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Charliecloud 0.21 Released

December 18, 2020 (release)

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 0.21 includes renaming of the internal builder, a new option to bind-mount directories during build, updates to CI testing, and more.

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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.

SUNDIALS 5.6.0 Released

December 11, 2020 (release)

SUNDIALS is a SUite of Nonlinear and DIfferential/ALgebraic equation Solvers. This release includes a new NVECTOR implementation, updates to the RAJA NVECTOR implementation, a new optional operation, and more.

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GLVis 4.0 Released

December 11, 2020 (release)

GLVis is a lightweight OpenGL tool for accurate and flexible finite element visualization. Version 4.0 includes:

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NeurIPS Features LLNL Papers and Software

December 07, 2020 (event) (story)

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.

New Repo: [Boost].MPI3

December 04, 2020 (new-repo)

MPI is a large library for run-time parallelism where several paradigms coexist. It was is originally designed as standardized and portable message-passing system to work on a wide variety of parallel computing architectures. The last standard, MPI-3, uses a combination of techniques to achieve parallelism, Message Passing (MP), Remote Memory Access (RMA),and Shared Memory (SM). [Boost].MPI3 is a C++ library wrapper for standard MPI3. While not an official MPI3 library, [Boost].MPI3 is designed following the principles of Boost and the STL. This repo provides a uniform interface and abstractions for MPI3 features by means of wrapper function calls and concepts brought familiar to C++ and the STL.

UnifyFS 0.9.1 Released

December 03, 2020 (release)

UnifyFS is a user-level burst buffer file system under active development. The repo supports scalable and efficient aggregation of I/O bandwidth from burst buffers while having the same life cycle as a batch-submitted job. More than a year in the making, version 0.9.1 includes improved HDF5 and MPI-IO support, optimization to satisfy read requests from local, support for relative paths, additional unit and integration tests, and much more.

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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.

Caliper 2.5.0 Released

December 01, 2020 (release)

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 the ability to run ConfigManager configs without the ConfigManager API, improvements to sampling and symbol lookup, loop profiling for the Spot config, documentation updates, and more.

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New Repo: Lestofire

November 30, 2020 (new-repo)

Lestofire implements the level set method in topology optimization. It combines the automated calculation of shape derivatives in Firedrake and pyadjoint with the Null space optimizer to find the optimal design.

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.

Umpire 5.0.0 Released

November 18, 2020 (release)

Umpire is a resource management library that allows the discovery, provision, and management of memory on next-generation architectures. v5.0.0 includes unified memory support for HIP, new allocator accessibility functionality, new getParent functionality, and more.

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Spack 0.16.0 Released

November 18, 2020 (release)

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 0.16.0 contains several new and experimental features, including

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RAJAPerf 0.10.0 Released

November 17, 2020 (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. Each kernel in the suite appears in multiple RAJA and non-RAJA (i.e., baseline) variants using parallel programming models such as OpenMP and CUDA. The v0.10.0 release changes the way kernel variants are managed.

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Hatchet 1.3.0 Released

November 12, 2020 (release)

Hatchet is a Python-based library that allows Pandas dataframes to be indexed by structured tree and graph data. Version 1.3.0 includes a new interactive tree visualization in Jupyter, new APIs, new graph output formats, an updated tutorial, and more.

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LLNL's First Computing Virtual Expo

November 11, 2020 (event-report)

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.

In addition to an exhibit booth about open source projects in general, the Expo featured booths for RADIUSS project and the Maestro Workflow Conductor. Ian Lee presented a lightning talk about the Lab’s open source community and policies, and Rob Neely gave a talk on RADIUSS.


New Repo: PF3DCOMM

November 06, 2020 (new-repo)

PF3DCOMM is an MPI benchmark that tests the performance of communication patterns used in pF3D, a laser-plasma simulation code developed at LLNL. The benchmark is intended for use in evaluating the effectiveness of HPC interconnects.

Aluminum 0.6.0 Released

November 04, 2020 (release)

Aluminum provides a generic interface to high-performance communication libraries with a focus on allreduce algorithms. Blocking and non-blocking algorithms and GPU-aware algorithms are supported. Aluminum also contains custom implementations of select algorithms to optimize for certain situations. The latest release includes improved progress engine binding logic, new benchmarks, initial support for vector collectives in the NCCL and MPI backends, and more.

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New Repo: Admiral

November 04, 2020 (new-repo)

Admiral is a package for developing agent based simulations and training them with multiagent reinforcement learning. A reinforcement learning experiment contains two main components: (1) a simulation environment and (2) learning agents, which contain policies that map observations to actions. These policies may be hard-coded by the researcher or trained by the RL algorithm. In Admiral, these two components are specified in a single Python configuration script. The components can be defined in-script or imported as modules.

SUNDIALS 5.5.0 Released

November 02, 2020 (release)

SUNDIALS is a SUite of Nonlinear and DIfferential/ALgebraic equation Solvers. This release includes a refactored build system (requires CMake 3.12.0 or newer) and support for SuperLU DIST 6.3.0 or newer.

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RAJAPerf 0.8.0 Released

November 02, 2020 (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. Each kernel in the suite appears in multiple RAJA and non-RAJA (i.e., baseline) variants using parallel programming models such as OpenMP and CUDA. The v0.8.0 release updates the RAJA submodule to v0.13.0 and the BLT submodule to match what is used in RAJA.

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MFEM 4.2 Released

November 02, 2020 (release)

MFEM is a lightweight, general, scalable C++ library for finite element methods. Its goal is to enable high-performance scalable finite element discretization research and application development on a wide variety of platforms, ranging from laptops to supercomputers. The latest release includes several improvements and new features, such as:

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Conduit 0.6.0 Released

November 02, 2020 (release)

Conduit provides an intuitive model for describing hierarchical scientific data in C++, C, Fortran, and Python. It is used for data coupling between packages in-core, serialization, and I/O tasks.

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RAJA 0.13.0 Released

October 30, 2020 (release)

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.0.13.0 release includes new features:

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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.

Twitter accounts to follow: @Livermore_Comp, @LLNL_OpenSource, @NatLabsHPC, @Livermore_Lab.

Check out LLNL’s full lineup of events. All initial broadcast times are listed in Eastern Standard Time.

New Repo: FAROS

October 21, 2020 (new-repo)

FAROS is a framework for benchmarking and analysis of compiler optimization. The repo contains a benchmark harness to fetch, build, and run programs with different compilation options for analyzing the impact of compilation on performance. The use case is contrasting OpenMP compilation with its serial elision to understand performance differences due to different compilation. The README file contains information about how the software works. The team has published a paper with more details and recently won the Best Paper Award at the 2020 International Workshop on OpenMP (IWOMP).

Charliecloud 0.20 Released

October 20, 2020 (release)

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 0.20 includes a significant improvement for unprivileged image build via ch-grow, meaning Dockerfiles will no longer fail or need to be altered in order to succeed.

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HiOp 0.3 Released

October 13, 2020 (release)

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:

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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.

Another version of this story is available as a blog post, penned by Ian Lee: Spotlight Story: Interns and Open Source: A Productive Combination.

libCEED 0.7 Released

September 30, 2020 (release)

The Center for Efficient Exascale Discretizations (CEED) within the US Department of Energy’s ECP is helping applications leverage future architectures by developing state-of-the-art discretization algorithms that better exploit the hardware and deliver a significant performance gain over conventional methods. libCEED is a high-order API library that provides a common algebraic low-level operator description, allowing a wide variety of applications to take advantage of the efficient operator evaluation algorithms in the different CEED packages. This major release includes a new HIP backend, revamped OCCA backend, restriction by offsets instead of blocked indices, improved solver ingredients, and numerous improvements to examples.

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CEED MS-35 Milestone Report Released

September 30, 2020 (release)

The Center for Efficient Exascale Discretizations (CEED) is part of the Department of Energy’s Exascale Computing Project (ECP). The Center helps applications leverage future architectures by developing discretization algorithms that better exploit the hardware and deliver a significant performance gain over conventional methods. CEED regularly releases milestone (MS) reports to document progress and ensure transparency throughout its multi-year efforts.

The MS-35 report details the CEED accomplishments towards the following goals:

LBANN 0.101 Released

September 29, 2020 (release)

The Livermore Big Artificial Neural Network toolkit (LBANN) is an open-source, HPC-centric, deep learning training framework that is optimized to compose multiple levels of parallelism. This release includes support for new network structures and layers, a Python front-end, several performance optimizations, increased model portability and usability, new datasets, and much more.

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New Repo: Kosh

September 28, 2020 (new-repo)

Kosh allows codes to store, query, share data via an easy-to-use Python API. Kosh lies on top of Sina and, as a result, can use any database backend supported by Sina. This software aims to make data access and sharing as simple as possible. The repo includes installation instructions.

New Repo: Spheral++

September 22, 2020 (new-repo)

Spheral++ (documentation) provides a steerable parallel environment for performing coupled hydrodynamical and gravitational numerical simulations. Hydrodynamics and gravity are modeled using particle based methods (SPH and N-Body). Features include:

MFEM Advances to the R&D 100 Award Finals

September 21, 2020 (story)

The annual R&D 100 Awards finalists have been announced. The MFEM (Modular Finite Element Methods) high-order math library is a finalist in the Software/Services category. Winners will be announced on October 1. Watch this video about MFEM’s impact on scientific simulations.

New Repo: PYB11Generator

September 21, 2020 (new-repo)

PYB11Generator is a python based code generator that creates pybind11 code for binding C++ libraries as extensions in Python. The software parses input that is very close to writing the desired interface in native python, turning this into the corresponding pybind11 C++ code. The repo includes documentation.

Celebrate Exascale Day

September 18, 2020 (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 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.

LLNL’s highlights include:

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.

New Repo: CAMP

August 25, 2020 (new-repo)

CAMP is a compiler-agnostic metaprogramming library providing concepts, type operations, and tuples for C++ and Cuda. The project collects a variety of macros and metaprogramming facilities for C++ projects.

CEED's Virtual Annual Meeting

August 12, 2020 (event-report)

As part of the Exascale Computing Project (ECP), the Center for Efficient Exascale Discretizations (CEED) is a research partnership between two U.S. Department of Energy laboratories and five universities. LLNL leads the Center. All of CEED’s software is open source.

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.

New Repo: mpibind

July 22, 2020 (new-repo)

mpibind is a memory-driven algorithm to map parallel hybrid applications to the underlying heterogeneous hardware resources transparently, efficiently, and portably. Unlike other mappings, its primary design point is the memory system, including the cache hierarchy. Compute elements are selected based on a memory mapping and not vice versa.

Spack Tutorial on AWS

July 20, 2020 (event-report)

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 Repo: SPIFY

July 13, 2020 (new-repo)

SPIFY is a C++ library for parsing input files to be used in scientific computing applications. The library allows an application developer to define a full set of required and optional input variable of different types and handles all of the parsing and validation. Examples are included in the repo.

New Repo: pLiner

July 08, 2020 (new-repo)

Compiler optimizations can alter significantly the numerical results of scientific computing applications. When numerical results differ significantly between compilers, optimization levels, and floating-point hardware, these numerical inconsistencies can impact programming productivity. pLiner is a framework that helps programmers identify locations in the source of numerical code that are highly affected by compiler optimizations. It uses a novel approach to identify such code locations by enhancing the floating-point precision of variables and expressions.

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!

New Repo: Quicksilver

July 02, 2020 (new-repo)

Quicksilver is a proxy application that represents some elements of the Mercury workload by solving a simplified dynamic Monte Carlo particle transport problem. Quicksilver attempts to replicate the memory access patterns, communication patterns, and the branching or divergence of Mercury for problems using multigroup cross sections. OpenMP and MPI are used for parallelization. Documentation is available.

New Repo: Babel

July 02, 2020 (new-repo)

Babel is a language interoperability tool intended for use by the high-performance scientific computing community. It supports the Scientific Interface Definition Language (SIDL) for the language-independent declaration of interfaces associated with scientific software packages. Although the project is no longer funded, it has recently moved to GitHub for ease of access by the HPC community. Documentation is available.

New Repo: PolyClipper

June 19, 2020 (new-repo)

PolyClipper is a C++ reimplementation of the geometric clipping operations in the R3D library originally written by Devon Powell, as documented in the paper Powell & Abell (2015). This repo focuses on clipping polygons (in 2D (x,y) coordinates) and polyhedra (in 3D (x,y,z) coordinates) with planes, returning new polygons/polyhedra as the result of this clipping. The input polygons/polyhedra may be non-convex and arbitrarily complex, but the only clipping operation supported is with planes. This is equivalent to intersecting one arbitrary (not necessarily convex) polygon/polyhedron with a convex polygon/polyhedron. Documentation is available.

New Repo: MaPPeRTrac

June 16, 2020 (new-repo)

MaPPeRTrac stands for Massively Parallel, Portable, and Reproducible Tractography. This repo provides a brain tractography workflow for high-performance computing. It incorporates novel technologies to simplify and accelerate neuroimaging research. Setup requires Python 3.5+ and SLURM job scheduling on a multi-node system.

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.

ISC Is Going Virtual

June 08, 2020 (event)

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.

New Repo: CARE

May 22, 2020 (new-repo)

CHAI and RAJA provide an excellent base on which to build portable code for different computing architectures. CARE expands on that functionality, adding new features such as loop fusion capability and a portable interface for many numerical algorithms. CARE provides all the basics for anyone wanting to write portable code.

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.

New Repo: BMSL

May 14, 2020 (new-repo)

BMSL, the Bayesian Multitask with Structure Learning model, is a repository that accompanies a paper: “Bayesian Multitask Learning Regression for Heterogeneous Patient Cohorts” from the Journal of Biomedical Informatics. Multitask learning (MTL) is a sub-field of machine learning in which individual models for performing potentially related tasks are learned jointly. The Bayesian MTL model infers the task relationship structure directly from the data.

New Repo: WCS

May 06, 2020 (new-repo)

WCS (short for Whole Cell Simulator) is a computational framework that enables seamless integration of diverse simulation methods used in creating a whole cell model (i.e., all the known biochemical processes in a cell). Its methods run simultaneously, not only for whole pathways but also for subsets of reactions.

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.

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.

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 (&lt101 core) desktop-sized projects to large (&gt105 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.

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.

Many open source technologies were featured in LLNL’s technical program. Read the full recap on LLNL’s main website.

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.

Among open source projects Lee highlighted in his talk were 2019 R&D 100 Award winners Spack and SCR (Scalable Checkpoint/Restart) and the software stack underpinning the Exascale Computing Project.

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).

Two Repos among 2019 R&D 100 Award Finalists

October 24, 2019 (story)

The annual R&D 100 Awards finalists have been announced. Among them are six LLNL-developed or co-developed technologies. In the Software/Services category, two open source projects have been recognized:SCR (Scalable Checkpoint/Restart) and Spack. Winners will be announced on October 29.

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.

New website features include:

*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.

LLNL's Third Annual Developer Day Focuses on Career Lifecycle and Best Practices

July 26, 2019 (story)

Initiated in 2017, Developer Day is a day-long, annual event that brings software developers together from all over LLNL. This year’s Dev Day included a panel discussion about onboarding new hires; short talks on topics ranging from staying engaged at work to learning unicode characters; and deep dives on software quality assurance and cloud services. The event featured a keynote address by Dr. Jeffrey Carver from the University of Alabama, who spoke about “Contemporary Peer Code Review Practices in Research Software.”

Why Do We Need Supercomputers and Who Is Using Them?

July 10, 2019 (story)

PC Magazine recently featured LLNL’s supercomputing facility to find out how the supercharged machines handle everything from virtual nuclear weapons tests to weather modeling. The article highlights examples of simulations performed on the Lab’s computers, such as a fusion energy research experiment generated by the MFEM-based BLAST shock hydrodynamics code and visualized with VisIt.

Redesign of Cardioid's Heartbeat Simulation Brings Code One Step Closer to Clinical Use

June 12, 2019 (multimedia) (story)

LLNL researchers have successfully optimized a code that models the human heartbeat for next-generation, GPU-based supercomputers, with an eye on developing it for virtual drug screening and modeling heart activity in clinical settings. Cardioid, a suite merging mathematical solvers for electrophysiology, fiber-generation, cardiac mechanics, torso-electrocardiograms (ECGs) and cardiac meshing tools, simulates the electrical current running through the heart tissue, triggering cells to contract like cascading dominoes and causing the heart to beat. It was originally developed by LLNL and IBM for Sequoia, at one time the world’s fastest supercomputer, and was a finalist for the 2012 Gordon Bell Prize, supercomputing’s top honor.

Learn more:

Video: LLNL at the 2019 Red Hat Summit

May 08, 2019 (event-report) (multimedia)

At the recent Red Hat Summit in Boston, LLNL’s Robin Goldstone discussed open-source technologies and the Sierra supercomputer. Goldstone, an HPC solutions architect, said “open source makes perfect sense” for scalability and performance in an HPC center like LLNL’s. She stated, “We have all that visibility and that software. If it doesn’t work for our needs, we can make it work for our needs. And then we can give it back to the community because even though people aren’t doing things at the scale that we are today, a lot of the things that we’re doing really do trickle down and be used by a lot of other people.” A transcript of her interview is included with the video, which runs 15:28.

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.

How Machine Learning Could Change Science

May 03, 2019 (story)

Artificial intelligence tools are revolutionizing scientific research and changing the needs of high performance computing. In an article from Data Center Dynamics, LLNL’s Fred Streitz and Brian Van Essen discuss the future of scientific computing, highlighting the Exascale Computing Project (ECP) and the Livermore Big Artificial Neural Network (LBANN).

The ECP is a multi-institutional Department of Energy collaboration aimed at achieving exascale computing capability. Many open source software projects, from LLNL and elsewhere, are crucial components of the ECP ecosystem.

LBANN is an open source deep learning toolkit developed at the Lab. It provides model-parallel acceleration through domain decomposition to optimize for strong scaling of network training.

Opening Supercomputing to All Agencies

April 24, 2019 (story)

LLNL’s Ian Lee discusses the importance of open-source software and cloud computing for HPC centers and government agencies in this article. He states, “We’ve been doing open source on big Unix systems for more than 20 years. Back then, if we produced open source software for our supercomputers, we were the only ones who could use that software. Now, the software can be ported out and mainstreamed, and it’s a lot easier to make use of supercomputing in other places.”

Spack Team Visits RIKEN

April 23, 2019 (event-report)

Spack’s first tutorial in Japan took place on April 23, 2019. With more than 40 participants, the onsite tutorial at RIKEN’s Kobe research center was the latest international event for the Spack team and collaborators. Read more about Spack’s European tour of HPC facilities. Everything you need to get started with Spack is available on the website.

Caliper Library Highlighted at 31st VI-HPS Tuning Workshop

April 15, 2019 (event-report)

The Virtual Institute – High Productivity Supercomputing (VI-HPS) conducts a long-running series of tuning workshops, where participants can learn about programming tools developed by the institute partners. Morning sessions consist of tool presentations and hands-on exercises. In the afternoon, users can apply the tools to their own codes with the help of the instructors. Whilst most of the workshops take place in Europe, the 31st tuning workshop was held at the University of Tennessee, Knoxville (UTK), on April 9–12, 2019.

As part of the workshop, LLNL computer scientist David Boehme conducted a 75-minute tutorial on Caliper, an open-source performance profiling library for HPC software. The session included hands-on exercises using the Lulesh proxy application as an example. There were around 15–20 participants, primarily HPC software developers from UTK and Oak Ridge National Laboratory, as well as the other HPC tool presenters. This tutorial marked the first time Caliper was presented within the VI-HPS tuning workshop series. Boehme’s tutorial was well received, and several participants were able to successfully apply Caliper to their programs.

The workshop also provided an opportunity to discuss common software infrastructure as well as integration and interoperability possibilities with other performance analysis tools. For example, the PAPI team plans to explore using Caliper’s data collection and processing functionality. Finally, as a VI-HPS member organization, LLNL’s participation in the tuning workshop series helped showcase the Lab’s strong portfolio of open-source programming tools among the VI-HPS partners and in the HPC community at large.

Learn more about Caliper:

CTR: An Introduction Using Recent Tech Refresh Experiences on VisIt

April 12, 2019 (story)

This LLNL-authored blog post describes the practice of continuous technology refreshment, or CTR – the periodic upgrade or replacement of infrastructure to deliver continued reliability, improved speed, capacity, and/or new features. Using the VisIt code’s recent migration to GitHub as an example, the post explains the development team’s process through wrangling binary content, revision control, issue tracking, documentation, and other refreshments.

Learn more:

The Linux Foundation's Open Source Leadership Summit

March 15, 2019 (event-report)

The Linux Foundation’s Open Source Leadership Summit occurred in Half Moon Bay, California, on Thursday, March 14. LLNL’s Todd Gamblin presented “Open Source in the Exascale Computing Project: Building a Software Ecosystem for Science.” Check out the conference schedule.

This presentation covered the challenges of building software for machines that don’t exist yet, and how government laboratories, academia, and industry are collaborating to build a highly optimized software distribution. From deploying services like GitLab CI and JupyterHub in high-security HPC centers, challenges for architecture-specific containers, the use of Spack to package and distribute optimized binaries, and the social hurdles of scientists and developers working together, this talk summarized the open source challenges in DOE’s largest-ever HPC software project.

The Great Migration: VisIt Moves from SVN to GitHub

March 08, 2019 (story)

Software development is often a story of teamwork and determination. It’s a tale of persistence through failure toward, ideally, success. At LLNL, this story plays out in countless daily iterations as software teams strive to advance the Lab’s national security mission. When it comes to supporting both stockpile stewardship and foundational science, the VisIt visualization tool is the backbone of LLNL’s computer simulation analysis and visualization capabilities.

For the VisIt team, migration is modernization. Some of VisIt’s original development technologies are now considered ancient. But migrating 2 million lines of code is easier said than done. Go behind the scenes as an LLNL team discusses the logistics, challenges, and benefits of VisIt’s complicated move to GitHub.

Learn more:

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.

Learn more:

ESGF Conference Caps a Productive Year

February 12, 2019 (event-report)

Held in Washington, DC, the Earth System Grid Federation’s (ESGF) 8th annual face-to-face conference was a lively, fruitful affair. The event packed 40 presentations, several plenary sessions, a poster session, guest speakers, an awards ceremony, and an executive committee meeting into the week.

The federation houses an enormous database of global observational and simulation data—more than 5 petabytes—and manages the HPC hardware and software infrastructure necessary for scientific climate research. In the nearly two decades since its launch, ESGF has grown to serve 25,000 users on 6 continents.

Among ESGF’s 2018 milestones were support for CMIP6 data (thanks to input4MIPs and obs4MIPs initiatives), beta v3.0 of the software stack installer, OAuth single sign-on integration, and progress in containerized architecture. Read more about the conference and check out ESGF’s GitHub repo.

ScrubJay: A Bird's-Eye View of Computing Performance

December 10, 2018 (story)

ScrubJay, an open-source performance data analysis tool, helps ensure that the Laboratory’s HPC center lives up to its name. Check out this new writeup in LLNL’s magazine, Science & Technology Review. Fork the repo on GitHub.

ScrubJay is an intuitive, scalable framework for automatic analysis of disparate HPC data. ScrubJay decouples the task of specifying data relationships from the task of analyzing data. Domain experts can store reusable transformations that describe the projection of one domain onto another. The program also automates performance analysis. Analysts provide a query over logical domains of interest, and ScrubJay automatically derives the needed steps to transform raw measurements. This process makes large-scale analysis tractable and reproducible, thus providing crucial insights into HPC facilities.

DOE Machines Dominate Record-Breaking SC18

November 20, 2018 (event-report)

Supercomputing ‘18 (SC18), held Nov. 11–16 in Dallas, broke records for attendees and exhibitors and saw LLNL once again make its presence felt on the world’s biggest HPC stage. For the first time in five years, the U.S. captured the top two spots on the TOP500 List of the world’s fastest supercomputers: Summit at ORNL and Sierra at LLNL.

Highlights from the conference include:

New Computing Cluster Coming to LLNL

November 13, 2018 (story)

The Lab is looking forward to Corona, a new unclassified HPC cluster that will provide unique capabilities for Lab researchers and industry partners to explore data science, machine learning, and big data analytics. Corona will help NNSA assess future architectures, fill institutional needs to develop leadership in data science and machine learning capabilities at scale, and provide access to HPC partners.

Read more about LLNL’s commodity clusters.

Sierra Supercomputer Dedicated and Ranked

November 12, 2018 (story) (multimedia)

LLNL recently unveiled the new 125-petaflop-capable Sierra supercomputer. Sierra will serve the NNSA’s three nuclear security laboratories: LLNL, Sandia National Laboratories, and Los Alamos National Laboratory, providing high-fidelity simulations in support of NNSA’s core mission of ensuring the safety, security, and effectiveness of the nation’s nuclear stockpile. Its arrival represents years of procurement, design, code development and installation, requiring the efforts of hundreds of computer scientists, developers and operations personnel working in close partnership with IBM, NVIDIA, and Mellanox.

Just a few weeks later, Sierra rose from third to second place on the TOP500 list of the world’s fastest computing systems after reaching 94.6 petaflops on the Linpack benchmark test. The latest rankings were announced at SC18.

See Sierra’s system details and watch a video of the dedication.

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.

Good Times at GitHub Universe

November 01, 2018 (event-report)

LLNL open-source champions Laura Weber, Ian Lee, and David Beckingsale attended the 2018 GitHub Universe conference in San Francisco. Billed as “a conference for the builders, planners, and leaders defining the future of software”, the team enjoyed hearing about upcoming GitHub enhancements and being able to network with GitHub Federal employees and other GitHub users.

One recurring theme was inner source, the use of open source software development best practices and the establishment of an open-source-like culture within organizations. With this practice the organization may still develop proprietary software, but internally opens up its development.

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.

See all news in the archive