CHAI and RAJA provide a foundation on which to build portable code. CARE expands that functionality, adding new features such as loop fusion capability, a portable interface for many numerical algorithms, and additional data structures. It provides all the basics for anyone wanting to write portable code.
spdlayers provides symmetric positive definite (SPD) enforcement layers for PyTorch. Examples, an API, and documentation are included in the repo.
MFEM Team Hosts First Community Workshop
November 12, 2021 (event-report) (multimedia)
The MFEM team held the first annual MFEM Community Workshop on October 20, 2021. MFEM, which stands for Modular Finite Element Methods, is an open source C++ software library that provides high-order mathematical algorithms for large-scale scientific simulations. The project’s discretization methods enable HPC systems to run these simulations more efficiently. More than 150 researchers from dozens of organizations and countries attended the one-day virtual workshop organized by Aaron Fisher, Tzanio Kolev, Will Pazner, and Mark Stowell. According to the registration survey, more than half of the participants were new users. An article about the workshop is available on LLNL’s Computing website, and links to videos of the presenters can be found at the MFEM website.
libROM 1.0.0 Released
November 12, 2021 (release)
libROM is lightweight, scalable C++ library for data-driven physical simulation methods from the intrusive projection-based reduced order models to non-intrusive black-box approaches. The first official release adds the capability to create a sample mesh and relevant DOF maps for samples in an arbitrary number of finite element spaces.
Pytaridx is a Python interface for reading and appending tar files, while keeping a fast index for finding and reading files in the archive. This interface has been successfully used to store and manage over one billion files in one of the Pilot-2 simulation campaigns.
CCT 1.0.13 Released
November 11, 2021 (release)
The Coda Calibration Tool (CCT) calculates reliable moment magnitudes for small- to moderate-sized seismic events. This release refactors the spectral plot displays for site and measurement tabs, adds group velocity lines to coda waveform plots, and more.
Spack is a flexible, configurable, Python-based, and open-source HPC package manager. Spack automates the installation and fine-tuning of simulations and libraries, operating on a wide variety of HPC platforms and enabling users to build many code configurations. Version 0.17.0 includes:
the new default concretizer default
existing package reuse
improvements to versioning, caching, and error messaging
Caliper is a program instrumentation and performance measurement framework. It is designed as a performance analysis toolbox in a library, allowing one to bake performance analysis capabilities directly into applications and activate them at runtime. The latest release includes native Windows support, initial support for Variorum, updated report configs, and more.
DataRaceBench is a benchmark suite designed to systematically and quantitatively evaluate the effectiveness of data race detection tools. It includes a set of microbenchmarks with and without data races. Parallelism is represented by OpenMP directives. This version adds data race ground truth encoding into all microbenchmarks, new C/C++ microbenchmarks and Fortran microbenchmarks, new high-precision evaluation scripts, and more.
The renowned worldwide competition announced the winners of the 2021 R&D 100 Awards, among them LLNL’s Flux workload management framework in the Software/Services category. Watch the Flux video to learn how it enables modern supercomputing workflows.
Celebrate Exascale Day 2021
October 18, 2021 (event) (multimedia)
Exascale computing will transform the ability to tackle some of the world’s most important challenge. The Exascale Computing Project (ECP) celebrates this new era of scientific discovery with the now-annual Exascale Day on October 18, or “10^18” to represent the exascale threshold of floating-point operations per second. This virtual event runs all week and provides multimedia and articles that educate explain the impact areas of exascale computing from the Department of Energy national laboratories (including LLNL), HPC manufacturers, and universities and industrial organizations. Much of the ECP’s software stack is open source.
Variorum is a platform-agnostic software library exposing monitor and control interfaces for several features in hardware architectures from IBM, ARM, and NVIDIA. In a two-part lecture series, the Variorum team demonstrates everything necessary to start using Variorum to write portable power management code. These videos were recorded as part of the Exascale Computing Project’s lecture series.
The Scalable Checkpoint/Restart (SCR) library enables MPI applications to utilize distributed storage on Linux clusters to attain high file I/O bandwidth for checkpointing, restarting, and writing large datasets. The second 3.0 release candidate includes:
added support for multiple outstanding asynchronous flushes
Reduced order models (ROMs) combine data and underlying first principles to accelerate physical simulations, reducing computational complexity without losing accuracy. The C++ software library called libROM provides data-driven physical simulation methods from intrusive projection-based ROMs to non-intrusive black-box approaches. The project has a new website that contains documentation and examples. Additionally, computational scientist Youngsoo Choi has recorded three user tutorials, with plans to record more in the future:
YGM is a general-purpose, pseudo-asynchronous communication library built on top of MPI in C++. The repo’s utility is provided through its mailbox abstractions, which are used for point-to-point and broadcast communications. When using YGM, individual cores queue messages into a mailbox instead of directly sending them.
SUNDIALS 5.8.0 Released
September 30, 2021 (release)
SUNDIALS is a SUite of Nonlinear and DIfferential/ALgebraic equation Solvers. This release includes
HiOp is an optimization solver for solving certain mathematical optimization problems expressed as nonlinear programming problems. This lightweight HPC solver leverages application’s existing data parallelism to parallelize the optimization iterations by using specialized linear algebra kernels. This version includes
interface update for running mixed dense-sparse problems in the device memory space
interface for PARDISO linear solver
porting of sparse linear algebra kernels to device
Spack is a flexible, configurable, Python-based, and open-source HPC package manager. Spack automates the installation and fine-tuning of simulations and libraries, operating on a wide variety of HPC platforms and enabling users to build many code configurations. Version 0.16.3 includes
LANL led with LLNL contributors, Charliecloud provides user-defined software stacks for HPC centers. It uses Linux user namespaces to run containers with no privileged operations or daemons and minimal configuration changes on center resources. Version 0.25 bundles the Python module Lark (which no longer needs to be installed externally), updates how SSH data is handled in the build, and includes several other fixes and improvements.
The Coda Calibration Tool (CCT) calculates reliable moment magnitudes for small- to moderate-sized seismic events. This release adds two significant features including energy calculations (BETA) and a new data table filter feature. The current beta code integrates theoretical spectra to determine empirically the necessary integration constant to give the correct energy value. In the final version of the code, this will be tied to the analytical form of the seismic energy.
The VisIt visualization and analysis tool has supported scalable, high-quality evaluation of simulation results for over 20 years. A Research Highlight article in the latest issue of Science & Technology Review describes the software’s history and importance. Eric Brugger, who has worked on VisIt since its inception, states, “Our software is used broadly throughout the Department of Energy complex, at universities, and at other supercomputing centers. It’s running on some of the world’s most powerful machines. VisIt strikes a balance between application support and capability development that appeals to the larger HPC community.” Read “Visualization Software Stands the Test of Time” on the S&TR website.
FMS 0.2 Released
September 10, 2021 (release)
As part of the Exascale Computing Project’sCEED software suite, FMS provides a high-order Field and Mesh Specification interface that allows a wide variety of applications and visualization tools to represent unstructured high-order meshes with general high-order finite element fields defined on them. FMS is intended as a lightweight format and API that can represent general finite elements within a common, easy to use framework. This includes high-order solutions and meshes as well as non-standard finite elements, such as Nedelec and Raviart-Thomas elements. Version 0.2 includes:
Lightweight API to represent general finite element meshes + fields
Quandary provides optimal control for open quantum systems via an optimization solver. The underlying quantum dynamics model open quantum systems, using the Lindblad master equation to evolve a density matrix in time. The control problem aims to find control pulses that drive the system to a desired target state. The README contains installation information as documentation is under development.
New Repo: Devil Ray
September 09, 2021 (new-repo)
Devil Ray is a visualization and analysis library for high-order element meshes targeting modern HPC architectures. It runs on both GPUs and many-core CPUs and leverages MPI for distributed-memory computations. The repo supports meshes consisting of hexs, quads, tets, and triangles of arbitrary polynomial order, with fast paths for constant, linear, quadratic, and cubic elements. Originally architected as a ray tracer, Devil Ray is capable of rendering volumes and surfaces and has been demonstrated running concurrently on over 4,000 GPUs.
SC21: Video Previews Hatchet Tutorial
September 08, 2021 (event) (multimedia) (story)
The Python-based library Hatchet will be part of a new Supercomputing 2021 (SC21) tutorial on performance tools. Hatchet allows Pandas dataframes to be indexed by structured tree and graph data and is intended for analyzing hierarchical performance data. The development team has released a video titled “User-Centric Automated Performance Analysis of Hybrid Parallel Programs” to preview the tutorial and give attendees an idea of what to expect. SC21 will take place in a hybrid format on November 14–19.
Vanessa Sochat Presents Keynote at SeptembRSE
September 06, 2021 (event-report) (multimedia)
LLNL computer scientist and open source advocate Vanessa Sochat delivered a keynote presentation titled “The Stories We Tell Ourselves” at the 5th Conference of Research Software Engineers on September 6. Sochat’s work includes developing container technologies, supporting tools, and fostering open source communities. She founded and hosts the Research Software Engineer Stories podcast and is an active member of the U.S. Research Software Engineer Association.
RAJAPerf 0.11.0 Released
September 01, 2021 (release)
The RAJA performance suite (RAJAPerf) is designed to explore performance of loop-based computational kernels found in HPC applications. Specifically, it is used to assess, monitor, and compare runtime performance of kernels implemented using RAJA and variants implemented using standard or vendor-supported parallel programming models directly. The v0.11.0 release adds new kernels, features, and runtime options.
mappgene is a SARS-CoV-2 genomic sequence analysis pipeline designed for parallel HPC. It wraps V-pipe and iVar with a collection of useful scripts for deployment in almost any Linux environment. Requires Python 3.7+ and Singularity.
GLVis 4.1 Released
August 31, 2021 (release)
GLVis is a lightweight OpenGL tool for accurate and flexible finite element visualization. Version 4.1 includes:
Interactive inline plots in Python and C++ Jupyter Notebooks
Support for native build on Windows and native Mac application bundle
At the AWS/Arm Cloud Hackathon, LLNL’s Todd Gamblin and Greg Becker discussed the essential skills and concepts needed to understand how to create and deploy Spack recipes to build scientific codes. The Hackathon was held July 12-16 and aimed to assemble the HPC community around a common goal of beginning the porting, testing, and tuning processes for dozens of codes to use Arm-based processors. The video runs 31:42.
Flux Software Selected Among R&D 100 Award Finalists
August 26, 2021 (story)
The annual R&D 100 Awards finalists have been announced. The Flux workload management software framework is a finalist in the Software/Services category. Winners will be announced later this fall. Watch the Flux video to learn how it enables modern supercomputing workflows.
Summer Hackathon Tradition Continues Virtually
August 23, 2021 (event-report)
Each new season brings another hackathon, and LLNL’s summer event took place on August 12–13. The event was sponsored by the Center for Applied Scientific Computing (CASC) and Livermore Computing (LC) divisions and organized by Stephanie Brink (CASC), Tammy Dahlgren (LC), and Stephen Herbein (LC). Additionally, Computing’s summer interns were encouraged to participate in the event. Ian Lee, open source advocate and Computing’s Alternate Organizational Information System Security Officer, kicked off the hackathon with a presentation titled “When a Hackathon Project Ends…Does It Make a Sound?” He gave participants a larger picture beyond the event’s concentrated 24 hours, detailing how he has shepherded hackathon projects into real-world applications with benefits to a wide group of users and developers across the Lab.
Introducing the Spackpedia
August 22, 2021 (story)
In a new twist on documentation, the Spack package manager team created the Spack Encyclopedia, or Spackpedia, to help users understand frequently used (and sometimes funny) terms. Click on a term to see a quick definition with an option to read more. Click “read more” for additional details about the term, an example of its usage, a link to Spack documentation, and related terms. Spackpedia is a separate repo within the Spack organization on GitHub, and contributions are welcome.
Umpire 6.0.0 Released
August 19, 2021 (release)
Umpire is a resource management library that allows the discovery, provision, and management of memory on next-generation architectures. v5.0.0 includes initial support for IPC Shared Memory, added support for named allocations, refactored pool coalesce heuristic API, updated allocations tracking, and much more.
RAJA is a software abstraction that systematically encapsulates platform-specific code to enable applications to be portable across diverse hardware architectures without major source code disruption. The v.0.14.0 release includes
CHAI is a C++ library providing an array object that can be used transparently in multiple memory spaces. CHAI can be used standalone, but is best when paired with the RAJA library, which has built-in CHAI integration that takes care of everything. This release bumps RAJA to v0.14.0, Umpire to v6.0.0, and BLT to v0.4.1.
The goal of the workshop is to foster collaboration among all MFEM users and developers, share the latest MFEM features with the broader community, deepen application engagements, and solicit feedback to guide future development directions for the project.
Additionally, we are looking for users to present the work they are doing utilizing MFEM. If you are interested in presenting please indicate that in the registration form.
New Repo: ISO-DART
August 17, 2021 (new-repo)
ISO-DART, which stands for Independent System Operator Data Automated Request Tool, allows the user to create multiple automated requests of ISO data from California, Midcontinent, and New York electric power transmission system operators. The repo also includes a weather module and solar data.
CEED held its fifth annual meeting (CEED5AM) virtually on August 3-4 . The goals of the meeting were to report on recent progress; deepen existing and establish new connections with ECP hardware vendors, ECP software technologies projects, and other collaborators; plan project activities; and work as a group to make technical progress. Presentations covered activities related to GPU support and GPU-enabled solvers, high-order methods and finite elements, software products including the AmgX linear solver library and libCEED algebraic library, benchmarking and optimization, various types of simulations enabled by CEED development, and much more.
Attendance included 97 researchers from 36 organizations:
8 national labs
Research in Traumatic Brain Injury Aided by Open Source Workflow
August 03, 2021 (story)
Traumatic brain injuries (TBIs) affect millions of people each year, whether from car accidents, sports injuries, or on the battlefield. LLNL is part of the Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) project, which aims to uncover fundamental new insights into how to diagnose and treat TBI as well as help deliver precision medicine to patients using advanced supercomputing and machine learning technologies. To this end, researchers have developed the open source MaPPeRTrac: the Massively Parallel, Portable, and Reproducible Tractography brain tractography workflow. MaPPeRTrac incorporates novel technologies to simplify and accelerate neuroimaging research. Read more about LLNL’s efforts to address TBI.
MFEM 4.3 Released
August 01, 2021 (release)
MFEM is a lightweight, general, scalable C++ library for finite element methods. It enables high-performance scalable finite element discretization research and application development on a wide variety of platforms, from laptops to supercomputers. The v4.3 release includes many improvements and new features, such as:
Variable order spaces, serial p- and hp-refinement
Low order refined discretizations, solvers and transfer
MuyGPys is a Gaussian process estimation method that affords fast hyperparameter optimization by way of performing leave-one-out cross-validation. MuyGPys achieves best-in-class speed and scalability by limiting inference to the information contained in k nearest neighborhoods for prediction locations for both hyperparameter optimization and tuning. Documentation and other resources are available at the MuyGPys Read the Docs site.
ECP Annual Meeting Videos Now Available: Spack, CEED, Flux
July 29, 2021 (event-report) (multimedia)
The Exascale Computing Project, a joint effort between the DOE Office of Science and NNSA, brings together several national laboratories to address many hardware, software, and application challenges inherent in the organizations’ scientific and national security missions. The ECP’s annual meeting was held virtually this year on April 12-16. Several sessions are available in a YouTube playlist. LLNL’s highlights feature open source projects that are crucial to the ECP’s collaborative goals:
Spack BoF (runtime 1:00:40): This “birds of a feather” gathering details major developments in Spack releases, collaborative work with the E4S team, roadmap for future development, and results from a community survey.
Using Spack to Accelerate Developer Workflows (runtime 6:14:42): This tutorial focuses on developer workflows, covering covered installation, package authorship, Spack’s dependency model, and Spack environments and configuration. Participants can learn new skills in this tutorial, even if they have participated in Spack tutorials in the past.
Characterizing Performance Improvements in the Center for Efficient Exascale Discretizations (runtime 1:00:04, CEED section begins at 25:05): Speakers from ECP Application Development areas talked about how they set figures of merit, determined key performance parameters, and calculated efficiency of codes. CEED is a co-design center led by LLNL and focusing on discretization algorithms that better exploit the hardware and deliver a significant performance gain over conventional low-order methods. The video concludes with a panel discussion with the speakers.
Using Flux to Overcome Scheduling Challenges of Exascale Workflows (runtime 2:16:48): The Flux team provides an in-depth tutorial that demonstrates how Flux is used in challenging HPC workflows, how to unify Flux with other scheduling and resource management software tools, and how Flux’s job and resource model works, along with hands-on uses cases and testing.
Dev Day Makes the Most of Virtual Format
July 29, 2021 (event-report)
Held virtually on July 15, our fifth annual Developer Day was a success. The morning session included lightning talks, a security-focused technical deep dive, and “quick takes” on remote-development resources. The afternoon session provided presentations about career paths and the Lab’s diversity and inclusion goals, capped by a career development panel discussion co-sponsored by the Data Science Institute.
Spack Tutorial from PEARC'21
July 19, 2021 (event-report)
The Spack team presented a tutorial at the 2021 Practice & Experience in Advanced Research Computing (PEARC’21) conference on July 19. You can view go through the tutorial yourself.
New Repo: Axom
June 17, 2021 (new-repo)
Axom provides robust, flexible software infrastructure for the development of multi-physics applications and computational tools. Supported by the Advanced Simulation and Computing program at LLNL and part of the Lab’s RADIUSS project, Axom is a library of robust “building block” software components that provide foundational capabilities needed for production simulation codes. The Axom team focuses on developing software infrastructure components that can be shared by HPC applications running on diverse computing platforms. Read more about Axom on the LLNL Computing website.
RAJA Portability Suite Enables Performance Portable CPU and GPU HPC Applications
June 14, 2021 (story)
A growing number of scientific computing applications must deliver high performance on central and graphics processing unit (CPU and GPU) hardware platforms. Compute node architectures are becoming more complex and diverse than earlier generation platforms as hardware vendors strive to deliver performance gains while adhering to physical constraints, such as power usage. Moreover, DOE laboratories are procuring machines with GPUs from three different hardware vendors. This environment makes developing applications that can run efficiently on multiple platforms increasingly time consuming and difficult.
The RAJA Portability Suite is a collection of open source software libraries that enable developers to build portable high performance applications. RAJA provides software abstractions that enable portable parallel numerical kernel execution and memory management for computing platforms with heterogeneous memory systems, specifically the Umpire and CHAI libraries. Development is supported by LLNL’s ASC Program, the RADIUSS project, and the DOE Exascale Computing Project. Read more about RAJA’s capabilities on the LLNL Computing website.
New Repo: MaPPeRTrac
June 11, 2021 (new-repo)
MaPPeRTrac (Massively Parallel, Portable, and Reproducible Tractography) is a brain tractography workflow for high performance computing. It incorporates novel technologies to simplify and accelerate neuroimaging research. MaPPeRTrac’s data and dependencies are de-coupled from code to enable rapid prototyping and modification. The container enables high-performance, parallel, parametrized, and portable generation of the brain’s neural connectomes that is fast, efficient, well-tested, robust, and easy-to-use.
Spack on CppCast
May 28, 2021 (multimedia)
The CppCast podcast recently hosted Spack creator Todd Gamblin and core developer Greg Becker to discuss a documentation tool, a blog post about floating point numbers, and ABI changes. The podcast is created by and for C++ developers. The episode runs 59:13.
New Repo: INGRID
May 28, 2021 (new-repo)
INGRID (Interactive Grid) is a Python-based tokamak edge plasma grid generator capable of automatic generation of grids for magnetic topologies with up to two x-points anywhere in the domain. INGRID can be utilized in a GUI mode and noninteractively via Python scripts; both modes of operation support the use of the YAML-formatted parameter file. The repo provides installation instructions and a guide to getting started. v2.0.0 is now available.
Flux: Enabling Modern Supercomputing Workflows
May 26, 2021 (multimedia)
Flux is an open-source software framework that manages and schedules computing workflows to maximize available resources to run applications faster and more efficiently. Flux’s fully hierarchical resource management and graph-based scheduling features improve the performance, portability, flexibility, and manageability of both traditional and complex scientific workflows on many types of computing systems—in the cloud, at remote locations, on a laptop, or on next-generation architectures. Watch this video to learn more about Flux (runtime 7:14).
New Repo: IREP
May 25, 2021 (new-repo)
IREP is a tool that enables mixed-language simulation codes to use a common, Lua-based format for their input decks. The repo contains link to build documentation and examples. v1.0.0 is the first official GitHub release.
Vanessa Sochat Is Building Research Software and Open Source Engagement
May 18, 2021 (profile)
Vanessa Sochat has built her software engineering and computer science career in an unconventional way. After earning an undergraduate degree in Psychology, her first research assistant job involved using command line software and writing scripts. “I had no idea what I was doing, nor did anyone teach me, but I thrived in this environment,” she says. Vanessa recently joined LLNL to work on the BUILD project, Spack package manager, and other open-source initiatives. She was one of the original developers of the Singularity container technology, and she created and continues to produce the RSE Stories podcast. Read Vanessa’s profile at LLNL Computing.
LLNL, IBM, and Red Hat Joining Forces
April 28, 2021 (story)
Under a new memorandum of understanding, researchers at LLNL, IBM, and Red Hat will aim to enable next-generation workloads by integrating LLNL’s open source Flux scheduling framework with Red Hat OpenShift to allow more traditional HPC jobs to take advantage of cloud and container technologies. “Cloud systems are increasingly setting the directions of the broader computing ecosystem, and economics are a primary driver,” said Bronis de Supinski, CTO of Livermore Computing at LLNL. “With the growing prevalence of cloud-based systems, we must align our HPC strategy with cloud technologies, particularly in terms of their software environments, to ensure the long-term sustainability and affordability of our mission-critical HPC systems.” Read more at LLNL News.
Called to a Valuable Function, Stephanie Brink Streamlines the Lab’s Code
April 27, 2021 (profile)
LLNL Computing relies on engineers like Stephanie Brink to keep the legacy codes running smoothly. “You’re only as fast as your slowest processor or your slowest function,” says Stephanie, who works in the Center for Applied Scientific Computing. By analyzing a legacy code’s performance, Stephanie and her team can reduce the amount of time it takes to run and allow for more critical science to be accomplished. Stephanie is a frequent contributor to open source software, including Hatchet and Variorum. Read the full profile at LLNL Computing.
S&TR Features Software for the Exascale Era
April 21, 2021 (story)
The latest issue of LLNL’s Science & Technology Review magazine showcases Computing in the cover story (see abstract below) and Commentary. Open source software plays a prominent role in the initiatives described in the story. The cover art shows an advection simulation powered by open source repos MFEM and GLVis.
Cover story: The Exascale Software Portfolio by Holly Auten and featuring Lori Diachin, Rob Neely, Jeff Hittinger, Ulrike Meier Yang, David Beckingsale, and Tzanio Kolev
Abstract: As a leader in high-performance computing, Lawrence Livermore wields a large portion of the Department of Energy’s HPC resources to advance national security and foundational science. The Sierra supercomputer supports the National Nuclear Security Administration’s Stockpile Stewardship Program by enabling more accurate, more predictive simulations. This generation of computers is known as heterogeneous, or hybrid, because their architectures combine graphics processing units and central processing units to achieve peak performance well above 100 petaflops. (A petaflop is 10^15 floating-point operations per second.) The next generation’s processing capability—at least an exaflop (10^18 flops)—will be many times greater. HPC software must adjust to these new hardware standards. As the exascale era begins, two major initiatives leverage and expand Livermore’s HPC capabilities, with a spotlight here on software. The Exascale Computing Project, a joint effort between the DOE Office of Science and NNSA, brings together several national laboratories to address many hardware, software, and application challenges inherent in the organizations’ scientific and national security missions. Within the Laboratory, the RADIUSS project aims to benefit scientific applications through a robust software infrastructure.
LLNL's Spring Hackathon Coming Up
April 20, 2021 (event)
Held since 2012, LLNL’s hackathons are 24-hour opportunities to brainstorm, foster creativity, prototype, and explore. Participants work in groups or individually and often strive to learn new skills, programming languages, and tools in service to LLNL’s missions. Like the hackathons of the past year, the spring event (April 29-30) will be held virtually using WebEx and Mattermost for collaboration. LLNL sponsors are two Computing divisions: Enterprise Applications Services and National Ignition Facility Computing.
New Repo: MTtime
April 16, 2021 (new-repo)
MTtime (Time Domain Moment Tensor Inversion in Python) is a python package developed for time domain inversion of complete seismic waveform data to obtain the seismic moment tensor. It supports deviatoric and full moment tensor inversions, and 1-D and 3-D basis Green’s functions. Documentation and a working example are provided.
New Project Aims to Solve the Software Complexity Puzzle
April 14, 2021 (story)
The HPC world is full of complexity—from applications to the software components they rely on and the hardware they need to run. With the first three exascale machines, including Livermore’s El Capitan, slated to come online in the next few years, addressing complexity challenges will be a heavier, more urgent lift. Like our current Sierra system, these exascale systems will derive most of their computational power from secondary accelerator processors called GPUs. Traditionally, HPC systems have used only CPUs. With these machines, developers will need to accommodate not just NVIDIA accelerators but also new offerings from AMD and Intel. Harnessing the power of these devices entails using rapidly evolving programming environments, which require new compilers, runtime libraries, and software packages whose relationships are not always well understood. Without automated approaches to integration, developers will fight these software stacks by hand—but manual integration and maintenance are unsustainable.
A new effort kicking off in fiscal year 2021 aims to develop a machine-verifiable model of package compatibility that will enable automated integration, reducing human labor and errors. The Binary Understanding and Integration Logic for Dependencies (BUILD) project will run for three years with computer scientist Todd Gamblin at the helm. He states, “This project will develop techniques that enable rapid integration of HPC software systems, especially for upcoming exascale machines.” The project will build on Spack—the widely adopted package manager with a repository of more than 5,000 packages. Created by Gamblin in 2013 and today supported by a core development team, Spack already incorporates package configuration capabilities with dependency solving techniques.
LLNL’s Rob Falgout Named to 2021 Class of SIAM Fellows
April 09, 2021 (profile) (story)
The Society for Industrial and Applied Mathematics (SIAM) has announced its 2021 Class of Fellows, including LLNL computational mathematician Rob Falgout. Falgout is best known for his development of multigrid methods and for Hypre, one of the world’s most popular parallel multigrid codes. LLNL News has the fully story about this honor.
New Repo: PairScore
April 06, 2021 (new-repo)
PairScore is a preliminary code to predict binding affinity from the pairwise distances between protein and ligand atoms. The repo contains an example.
Spack and the NoTearsHPC Cluster at AWS
March 25, 2021 (multimedia) (story)
From HPC Tech Shorts, this video (25:09) shows Amazon Web Services team members discussing the NoTearsHPC cluster solution for 1-click launches. Evan Bollig and Sean Smith talk about how the cluster works, what it provides, and how to do complicated tasks quickly. They used Spack for installation.
New Computing Website Tags Content as Open Source
March 19, 2021 (story) (this-website)
LLNL’s computing website recently underwent a major overhaul to its design and information architecture. The site now features a taxonomy of Focus Areas that connect related content. These topics are tagged on News, People Highlights, and Projects. One of the topics is open source software. The site’s Livermore Computing page also directs users to this website for more information about open source projects.
Novel Deep Learning Framework Includes New Repo
March 18, 2021 (new-repo) (story)
LLNL computer scientists have developed a new framework and an accompanying visualization tool that leverages deep reinforcement learning for symbolic regression problems, outperforming baseline methods on benchmark problems. The paper was recently accepted as an oral presentation at the International Conference on Learning Representations (ICLR 2021), one of the top machine learning conferences in the world. The conference takes place virtually May 3-7, and the team’s deep symbolic regression code is available in a GitHub repo.
New Repo: Juqbox.jl
March 02, 2021 (new-repo)
Juqbox.jl is a package for solving quantum optimal control problems in closed quantum systems, where the evolution of the state vector is governed by Schrodinger’s equation. See the project’s README for installation instructions and workflow details. A few examples are also provided.
Videos from Wild West Hackin' Fest
February 24, 2021 (multimedia)
LLNL computer engineer Ian Lee presented at Wild West Hackin’ Fest (WWHF) 2020, and both of his talks are now available on YouTube:
Intro to Git for Security Professionals (2:01:58). This workshop provides an overview and introduction to the version control system Git for security professionals who may have no background in software development and who would like to start using their favorite open source tool.
Releasing Your First (Python) Open Source Project to the Masses! (2:08:02). This video picks up from having just learned how to start using Git, and works through how to take that knowledge to start your own first open source project. This Hackin’ Cast is appropriate for attendees of all levels, and no prior knowledge (other than very basic command line and git usage) is expected.
WWHF offers high-quality information security education to beginners and seasoned professionals alike. A stated goal is to lower the barrier to entry for those seeking to enter into the world of information security.
New Repo: Saloon
February 17, 2021 (new-repo)
Saloon is a Vim plugin that simplifies Python code linter/fixer configuration and usage. Saloon’s menu lets developers toggle which static analysis tools to use and delegates those changes to ALE’s API. Since prospector already handles multiple tools, and is integrated with ALE, most of the actual linting will initially be handled via prospector calls. See the project’s README for information about how to get started using Saloon.
MFEM GPU Tips & Tricks
February 17, 2021 (story)
The MFEM team has created a helpful page of tips and tricks that explain how to make the most of GPUs when running finite element algorithms. This support documentation includes information about optimizing porting and performance. Learn more about these features and processes:
MFEM’s internal memory manager to simplify the use of host/device memory
MFEM_FORALL macro to enable performance portability
Maximizing the main memory bandwidth
Profiling on NVIDIA GPUs to improve the performance of a memory bound kernel
Roofline model for predicting the peak performance achievable by a specific algorithm
Held since 2012, LLNL’s hackathons are 24-hour opportunities to brainstorm, foster creativity, prototype, and explore. Participants work in groups or individually and often strive to learn new skills, programming languages, and tools in service to LLNL’s missions. Like the spring and summer hackathons of 2020, this year’s winter event (February 11-12) was held virtually using WebEx and Mattermost for collaboration. With LLNL’s Data Science Institute (DSI) sponsoring the hackathon, the agenda included guest speakers (below) discussing data science topics relevant to the Lab’s missions as well as a deep learning tutorial. (Participants were not required to attend the talks.) Read the recap on the DSI website.
Brian Van Essen: COVID-19 Rapid Drug Discovery
Jose Cadena Pico: Modeling the Temporal Network Dynamics of Neuronal Cultures
Benjamin Priest: Querying Massive Graphs with Sketching Algorithms
Kelli Humbird: Data-Driven Design for Inertial Confinement Fusion
Cindy Gonzales and Luke Jaffe: Introduction to Deep Learning for Image Classification
Award-Winning Computer Vision Research Includes New Repo
January 08, 2021 (new-repo) (story)
The 2021 IEEE Winter Conference on Applications of Computer Vision (WACV 2021) announced that a paper co-authored by Rushil Anirudh received the conference’s Best Paper Honorable Mention award based on its potential impact to the field. The paper, titled “Generative Patch Priors for Practical Compressive Image Recovery,” introduces a new kind of prior—a characterization of the space of natural images—for compressive image recovery that is trained on patches of images instead of full-sized images. Unlike existing generative methods that are applicable only to images similar to the training dataset—i.e., similar kinds of objects, image sizes or aspect ratios—the generative patch prior (GPP) can recover a wide variety of natural images and compares favorably to other existing methods, researchers said. Anirudh presented the paper on behalf of the group during an awards session hosted by the virtual conference, the premier event of its kind in the world. The conference received about 1,100 paper submissions—only 5 were honored with awards. The code used in the paper is available on the open source repository GPP on GitHub.
New Repo: SPOT Suite
January 07, 2021 (new-repo)
SPOT is a web-based visualization tool for performance data. One use case is to link the Caliper performance library into an application, and every run of the application will produce a .cali performance data file. SPOT will then visualize the collective performance of an application across many runs. This could involve tracking performance changes over time, comparing the performance achieved by different users, running scaling studies across time, and so on.
We now have three repos that provide different functionality around SPOT:
To get started, fork spot2_container and let it check out the other two repos as submodules.
New Repo: ns3-if77-module
December 17, 2020 (new-repo)
The ns3-if77-module provides an implementation of the ns3::PropagationLossModel, which uses the If77 propagation model developed by G. D. Gierhart and M. E. Johnson. The If77 propagation model was developed in the 1970s to estimate the service coverage for radio systems. It can be used to calculate propagation loss for ground/air, air/air, ground/satellite, and air/satellite systems for frequencies in the 0.1Mhz to 20Ghz range.
NeurIPS Features LLNL Papers and Software
December 07, 2020 (event)
The 34th Conference on Neural Information Processing Systems (NeurIPS)features two LLNL papers advancing the reliability of deep learning for the Lab’s mission-critical applications. The most prestigious machine learning conference in the world, NeurIPS began virtually on December 6. The first paper describes a framework for understanding the effect of properties of training data on the generalization gap of machine learning (ML) algorithms—the difference between a model’s observed performance during training versus its “ground-truth” performance in the real world. The second NeurIPS paper introduces an automatic framework to obtain robustness guarantees of any deep neural network structure using the open source Linear Relaxation-based Perturbation Analysis (LiRPA) repo. Developed with colleagues at Northeastern University, China’s Tsinghua University, and UCLA, LiRPA algorithms can provide guaranteed upper and lower bounds for a neural network function with perturbed inputs.
Spack User Survey Results
December 02, 2020 (story)
The Spack development team ran a user survey from September 28 to October 9 and received 169 responses. The survey covered user demographics, use cases, feature priorities, community involvement, and more. For example, responses indicated strong interest in a future virtual workshop. The full analysis is available on the Spack website, and the survey data is housed in its own repo.
New Templates for Community Health Files
November 24, 2020 (this-website)
Our .github repo houses file templates and other content that can be used by LLNL open source projects. The goal is to help standardize the presentation and organization of certain types of content across the LLNL organization. New this month are community health files that developers can copy and/or modify as needed to ensure their repos adhere to certain guidelines regarding licenses and other aspects of releasing and maintaining open source software. New files include Contributing Guidelines, a Notice, a Code of Conduct, and templates for opening issues and submitting pull requests. More information is available on the .github README.
LLNL's First Computing Virtual Expo
November 11, 2020 (event-report) (multimedia)
The LLNL Computing Virtual Expo was an end-to-end digital experience with interactive booths, networking opportunities, and on-demand presentations, held on September 30. Lab employees and the public were invited to learn about new initiatives while networking and engaging with the Computing community, including computer scientists, IT experts, HPC contacts, and software developers and engineers.
FAROS Team Wins Best Paper Award at OpenMP Workshop
October 30, 2020 (story)
A team of LLNL computer scientists and a collaborator from Argonne National Laboratory (ANL) won the Best Paper Award at the International Workshop on OpenMP (IWOMP) 2020 in September. Giorgis Georgakoudis, Ignacio Laguna, Tom Scogland (LLNL), and Johannes Doerfert (ANL) accepted the award for their paper, “FAROS: A Framework to Analyze OpenMP Compilation Through Benchmarking and Compiler Optimization Analysis.” The paper showcases the new Livermore-developed framework, FAROS, which pinpoints missing compiler optimizations due to OpenMP compilation and measures the impact on performance. FAROS is the result of a previously funded Laboratory Directed Research and Development Feasibility Study, which was led by Georgakoudis. Read more about the award.
LLNL Heads to SC20
October 28, 2020 (event)
The 32nd annual Supercomputing Conference (SC20) will be held virtually throughout November 9–19. This year the conference groups event types (e.g., tutorials, posters) into specific days. Much of the content is pre-recorded and will remain available online for six months. Tutorials will be live-streamed. As always, LLNL teams are looking forward to the event.
Podcast: Power Up Your Java Using Python With JPype
October 26, 2020 (multimedia)
Python and Java are two of the most popular programming languages in the world, and have both been around for over 20 years. In that time there have been numerous attempts to provide interoperability between them, with varying methods and levels of success. One such project is JPype, which allows you to use Java classes in your Python code. In this Python podcast episode, lead developer Karl Nelson from LLNL explains why he chose it as his preferred tool for combining these ecosystems, how he and his team are using it, and when and how you might want to use it for your own projects. He also discusses the work he has done to enable use of JPype on Android, and what is in store for the future of the project. The episode runs 48:39.
Video: Build All the Things with Spack
October 20, 2020 (multimedia)
LLNL computer scientist Todd Gamblin presented a brief overview of Spack at CppCon. CppCon is an annual, week-long gathering for the C++ community. This video runs 6:53.
Open-Source Software Community Welcomes Virtual Internships
October 01, 2020 (story) (this-website)
LLNL hosts hundreds of student interns annually—even during a year distinguished by the COVID-19 pandemic. This summer, the Computing Scholar Program welcomed 160 undergraduate and graduate students into virtual internships. The Lab’s open source community was already primed for student participation. A Computing news article describes three open source projects that benefitted from interns’ help: Ascent, MFEM, and this website. Mentors discuss the challenges of mentoring remotely, while students describe their experiences including skill development.
Exascale computing will transform the ability to tackle some of the world’s most important challenge. The Exascale Computing Project (ECP) celebrates this new era of scientific discovery with Exascale Day on October 18, or “10^18” to represent the exascale threshold of floating-point operations per second. This virtual event will provide videos, audio discussions, and articles that will educate participants about impact areas of exascale computing from the Department of Energy national laboratories, HPC manufacturers, and leading universities and industrial organizations. LLNL will be participating, and much of the ECP’s software stack is open source.
The FLOSS for Science podcast showcases open source software uses in science. Episode 30 covered the philosophy of Spack, its package management capabilities in HPC clusters, supported operating systems, and much more. The episode runs 52:26.
News Filters Added to Software Portal
September 02, 2020 (this-website)
This site’s News and Archive pages have been updated with filters for selecting news posts by category. These categories appear next to the date on each post. We have nearly five years’ worth of news, so this feature improves the navigation of different types of news. These filters were implemented by our 2020 summer intern.
New Visualizations of Popular Repositories
August 31, 2020 (this-website)
The Explore section of this website has again expanded to include a new page that breaks down the popularity (i.e., stars) of LLNL repositories in a few ways: repos with the highest number of stars, creation history of those repos, increase of stars over time, commit activity of popular repos, and licenses of those repos. This new page, created by our 2020 summer intern, helps us better understand repos that have made a big impact in the open source community.
Video: Flux Framework Featured on Next Platform TV
August 18, 2020 (multimedia)
LLNL computer scientist Stephen Herbein discusses the open-source Flux Framework HPC software on this video episode of Next Platform TV. His segment begins at 27:34.
CEED held its 4th annual meeting on August 11-12 using ECP Zoom for videoconferencing and Slack for side discussions. The goals of the meeting were to report on the progress in the Center; deepen existing and establish new connections with ECP hardware vendors, ECP software technologies projects, and other collaborators; plan project activities; and brainstorm/work as a group to make technical progress. In addition to gathering together many CEED researchers, the meeting included representatives of ECP management, hardware vendors, software technology, and other interested projects. The full meeting agenda is available on the CEED website.
New Dependencies Page on Software Portal
July 28, 2020 (this-website)
The Explore section of this website has grown to include a new page that visualizes our software catalog’s dependencies. LLNL software repos are shown in the context of repositories with dependencies, External Packages, and internal packages. You can move the slider to change the connections between repos, organizations, and dependencies as well as click on a circle to isolate its specific connections in an expansion panel on the right side of the page. This work, which enables us to learn more about our repos and how they are related, was done by our 2020 summer intern.
Tool Time: Caliper - A Performance Analysis Toolbox in a Library
July 27, 2020 (story)
The Performance Optimisation and Productivity blog published a post by LLNL’s David Boehme, who described the open source Caliper program instrumentation and performance measurement framework. Caliper can be used for lightweight always-on profiling or advanced performance engineering use cases, such as tracing, monitoring, and auto-tuning. It is primarily aimed at HPC applications, but works for any C/C++/Fortran program on Unix/Linux. The blog post outlines Caliper’s instrumentation and API with examples.
Spack Tutorial on AWS
July 20, 2020 (event-report) (multimedia)
Amazon Web Services hosted a free two-day Spack tutorial broadly targeted at HPC users, developers, and user support teams. Each day consisted of two 1.5-hour sessions with a 30-minute break in the middle. The first day covered Spack basics, while the second day drilled down on advanced features. Videos from day 1 (3:19:18) and day 2 (3:30:18) are available.
LLNL's Summer Hackathon Will Be Virtual
July 18, 2020 (event)
Held since 2012, LLNL’s hackathons are 24-hour opportunities to brainstorm, foster creativity, prototype, and explore. Participants work in groups or individually and often strive to learn new skills, programming languages, and tools in service to LLNL’s missions. Like the spring hackathon earlier this year, the summer event (August 6-7) will be held virtually using WebEx and Mattermost for collaboration. LLNL sponsors are Livermore Computing and the Center for Applied Scientific Computing. Registration closes on July 31.
Webinar: What’s New in Spack?
July 15, 2020 (event-report) (multimedia)
The IDEAS Productivity project, in partnership with the DOE Computing Facilities of the ALCF, OLCF, and NERSC and the DOE Exascale Computing Project, hosts a webinar series on Best Practices for HPC Software Developers. A webinar titled “What’s New in Spack?” was presented by LLNL’s Todd Gamblin on July 15. Slides and a video (1:26:33) from the session are available.
New Consolidated FAQ on Software Portal
July 08, 2020 (this-website)
Much of the content under the About section of this website has been consolidated into an easy-to-navigate FAQ page. The FAQ explain how to get started on GitHub, become part of the LLNL organization, manage repositories, and much more. We encourage readers to provide feedback or new questions by contacting the LLNL GitHub admins or submitting a pull request.
New Data Visualizations on Software Portal
July 07, 2020 (this-website)
The Explore section of this website is benefitting from new development by our summer intern. Data we collect from GitHub is visualized in various ways, with additional visualizations planned. These efforts help us understand our repos’ activity, how they are being used, development trends, and more. Check out the new “Repo Licenses” viz and stay tuned for more!
Video: MFEM: Advanced Simulation Algorithms for HPC Applications
June 24, 2020 (multimedia)
MFEM is an open-source software library that provides advanced mathematical algorithms for use by scientific applications. By relying on MFEM, application scientists can quickly develop highly accurate physics simulation codes on a variety of platforms—from laptops to the world’s largest supercomputers. MFEM version 4.0 incorporates the most advanced techniques from the scientific computing research community, and its methods are widely applicable, highly impactful, and easy to use. A new video (runtime 7:07) features members of the LLNL development team, who describe how the software library works.
LLNL to Host Online Developer Day
June 09, 2020 (event)
Initiated in 2017, Developer Day is a day-long, annual event that brings software developers together from all over LLNL. The fourth installment of the popular event will be held virtually on July 30. Read more about Dev Day in last year’s recap.
Podcast: The MFEM Finite Element Library Broadens GPU Support
June 08, 2020 (multimedia) (release)
MFEM is a lightweight, general, scalable C++ library for finite element methods. v4.1 was released in March. LLNL computational mathematician and MFEM PI Tzanio Kolev joined the Let’s Talk Exascale podcast to talk about the release and MFEM’s expanded GPU support. The podcast episode runs 6:28.
Although in-person conferences are not feasible this summer, LLNL will participate in the online ISC High Performance Conference (ISC20) on June 22–25. The event brings together the HPC community—from research centers, commercial companies, academia, national laboratories, government agencies, exhibitors, and more—to share the latest technology of interest to HPC developers and users. View details about LLNL’s papers, poster, and workshops.
Webcast: Open Source Doesn't Have to Be Scary
May 23, 2020 (event-report) (multimedia)
LLNL’s Ian Lee recently appeared on the Thought Leadership Consortium webcast entitled “Open Source Doesn’t Have to Be Scary.” Registration is free to watch the Zoom replay (01:25:00) on demand.
Podcast: Spack Attack!
May 22, 2020 (multimedia)
In a recent RSE Stories podcast, LLNL’s Todd Gamblin shares his journey at a national Lab and how getting angry at software led to development of a hugely popular package manager, Spack. The “Spack Attack!” episode runs 21:25. RSE is affiliated with the U.S. Research Software Engineer Association.
Working Remotely: The Spack Team
May 16, 2020 (story)
Better Scientific Software’s blog features a post about the Spack team’s experience working remotely and interacting with the Spack community. LLNL’s Todd Gamblin offers insight into making the most of online communication opportunities and stresses the importance of providing robust documentation so users can help themselves.
Maestro Workflow Conductor
May 04, 2020 (story)
Maestro Workflow Conductor is a lightweight Python tool that can launch multi-step software simulation workflows in a clear, concise, consistent, and repeatable manner. It does this locally as well as on supercomputers. LLNL Computing recently published a project description, highlighting the challenges in scientific workflows that Maestro solves. “Before Maestro, it took a long time to stand up new workflows. Maestro has changed that by providing a consistent framework that can break down workflows into smaller pieces, and facilitate automated execution,” said project leader Frank Di Natale. Check out the Maestrowf repo.
Podcast: Flexible Package Manager Automates the Deployment of Software on Supercomputers
April 28, 2020 (multimedia)
In this podcast episode (5:54) produced by the Exascale Computing Project, LLNL’s Todd Gamblin talks about Spack: its role in the ECP’s software stack, the Spack-related events at last fall’s SC19, and the package manager’s R&D 100 Award.
Podcast: Reducing the Memory Footprint and Data Movement on Exascale Systems
April 16, 2020 (multimedia)
In this podcast episode (12:36) produced by the Exascale Computing Project, LLNL’s Peter Lindstrom talks about ZFP project, which is a compressed representation of multidimensional floating-point arrays that are ubiquitous in high-performance computing.
LLNL to Host First Virtual Hackathon
April 12, 2020 (event)
Held since 2012, LLNL’s hackathons are 24-hour opportunities to brainstorm, foster creativity, prototype, and explore. Participants work in groups or individually and often strive to learn new skills, programming languages, and tools in service to LLNL’s missions. This year’s spring hackathon (April 30 through May 1) will be held virtually. In true hackathon spirit, several tech solutions will enable participants to collaborate remotely. Charalynn Macedo, division leader for LLNL’s Enterprise Applications Services, will kick off the event with a brief keynote presentation.
Podcast: Delivering Exascale Machine Learning Algorithms and Tools for Scientific Research
March 12, 2020 (multimedia)
In this podcast episode (10:42) produced by the Exascale Computing Project, LLNL’s Brian Van Essen joins Brookhaven and LBNL colleagues to discuss an ECP co-design center called ExaLearn. ExaLearn leverages machine learning and artificial intelligence to inform the requirements for exascale machines.
Podcast: Helping Applications Use Future Architectures with First-Rate Discretization Libraries
February 26, 2020 (multimedia)
In this podcast episode (9:47) produced by the Exascale Computing Project, LLNL’s Tzanio Kolev, discusses ECP’s Center for Efficient Exascale Discretizations (CEED), which is a hub for high-order mathematical methods to increase application efficiency and performance.
Video: Spack at FOSDEM '20
February 02, 2020 (event-report) (multimedia)
FOSDEM is an annual two-day event promoting the widespread use of free and open source software. The 2020 conference took place in Brussels, Belgium, on February 1–2. Videos of speakers, lightning talks, and other sessions are available on the FOSDEM website. LLNL’s Todd Gamblin led two sessions about the package manager Spack:
MFEM and VisIt Benefits Engineer in LLNL’s Design Optimization Laboratory
December 10, 2019 (story)
MFEM and VisIt are key design codes in LLNL’s Center for Design and Optimization, which is developing algorithms that can optimize immensely complex systems in HPC environments. The MFEM library enables application scientists to prototype parallel physics application codes quickly, based on partial differential equations discretized with high-order finite elements. VisIt—a visualization, animation, and analysis tool—helps scientists and engineers interactively visualize and analyze data, from small (<101 core) desktop-sized projects to large (>105 core) leadership-class computing facility simulation campaigns. Learn more about the Center in the Science & Technology Review article “Leading a Revolution in Design.”
On the Spack Track at SC19
December 06, 2019 (story)
At the annual supercomputing conference (SC19) in Denver, Colorado, Spack events were held each day. As a reflection of its grassroots heritage, nine sessions were planned by more than a dozen thought leaders from seven organizations, including three 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 meetings, three papers, and more. This HPCwire article describes Spack’s history, functionality, impact, and user community through the many Spack-related events at SC19.
In this podcast episode (12:18) produced by the Exascale Computing Project, LLNL’s Kathryn Mohror and Elsa Gonsiorowski talk about what SCR is and does, the challenges involved in creating it, and the impact it is expected to have on HPC performance.
LLNL’s Presence in HPC Shines Bright at SC19
December 05, 2019 (event-report)
The 2019 International Conference for High Performance Computing, Networking, Storage, and Analysis—better known simply as SC19—returned to Denver, and once again LLNL made its presence known as a force in supercomputing. The conference, held November 17 through 22, was attended by nearly 14,000 people representing 118 countries.
Podcast: Software Enables Use of Distributed In-System Storage and Parallel File System
December 05, 2019 (multimedia)
For decades, HPC applications used a shared parallel file system for input/output (I/O), but the recent addition of new storage devices in systems—burst buffers, for example—has enabled the creation of a storage hierarchy. The hierarchy can be arranged such that in-system storage is the first level, and the parallel file system the second. For optimal performance, applications must change along with the architectures.
In this podcast episode (11:28) produced by the Exascale Computing Project, LLNL’s Kathryn Mohror and ORNL’s Sarp Oral talk about the open source tool UnifyFS, which can provide I/O performance portability for applications, enabling them to use distributed in-system storage and the parallel file system.
LLNL-Led Team Wins SC19 Best Paper Award
November 22, 2019 (event-report) (story)
On November 22, a panel of judges at the International Conference for High Performance Computing, Networking, Storage and Analysis (SC19) awarded a multi-institutional team led by LLNL computer scientists with the conference’s Best Paper award. The paper, entitled “Massively Parallel Infrastructure for Adaptive Multiscale Simulations: Modeling RAS Initiation Pathway for Cancer,” describes the workflow driving a first-of-its-kind multiscale simulation on predictively modeling the dynamics of RAS proteins—a family of proteins whose mutations are linked to more than 30 percent of all human cancers—and their interactions with lipids, the organic compounds that help make up cell membranes.
The team’s software, called MuMMI (Multiscale Machine-Learned Modeling Infrastructure), will soon be released as open source. Read more about the award on LLNL news.
Software Engineering 101: I have some code! Now what?
November 12, 2019 (event-report) (story) (this-website)
As part of LLNL’s Computing 101 speaker series, Ian Lee gave a talk to employees on November 12 titled “Software Engineering 101: I have some code! Now what?” The presentation reviewed the Lab’s resources for supporting software engineering and open source development.
Lee, who manages this website and leads many initiatives in the Lab’s open source community, aimed his remarks at relative newcomers to the software development landscape. He also updated the audience on the state of open source development at the Lab.
The Lab provides a wide range of support and solutions for just about any task a developer does: programming languages, package managers, computing platforms, code editors, version control systems, project communication, project tracking, documentation, and much more. Lee provided an overview of these options, offered advice about how to navigate the Lab’s software resources, and encouraged developers to take advantage of colleagues’ knowledge and experience.
Lee summarized the Lab’s recent open source activity, which echoes a trend toward developing “out in the open,”—i.e., not waiting for code to mature before releasing it for community feedback and contributions. (As this website shows, the Lab and affiliated GitHub organizations have almost 600 repos.) Accordingly, the Lab has updated its open source release policies to support modern code development practices.
Lee also demoed this website’s category-driven design changes, LLNL’s open source logo (and stickers), the @LLNL_OpenSource Twitter account, and Slack channels. He noted that LLNL may have a booth at PyCon 2020, which will be held April 15-23 in Pittsburgh. (Conferences such as PyCon provide LLNL’s open source software community with opportunities for networking, collaboration, and technical skills development. Lab employees interested in attending similar events may contact Ian Lee for funding.)
ESGF Architecture Workshop
November 08, 2019 (event-report)
Members of the Earth System Grid Federation (ESGF) gathered in Abingdon, England, on November 5-7 to kick off the redesign process for the Federation’s computing architecture. Since the original system was designed a decade ago, the number of ESGF’s supported projects and disciplines has grown and diversified. Furthermore, operational requirements are clearer for the ESGF to support an international federated archive of this size. Many of the ESGF nodes now have other functions beyond CMIP (the Coupled Model Intercomparison Project), and the landscape of data repository and science needs has changed.
Led by ESGF’s Executive Committee, the workshop team discussed improvements to the user experience, data repository and management, data compute requirements, and platform and system administration. This workshop concluded with a high-level roadmap for future architecture directions, which will be presented at the larger ESGF conference in March. LLNL’s delegates to the workshop were Ghaleb Abdulla (principal investigator and co-chair of the Executive Committee), Sasha Ames (member of multiple ESGF Working Teams) and Jason Boutte (Compute Working Team member).
JuliaCon Recap and Videos
August 22, 2019 (event-report) (multimedia)
LLNL’s Seth Bromberger attended JuliaCon 2019 on July 22–25 in Baltimore, Maryland. He gave a talk on July 24 to a full house: “Using Julia in Secure Environments” (abstract, YouTube video). The focus of the presentation was engaging the community in thinking about transitive package dependencies and the security of the source code supply chain.
Other notable events at the conference included a keynote address by Steven Lee, applied mathematics program manager for Advanced Scientific Computing Research (ASCR) within the U.S. Department of Energy’s Office of Science. His presented his office’s computing priorities and mentioned related LLNL work (YouTube video). In addition, LLNL’s Jane Herriman received a Julia Community Prize for her “teaching, outreach, and community stewardship.”
Conferences such as JuliaCon provide LLNL’s open source software community with opportunities for networking, collaboration, and technical skills development. Lab employees interested in attending similar events may contact Ian Lee for funding.
Software Portal Redesign and GitHub Integration
July 30, 2019 (this-website)
Recently this website received several changes that improve the user’s experience, keep the content fresh, and help the admin team monitor and track all repositories under the LLNL organization on GitHub. We are excited to improve user access to LLNL’s 500+ open source repositories and appreciate the help of our summer intern, Angela Flores, who is pursuing a B.S. in computer science with a minor in cybersecurity from Cal State Long Beach.
*LLNL’s RADIUSS project—Rapid Application Development via an Institutional Universal Software Stack—aims to broaden usage across LLNL and the open source community of a set of libraries and tools used for HPC scientific application development.
OSS Project Lead Kathryn Mohror Completes Tenure as S&TR Scientific Editor
May 07, 2019 (profile)
Like many LLNL computer scientists, Kathryn Mohror juggles multiple responsibilities both at her workplace and in the scientific community. She recently completed a 12-month term as scientific editor of LLNL’s Science & Technology Review magazine. Read about her experience with the publication while still keeping up with her own research in scalable fault-tolerant computing and input/output for next-generation computing systems – not to mention her two open source projects, SCR and UnifyCR.
Inaugural NAHOMCon19 Coming to San Diego
February 14, 2019 (event)
To all computational scientists, mathematicians, scientists, and engineers interested in high-order methods and PDEs: Several institutions have joined together to organize the inaugural North American High Order Methods Conference (NAHOMCon19). The conference will be held in San Diego in the summer of 2019 and will focus on the many developments in high-order discretizations and applications taking place in North America.
The DOE co-design Center for Efficient Exascale Discretizations (CEED) is pleased to participate in the conference. CEED is a partnership between two U.S. DOE laboratories (Livermore & Argonne) and five universities in support of the Exascale Computing Project.
Earth System Grid Federation's Annual Conference Coming Up
November 03, 2018 (event)
The LLNL-led international Earth System Grid Federation (ESGF) will meet December 3-7 in Washington, DC, to plan the future of Earth system data analysis and more. Registration info is available on the ESGF website along with the conference agenda. Fork this 2017 R&D 100 winner on GitHub.
Flux and Spack Events Coming to Supercomputing '18
October 27, 2018 (event)
LLNL staff are heading to Dallas, Texas, for the 30th annual Supercomputing Conference (SC18) on November 11–16. LLNL is leading 6 tutorials and 16 workshops with topics ranging from data analytics and data compression to performance analysis and productivity. LLNL-developed open-source tools Flux and Spack are subjects of a workshop and a tutorial, respectively. We hope to see you there!
Read more about our past experiences and tips for first-timers, and a complete list of LLNL-led sessions can be found on the LLNL Computing website (links unpublished in 2020). All times are listed in Central Standard Time.
Open-Source Developer Greg Becker Scales Projects and Mountains
October 26, 2018 (profile)
Is there a connection between rock climbing and software development? In this profile, LLNL’s Greg Becker describes his career path, motivation for improving HPC tools, and recent work with open-source projects like SCR, Caliper, and Spack.