale HPC and AI workflows; for this, together with our industry partner Fujitsu, we developed an HPC optimized Arm chip A64FX, that is three times as fast, and three times more power efficient than any other CPUs, as acknowledged by recent Green500 and other benchmarks. A64FX machines will be commercialized not only by Fujitsu but also Cray/HPE,” said RIKEN Center for Computational Science Director Satoshi Matsuoka (above photo, center). A64FX complies with Arm V8 and server standards; and Fugaku’s software stack is built on top of Red Hat Enterprise Linux. RIKEN and Fujitsu collaborate closely with the Spack development team to fix issues associated with aarch64; Arm 64-bit builds. Being one of the first exascale or near-exascale machines, both hardware and software must scale to an unprecedented magnitude of more than 150,000 nodes. Largely due to such effort centered around Spack, Matsuoka expects that everything running on current Arm and X86 clusters will ultimately run on Fugaku and other A64FX machines, but much, much faster.

According to Matsuoka, Fugaku’s first six racks will arrive at RIKEN this week (December 3, 2019), and by summer 2020, more than 400 racks will be in place. Early adopters will use the system this winter, and once performance benchmark are satisfied in December 2020, the system will go into full production in early 2021.

Glenn Johnson, UI

But not all Spack contributors work at large laboratories with massive systems; in fact, the largest number of contributors work with small to mid-sized clusters in academic research computing environments. HPC Architect Glenn Johnson (University of Iowa) was recognized as a feature contributor on Spack’s DOE R&D 100 Award (Software & Services). He is using Spack on Iowa’s Argon system that features 15,000 cores and 250 GPUs.

What motivates Johnson to contribute? He said, “Building and distributing scientific software applications is very challenging and becoming more so over time,” said Johnson. “Spack provides a tool, and a community, to develop best practices and standards for building and distributing scientific software, while still allowing for site variability. With Spack, as a tool, it is possible to benefit from the work of others while Spack, as a community, provides the opportunity to contribute back and realize the satisfaction that comes from having others benefit from your work,” he added.

As for Spack’s roadmap, DOE labs are leading the effort to detect and label installs for microarchitectures (Skylake, Zen, etc.). They’re optimizing packages for both cloud and static HPC environments and planning to focus on container integration; multi-mode, parallel builds; and better external package detection. They’re also developing a prototype for a new concretizer. In 2020, they will launch a multi-stage container builds that automatically exclude build dependencies from artifacts.

When asked if Spack is sustainable, Gamblin said that the DOE Advanced Simulation and Computing (ASC) program and Exascale Computing Project are funding a strong core team of developers, and are fully committed. The collaboration with Sylabs, which has a user base of 2.5 million developers worldwide, will help establish an even broader base of adoption.

A National Science Foundation/DOE tutorial will soon be added to their website: spack.io.

Photos by Leake, LLNL, and Fumikazu KONISHI. 

About the Author

HPCwire Contributing Editor Elizabeth Leake is a consultant, correspondent and advocate who serves the global high performance computing (HPC) and data science industries. In 2012, she founded STEM-Trek, a global, grassroots nonprofit organization that supports workforce development opportunities for science, technology, engineering and mathematics (STEM) scholars from underserved regions and underrepresented groups.

As a program director, Leake has mentored hundreds of early-career professionals who are breaking cultural barriers in an effort to accelerate scientific and engineering discoveries. Her multinational programs have specific themes that resonate with global stakeholders, such as food security data science, blockchain for social good, cybersecurity/risk mitigation, and more. As a conference blogger and communicator, her work drew recognition when STEM-Trek received the 2016 and 2017 HPCwire Editors’ Choice Awards for Workforce Diversity Leadership.

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!

NIST/Xanadu Researchers Report Photonic Quantum Computing Advance

March 3, 2021

Researchers from the National Institute of Standards and Technology (NIST) and Xanadu, a young Canada-based quantum computing company, have reported developing a full-stack, photonic quantum computer able to carry out th Read more…

By John Russell

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 even to this day, the largest climate models are heavily con Read more…

By Oliver Peckham

Deloitte Outfits New AI Computing Center with Nvidia DGX Gear

March 3, 2021

With AI use continuing to grow in adoption throughout enterprise IT, Deloitte is creating a new Deloitte Center for AI Computing to advise its customers, explain the technology and help them use it in their ongoing busin Read more…

By Todd R. Weiss

HPE Names Justin Hotard New HPC Chief as Pete Ungaro Departs

March 2, 2021

HPE CEO Antonio Neri announced today (March 2, 2020) the appointment of Justin Hotard as general manager of HPC, mission critical solutions and labs, effective immediately. Hotard replaces long-time Cray exec Pete Ungaro Read more…

By Tiffany Trader

ORNL’s Jeffrey Vetter on How IRIS Runtime will Help Deal with Extreme Heterogeneity

March 2, 2021

Jeffery Vetter is a familiar figure in HPC. Last year he became one of the new section heads in a reorganization at Oak Ridge National Laboratory. He had been founding director of ORNL's Future Technologies Group which i Read more…

By John Russell

AWS Solution Channel

Moderna Accelerates COVID-19 Vaccine Development on AWS

Marcello Damiani, Chief Digital and Operational Excellence Officer at Moderna, joins Todd Weatherby, Vice President of AWS Professional Services Worldwide, for a discussion on developing Moderna’s COVID-19 vaccine, scaling systems to enable global distribution, and leveraging cloud technologies to accelerate processes. Read more…

HPC Career Notes: March 2021 Edition

March 1, 2021

In this monthly feature, we’ll keep you up-to-date on the latest career developments for individuals in the high-performance computing community. Whether it’s a promotion, new company hire, or even an accolade, we’ Read more…

By Mariana Iriarte

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…

By Oliver Peckham

HPE Names Justin Hotard New HPC Chief as Pete Ungaro Departs

March 2, 2021

HPE CEO Antonio Neri announced today (March 2, 2020) the appointment of Justin Hotard as general manager of HPC, mission critical solutions and labs, effective Read more…

By Tiffany Trader

ORNL’s Jeffrey Vetter on How IRIS Runtime will Help Deal with Extreme Heterogeneity

March 2, 2021

Jeffery Vetter is a familiar figure in HPC. Last year he became one of the new section heads in a reorganization at Oak Ridge National Laboratory. He had been f Read more…

By John Russell

HPC Career Notes: March 2021 Edition

March 1, 2021

In this monthly feature, we’ll keep you up-to-date on the latest career developments for individuals in the high-performance computing community. Whether it Read more…

By Mariana Iriarte

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…

By Oliver Peckham

Japan to Debut Integrated Fujitsu HPC/AI Supercomputer This Spring

February 25, 2021

The integrated Fujitsu HPC/AI Supercomputer, Wisteria, is coming to Japan this spring. The University of Tokyo is preparing to deploy a heterogeneous computing Read more…

By Tiffany Trader

Xilinx Launches Alveo SN1000 SmartNIC

February 24, 2021

FPGA vendor Xilinx has debuted its latest SmartNIC model, the Alveo SN1000, with integrated “composability” features that allow enterprise users to add their own custom networking functions to supplement its built-in networking. By providing deep flexibility... Read more…

By Todd R. Weiss

ASF Keynotes Showcase How HPC and Big Data Have Pervaded the Pandemic

February 24, 2021

Last Thursday, a range of experts joined the Advanced Scale Forum (ASF) in a rapid-fire roundtable to discuss how advanced technologies have transformed the way humanity responded to the COVID-19 pandemic in indelible ways. The roundtable, held near the one-year mark of the first... Read more…

By Oliver Peckham

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…

By John Russell

Esperanto Unveils ML Chip with Nearly 1,100 RISC-V Cores

December 8, 2020

At the RISC-V Summit today, Art Swift, CEO of Esperanto Technologies, announced a new, RISC-V based chip aimed at machine learning and containing nearly 1,100 low-power cores based on the open-source RISC-V architecture. Esperanto Technologies, headquartered in... Read more…

By Oliver Peckham

Azure Scaled to Record 86,400 Cores for Molecular Dynamics

November 20, 2020

A new record for HPC scaling on the public cloud has been achieved on Microsoft Azure. Led by Dr. Jer-Ming Chia, the cloud provider partnered with the Beckman I Read more…

By Oliver Peckham

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…

By Tracey Bryant

NICS Unleashes ‘Kraken’ Supercomputer

April 4, 2008

A Cray XT4 supercomputer, dubbed Kraken, is scheduled to come online in mid-summer at the National Institute for Computational Sciences (NICS). The soon-to-be petascale system, and the resulting NICS organization, are the result of an NSF Track II award of $65 million to the University of Tennessee and its partners to provide next-generation supercomputing for the nation's science community. 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…

By Doug Black

Top500: Fugaku Keeps Crown, Nvidia’s Selene Climbs to #5

November 16, 2020

With the publication of the 56th Top500 list today from SC20's virtual proceedings, Japan's Fugaku supercomputer – now fully deployed – notches another win, Read more…

By Tiffany Trader

Gordon Bell Special Prize Goes to Massive SARS-CoV-2 Simulations

November 19, 2020

2020 has proven a harrowing year – but it has produced remarkable heroes. To that end, this year, the Association for Computing Machinery (ACM) introduced the Read more…

By Oliver Peckham

Leading Solution Providers

Contributors

Texas A&M Announces Flagship ‘Grace’ Supercomputer

November 9, 2020

Texas A&M University has announced its next flagship system: Grace. The new supercomputer, named for legendary programming pioneer Grace Hopper, is replacing the Ada system (itself named for mathematician Ada Lovelace) as the primary workhorse for Texas A&M’s High Performance Research Computing (HPRC). Read more…

By Oliver Peckham

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…

By Oliver Peckham

Intel Xe-HP GPU Deployed for Aurora Exascale Development

November 17, 2020

At SC20, Intel announced that it is making its Xe-HP high performance discrete GPUs available to early access developers. Notably, the new chips have been deplo Read more…

By Tiffany Trader

Intel Teases Ice Lake-SP, Shows Competitive Benchmarking

November 17, 2020

At SC20 this week, Intel teased its forthcoming third-generation Xeon "Ice Lake-SP" server processor, claiming competitive benchmarking results against AMD's second-generation Epyc "Rome" processor. Ice Lake-SP, Intel's first server processor with 10nm technology... Read more…

By Tiffany Trader

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…

By John Russell

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…

By Tiffany Trader

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…

By Oliver Peckham

It’s Fugaku vs. COVID-19: How the World’s Top Supercomputer Is Shaping Our New Normal

November 9, 2020

Fugaku is currently the most powerful publicly ranked supercomputer in the world – but we weren’t supposed to have it yet. The supercomputer, situated at Japan’s Riken scientific research institute, was scheduled to come online in 2021. When the pandemic struck... Read more…

By Oliver Peckham

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire