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VisIt 3.0.2 Released September 24, 2019

VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. Among the enhancements included in v3.0.2 are:

  • Openssl added to the list of required libraries in build_visit
  • Added turbo color table
  • Host profiles added for the Oak Ridge National Laboratory’s Summit supercomputer
  • Binary distributions added for Ubuntu 16, Ubuntu 18, Debian 9, and Fedora 27
  • and much more!

Learn more:

New Repo: FPP September 24, 2019

FPP (Function Preserving Projection) is a linear projection technique for finding a 2D view that captures interpretable patterns of the given function in a high-dimensional domain. The function can be univariate or multivariate, continuous (regression), or discrete (classification).

SUNDIALS 5.0.0-dev.2 Released September 18, 2019

SUNDIALS is a SUite of Nonlinear and DIfferential/ALgebraic equation Solvers. This release includes:

  • new optional operation to the SUNLINEARSOLVER API
  • performance improvements to the CUDA NVECTOR
  • two new Set functions to MRIStep
  • new SUNLinearSolver implementation
  • three new accessor functions to the SUNLinSol_KLU module

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libCEED 0.5 Released September 18, 2019

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. libCEED is a C99 library with no external dependencies.

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Charliecloud 0.11 Released September 17, 2019

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. This simple approach avoids most security risks while maintaining access to the performance and functionality already on offer.

This release contains new features along with documentation and test suite improvements:

  • Charliecloud is now in Fedora and EPEL
  • ch-grow: support ARG instruction
  • ch-run: /etc/resolv.conf on the host is now optional

Learn more:

Umpire 1.1.0 Released September 16, 2019

Umpire is a resource management library that allows the discovery, provision, and management of memory on next-generation architectures. v1.1.0 includes upgrades to detect version mismatches when linking multiple libraries, fixes to signature of C function, and updated pool algorithm.

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New Repo: UEDGE September 13, 2019

UEDGE is an interactive suite of physics packages using the Python or BASIS scripting systems. The plasma is described by time-dependent 2D plasma fluid equations that include equations for density, velocity, ion temperature, electron temperature, electrostatic potential, and gas density in the edge region of a magnetic fusion energy confinement device. slab, cylindrical, and toroidal geometries are allowed, and closed and open magnetic field-line regions are included. Classical transport is assumed along magnetic field lines, and anomalous transport is assumed across field lines. Multi-charge state impurities can be included with the corresponding line-radiation energy loss.

New Repo: MI-ChemVis September 01, 2019

Domain-specific applications often require specially designed visualization systems. MI-ChemVis is a browser-based visualization of chemistry papers, specifically morphology, material, and chemical data extracted from them. The UI is made with nanomaterial synthesis papers in mind.

JuliaCon Recap and Videos August 22, 2019

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.

CCT 1.0.5 Released August 14, 2019

The Coda Calibration Tool (CCT) calculates reliable moment magnitudes for small- to moderate-sized seismic events. This release contains performance improvements and other updates, namely:

  • Added REST endpoint on the envelope service to request to just get stacked files back rather than envelopes
  • 10–30% performance improvements when making many (>10K) high sample rate (>100hz) envelopes at once

Learn more:

New Repo: ExaCMech August 05, 2019

ExaCMech is a GPU-friendly library of constitutive models. The models are based on standard continuum mechanics concepts. Crystal-mechanics-based and porosity-mechanics-based models are a principal focus. Models are meant for standard crystalline metallic materials deforming under quasi-static conditions. Constitutive model response is a main ingredient in the simulation of deformation of material, and the constitutive model has two main jobs: It provides the stress tensor that goes into the balance of linear momentum, and it updates the evolving state of the material. This state can be tracked by variables for the stress, dislocation density, orientation of crystal lattices, grain size, and so on. For context, the GitHub repository includes links to relevant journal articles that reference similar models and algorithms.

CHAI 1.2.0 Released August 05, 2019

The CHAI library handles automatic data migration to different memory spaces behind an array-style interface. It was designed to work with RAJA and integrates with it. CHAI may be used with other C++ abstractions as well. v1.2.0 contains support for AMD devices using HIP as well as updates for the 1.0.0 release of Umpire.

Umpire 1.0.0 Released August 03, 2019

Umpire is a resource management library that allows the discovery, provision, and management of memory on next-generation architectures. With v1.0.0, Umpire is MPI-aware, and AllocationStrategies may be wrapped with multiple extra layers. Additional changes include directing log and replay output to files, one per process.

Learn more:

New Repo: PySABER August 02, 2019

PySABER is a python package for characterizing the X-ray source and detector blur in cone-beam X-ray imaging systems. SABER is an abbreviation for Systems Approach to Blur Estimation and Reduction. Note that even parallel beam X-rays in synchrotrons are in fact cone beams albeit with a large source to object distance. X-ray images, also called radiographs, are simultaneously blurred by both the X-ray source spot blur and detector blur. This package uses a numerical optimization algorithm to disentangle and estimate both forms of blur simultaneously.

New Repo: HELICS-FMI August 01, 2019

Energy systems and their associated information and communication technology systems are becoming increasingly intertwined. As a result, effectively designing, analyzing, and implementing modern energy systems increasingly relies on advanced modeling that simultaneously captures both the cyber and physical domains in combined simulations. It is designed to increase scalability and portability in modeling advanced features of highly integrated power system and cyber-physical energy systems.

LLNL’s Hierarchical Engine for Large-scale Infrastructure Co-Simulation (HELICS) was originally developed for electric power systems use cases, and now it can be used for co-simulation in other domains. The HELICS library provides a general-purpose, modular, highly-scalable co-simulation framework that runs cross-platform. A new repository has been added to the HELICS suite, HELICS-FMI, which allows functional mockup units to interact with HELICS.

Software Portal Redesign and GitHub Integration July 30, 2019

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:

  • Home page leaderboard image
  • Dynamic catalog navigation by categories and their “overflow” pages (e.g., Applications)
  • Standardized use of topic tags on repos, which drive the categories
  • RADIUSS catalog,* a subset of the full catalog
  • Embedded Twitter feed on the News and News Archive pages
  • Automatic twice-daily GitHub data update, which updates the repos listed under each category as well as the visualizations on the Explore page
  • and much more!

*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

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.”

RAJA 0.9.0 Released July 25, 2019

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.0.9.0 release includes new features:

  • Change in atomic operations
  • Extension of the lambda statement interface in the RAJA kernel API
  • Support of tuple index values by minloc and maxloc reductions

Learn more:

New Repo: Bridge Kernel July 25, 2019

Bridge Kernel is a Jupyter kernel for connecting to backends that implement the bridge kernel (bk) protocol. The bk protocol is a small client-server protocol that emphasizes minimal dependencies, easier embedding with MPI, secure connections, secure authentication, and automatic tunneling.

New Repo: SPIFY July 20, 2019

SPIFY, which stands for Spify Parser of Input Files with YAML syntax, 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.

New Repo: GIDIplus July 18, 2019

GIDIplus provides C++ libraries for accessing nuclear data from the Generalized Nuclear Database Structure (GNDS).

CEED’s Impact on Exascale Computing Project Efforts Is Wide-Ranging July 17, 2019

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. The focus is on high-order methods for high-fidelity and better machine utilization, with a range of orders providing flexibility in uncertain hardware and software environments.

The recent release of CEED v2.0 includes many open source projects such as 12 integrated Spack packages for libCEED, MFEM, Nek5000, NekCEM, Laghos, NekBone, HPGMG, OCCA, MAGMA, gslib, PETSc, and PUMI, plus an updated CEED “meta-package.”

Video: CASC Accelerates Scientific Discovery July 17, 2019

LLNL’s Center for Applied Scientific Computing (CASC) serves as a window to the broader computer science, computational physics, applied mathematics, and data science research communities. A new video showcasing CASC’s computational mathematics research debuted at the International Council for Industrial and Applied Mathematics (ICIAM) conference in July. Among the featured projects are open source repos MFEM, a library of scalable finite-element discretization and solver algorithms, and [XBraid] (https://github.com/XBraid/xbraid), a library of parallel-in-time solvers.

Charliecloud 0.10 Released July 16, 2019

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.

This release contains two important new features:

  • Completely unprivileged end-to-end workflow, with no root, no sudo, and no setuid/setcap helper programs
  • SquashFS wrapper scripts to facilitate a workflow based on SquashFS files rather than tarballs

Learn more:

VisIt 3.0.1 Released July 15, 2019

VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. Among the enhancements included in v3.0.1 are:

  • Rewrite of the Mili database reader
  • New database readers for ADIOS2 v2.4.0
  • Default color map settings
  • Enhanced default volume renderer
  • Ability for internallauncher to launch single-processor parallel engines

Learn more:

New Repo: CSLD July 13, 2019

Compressive Sensing Lattice Dynamics, or CSLD, provides a comprehensive package to study lattice dynamics from first-principles. The interatomic force constants were fitted using the compressive sensing algorithm. CSLD requires Python, C++, and Fortran 90 compilers for installation.

Why Do We Need Supercomputers and Who Is Using Them? July 10, 2019

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.

MacPatch 3.3.0.2 released July 08, 2019

MacPatch – used at LLNL to manage 3,000+ computers – simplifies the act of patching and installing software on Mac OS X based systems. The client relies on using the built-in software update application for patching the Mac OS X system updates and its own scan and patch engine for custom patches. v3.3.0.2 is a major release with a completely new UI and the backend updated to Python 3.

Learn more:

New Repo: Zero-Order Reaction Kinetics (Zero-RK) July 01, 2019

Zero-Order Reaction Kinetics, or Zero-RK is a software package that simulates chemically reacting systems in a computationally efficient manner. The fundamental advance embodied in Zero-RK is the numerical approach, which results in orders-of-magnitude reduction in simulation time while maintaining the accuracy of the results.

New Repo: H5Z-ZFP June 28, 2019

H5Z-ZFP is a highly flexible floating-point and integer compression plugin for the HDF5 library using ZFP compression. The plugin supports ZFP versions 0.5.0 through 0.5.5. It also supports all 4 modes of the ZFP compression library as well as 1D, 2D, and 3D datasets of single and double precision integer and floating-point data. Check out the GitHub repo and the v1.0.0 release.

umap 2.0.0 Released June 26, 2019

Umap is a library that provides an mmap()-like interface to a simple, user- space page fault handler based on the userfaultfd Linux feature. The use case is to have an application specific buffer of pages cached from a large file (i.e. out-of-core execution using memory map). This release includes:

  • Performance improvements
  • Support for multiple umap regions
  • Support for page prefetch
  • Support for page read-ahead

Learn more:

Caliper 2.1.0 Released June 25, 2019

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. This release includes several improvements and new features:

  • Simplified linking of all modules
  • ConfigManager for enabling configuration profiles
  • ChannelController for creating custom configuration profiles
  • RegionProfile for accessing timing information
  • cpuinfo service reports
  • Gotcha 1.0.2 bundled

Learn more:

SUNDIALS 5.0.0-dev.1 Released June 24, 2019

SUNDIALS is a SUite of Nonlinear and DIfferential/ALgebraic equation Solvers. This version is a beta release of the next major SUNDIALS version and offers a preview of what is to come, including

  • new Fortran 2003 interface modules
  • new linear solver interface functions
  • a new N_Vector implementation, NVECTOR_MPIPLUSX
  • and much more!

Learn more:

Kripke 1.2.4 Released June 18, 2019

Kripke is a simple, scalable, 3D Sn deterministic particle transport code. Its primary purpose is to research how data layout, programming paradigms and architectures effect the implementation and performance of Sn transport. A main goal of Kripke is investigating how different data-layouts effect instruction, thread and task level parallelism, and what the implications are on overall solver performance. v1.2.4 changes the software license to BSD 3-clause.

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BLT 0.2.5 Released June 14, 2019

BLT (Building, Linking, and Testing) is a streamlined CMake build system foundation for developing HPC software. BLT makes it easy to get up and running on a wide range of HPC compilers (e.g., gcc, clang), operating systems (e.g., Linux, Mac OS, Windows), and technologies (e.g., MPI, OpenMP, CUDA). BLT also includes unit testing and benchmarking.

LLNL initially released BLT in 2017, and now v0.2.0 and v0.2.5 are available.

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Redesign of Cardioid's Heartbeat Simulation Brings Code One Step Closer to Clinical Use June 12, 2019

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.

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Video: SCR Framework, Accelerating Resilience and I/O for Supercomputing Applications June 07, 2019

The SCR software framework provides efficient, scalable checkpoint/restart capability for simulation codes, ensuring faster time to solution and allowing scientists to focus on the science. SCR caches checkpoint data in storage on the compute nodes of a Linux cluster to provide a fast, scalable checkpoint restart capability for MPI codes.

In this video, LLNL’s Kathryn Mohror explains how SCR works. Physicist Denise Hinkel then discusses how SCR has impacted simulation capabilities at the National Ignition Facility.

Video: Spack, a Flexible Package Manager for HPC Software June 06, 2019

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.

In this video, LLNL’s Todd Gamblin and Greg Becker describe how Spack works and how its open source community has grown. They are joined by Lori Diachin, deputy director for the U.S. Department of Energy’s Exascale Computing Project, or ECP, who explains Spack’s value to the ECP software stack.

Magpie 2.3 Released June 01, 2019

Magpie contains a number of scripts for running big data software in HPC environments. It currently supports running over the parallel file system Lustre and running over any generic network filesystem. There is scheduler/resource manager support for Slurm, Moab, Torque, and LSF.

This release focuses on adding experimental support for Ray. Learn more:

MFEM 4.0 Released May 24, 2019

Version 4.0 of MFEM, a lightweight, general, scalable C++ library for finite element methods, is now available at: http://mfem.org

The goal of MFEM is to enable high-performance scalable finite element discretization research and application development on a wide variety of platforms, ranging from laptops to exascale supercomputers.

For the first time ever, MFEM-4.0 adds support for GPU acceleration in the library:

  • Device kernels can be written in CUDA, OCCA, RAJA or OpenMP.
  • Several examples have been ported with minimal code changes.
  • Many linear algebra and finite element operations can use device acceleration by simply replacing loops with the MFEM_FORALL macro.
  • The library provides seamless device/host memory management.

Some other new additions in version 4.0 are:

  • Partially assembled finite element operators in the core library.
  • Support for wedge/prism elements and meshes with mixed element types.
  • General “low-order refined”-to-“high-order” field transfer.
  • Seven new examples and miniapps.

The MFEM library has many more features, including:

  • 2D and 3D, arbitrary order H1, H(curl), H(div), L2, NURBS elements.
  • Parallel version scalable to hundreds of thousands of MPI cores.
  • Conforming/nonconforming adaptive mesh refinement (AMR), including anisotropic refinement, derefinement and parallel load balancing.
  • Galerkin, mixed, isogeometric, discontinuous Galerkin, hybridized, and DPG discretizations.
  • Support for triangular, quadrilateral, tetrahedral and hexahedral elements, including arbitrary order curvilinear meshes.
  • Scalable algebraic multigrid, time integrators, and eigensolvers.
  • Lightweight interactive OpenGL visualization with the MFEM-based GLVis tool.

MFEM is being developed in CASC, LLNL and is freely available under LGPL 2.1.

For more details, see the interactive documentation and the full CHANGELOG.

ZFS on Linux 0.8.0 Released May 23, 2019

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.

v0.8.0 includes many performance updates, new features, and improvements, such as:

  • Native encryption
  • Raw encrypted ‘zfs send/receive’
  • Pool TRIM and initialization
  • Project accounting and quota
  • Channel programs
  • Pyzfs and Python 3 compatibility

Learn more:

LBANN 0.99 Released May 14, 2019

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 training algorithms, performance optimizations, I/O and data readers, updates to the Python front-end, and much more.

Learn more:

Charliecloud 0.9.10 Released May 14, 2019

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.

This release includes:

  • New OpenMPI examples
  • Updated Travis CI tests
  • New interface for ch-build2dir

Learn more:

Video: LLNL at the 2019 Red Hat Summit May 08, 2019

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

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.

CCT 1.0.4-M3 Released May 07, 2019

The Coda Calibration Tool (CCT) calculates reliable moment magnitudes for small- to moderate-sized seismic events. This release contains many improvements and updates, including:

  • Overall optimization for the GUI and calibration modules (faster while using less memory)
  • Configurable group velocities used for selection criteria during calibration
  • Filter data from use in calibration
  • Auto (re)center of the map
  • Three new plots on the Mw tab
  • and much more!

Learn more:

LMT 3.2.6 Released May 06, 2019

The Lustre Monitoring Tools (LMT) repo is a distributed system that provides a “top”-like display of the activity levels of the server-side (MDS, OSSes, and LNET routers) nodes of one or more Lustre-based filesystems. This release includes support for Lustre 2.12.0.

Learn more:

zfp 0.5.5 Released May 05, 2019

zfp is a library for compressed numerical arrays that support high-throughput read and write random access. zfp also supports streaming compression of integer and floating-point data, e.g., for applications that read and write large data sets to and from disk. zfp is primarily written in C and C++ but also includes Python and Fortran bindings.

This release includes these additions to the code:

  • Support for reversible (lossless) compression of floating-point and integer data
  • Methods for serializing and deserializing zfp’s compressed arrays
  • Python bindings for compressing NumPy arrays
  • Fortran bindings to zfp’s high-level C API

Learn more:

How Machine Learning Could Change Science May 03, 2019

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.

VisIt 3.0 Released May 01, 2019

This is a huge release for LLNL’s VisIt visualization tool. The many new features include:

  • Support for outputting Cinema databases
  • Support for rendering 3D images using the OSPRay
  • Enhancements that leverage VTK-m for some operations
  • Custom animation behaviors in plots
  • Ability to build expressions with support for OpenMP, letting them parallelize over multiple threads

The release notes also detail changes in GUI behavior, file format reader, plots, operators, expression language, configuration, and more.

Learn more:

MSR-SAFE 1.3.0 Released April 29, 2019

MSR-SAFE allows safer access to model-specific registers. v1.3.0 includes updates to the spank plugin, msrsave and msrrestore functions, and command line parameters. The release also adds an initial Travis CI yaml configuration file to test against multiple OS.

Learn more:

Magpie 2.2 Released April 25, 2019

Magpie contains a number of scripts for running big data software in HPC environments. It currently supports running over the parallel file system Lustre and running over any generic network filesystem. There is scheduler/resource manager support for Slurm, Moab, Torque, and LSF.

This release includes:

  • New submission script type “sbatchmpirun”
  • Experimental support for Tensorflow
  • Support for additional versions of Spark and Hadoop

Learn more:

PnMPI 1.8.1 Released April 24, 2019

PnMPI is a dynamic MPI tool infrastructure that builds on top of the standardized PMPI interface. With it you can run multiple PMPI tools concurrently, activate PMPI tools without relinking, multiplex toolsets during a single run, and write cooperative PMPI tools.

Learn more:

Opening Supercomputing to All Agencies April 24, 2019

LLNL’s Ian Lee discusses the importance of open-source software and cloud computing for HPC centers and government agencies in this GCN.com 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

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.

MemSurfer 1.0 Released April 17, 2019

This is MemSurfer’s initial release. MemSurfer is an efficient and versatile tool to compute and analyze membrane surfaces found in a wide variety of large-scale molecular simulations. MemSurfer works independent of the type of simulation, directly on the 3D point coordinates, and can handle a variety of membranes as well as atomic simulations. It provides many in-built analysis tasks, such as computing the membrane curvature, density and normals of lipids, and area per lipid.

Learn more:

Caliper Library Highlighted at 31st VI-HPS Tuning Workshop April 15, 2019

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:

Charliecloud 0.9.9 Released April 13, 2019

Charliecloud provides user-defined software stacks (UDSS) for HPC centers. It uses Linux user namespaces to run containers with no privileged operations or daemons and minimal configuration changes on center resources.

This release includes:

  • Docker environment variables available in images
  • Alpine example images upgraded to 3.9
  • Documentation improvements and more

Learn more:

CTR: An Introduction Using Recent Tech Refresh Experiences on VisIt April 12, 2019

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:

RAJAPerf 0.5.1 Released April 12, 2019

The RAJA performance suite (RAJAPerf) is designed to explore performance of loop-based computational kernels found in HPC applications. 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.

v0.5.1 contains several documentation updates and changes to default CMake configuration so that RAJA tests and examples are not built unless explicitly turned on by passing the proper options to CMake.

Learn more:

Umpire 0.3.3 Released April 11, 2019

Umpire is a resource management library that allows the discovery, provision, and management of memory on next-generation architectures.

v0.3.3 includes:

  • NUMA strategy that allows allocating memory to specific NUMA nodes
  • Updates to the replay tool
  • GitHub workflow to check for CHANGELOG updates
  • Dockerfile for multi-stage builds
  • and much more!

Learn more:

SCR 2.0 Released March 29, 2019

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 2.0 release marks a milestone in SCR’s long history of bringing dependable, scalable, file set management to multiple HPC platforms.

Some highlights include:

  • Support for multiple platform specific hardware technologies, including Cray DataWarp
  • Portability across many HPC centers via scheduler integration
  • Scalable checkpoint resilience and restart capabilities

Learn more:

SUNDIALS 5.0.0-dev.0 Released March 28, 2019

SUNDIALS is a SUite of Nonlinear and DIfferential/ALgebraic equation Solvers. In this release, an additional N_Vector implementation, NVECTOR_MANYVECTOR, was created to support flexible partitioning of solution data among different processing elements (e.g., CPU + GPU) or for multi-physics problems that couple distinct MPI-based simulations together. Eleven new optional vector operations have also been added to the N_Vector API to support the new NVECTOR_MANYVECTOR implementation.

Learn more:

RAJA 0.8.0 & RAJAPerf 0.5.0 Released March 28, 2019

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 RAJA performance suite (RAJAPerf) is designed to explore performance of loop-based computational kernels of the sort found in HPC applications.

In RAJA v0.8.0, the build system was updated to use the latest version of BLT (or close to it). Depending on how one builds RAJA, this could require changes to how information is passed to CMake. The RAJAPerf 0.5.0 release contains several new kernels, plus substantial changes to many CUDA kernel variants to improve performance.

Learn more:

The Linux Foundation's Open Source Leadership Summit March 15, 2019

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.

New Repo: FGPU March 14, 2019

FGPU is a collection of code examples focusing on porting FORTRAN codes to run on GPU architectures. The repo includes learning aids for developers and a regression test for compilers supporting OpenMP4.5, OpenACC, CUDA FORTRAN, and more. While FGPU’s examples have a heavy FORTRAN emphasis, some examples also include C++ usage. Check out the GitHub repo and LLNL project summary.

Charliecloud 0.9.8 Released March 11, 2019

Charliecloud provides user-defined software stacks (UDSS) for HPC centers. It uses Linux user namespaces to run containers with no privileged operations or daemons and minimal configuration changes on center resources.

This release includes:

  • New RPM spec file and supporting scripts
  • New example workflow using Buildah
  • ch-tar2dir: support tarball extension
  • Refactoring and more

Learn more:

The Great Migration: VisIt Moves from SVN to GitHub March 08, 2019

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:

CCT 1.0.4-M2.1 Released March 06, 2019

The Coda Calibration Tool (CCT) calculates reliable moment magnitudes for small- to moderate-sized seismic events. After the January 25 release, you spoke and we listened! This is a minor bugfix and feature update release based on community feedback. Changes include:

  • Make optimization for Path correction significantly more aggressive
  • Reweight GT spectra with stress drop values defined to be 1.0 across all frequencies
  • Make noise floor display consistent across the board
  • Show ‘bad’ autopicks so humans get more feedback on what the autopicker is doing
  • Remove AP pick if a human moves them (consider as ‘reviewed’)

Learn more:

Caliper 2.0 Released March 04, 2019

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. Caliper is primarily aimed at HPC applications but works for any C/C++/Fortran program on Unix/Linux.

Functionality in v2.0 includes the new Channel API, which allows multiple, independent measurement configurations to be active at the same time.

Learn more:

Magpie 2.1 Released March 02, 2019

Magpie allows Hadoop and similar data analytics frameworks to run on LLNL’s HPC systems. Magpie instantiates the framework within the context of a batch job – rather than on a persistent, dedicated cluster – and by reading and writing from the Lustre parallel HPC file system instead of local disk drives.

v2.1 includes support for several versions of Hbase, Spark, Hadoop, and Zeppelin.

Learn more:

Conduit 0.4 Released March 01, 2019

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. The Core API provides a flexible way to describe and access hierarchical data. v0.4 includes several new functions, new Blueprint protocols, and enhanced Relay support.

Learn more:

Umpire 0.3.2 Released February 25, 2019

Umpire is a resource management library that allows the discovery, provision, and management of memory on next-generation architectures. (Please download the umpire-0.3.2.tar.gz file, rather than the automatically generated files. These do not include all the necessary submodule code.)

v0.3.1 includes:

  • Added a “cookbook” of examples on using Umpire in complex situations
  • Allow users to provide a heuristic to modify pool behavior, determining when unused blocks will be coalesced
  • Modify the CudaAdvice* operations to take a specific device id
  • Improve error message when running a CUDA-enabled version of Umpire on a machine without GPUs

v0.3.2 includes:

  • New functions to create Allocators to the C interface and ensure all C interface files are correctly installed
  • New tool to only replay AllocationMap operations

Learn more:

New Repo: UMAP February 20, 2019

UMAP is a library that provides an mmap()-like interface to a simple, user- space page fault handler based on the userfaultfd Linux feature (starting with 4.3 linux kernel). The use case is to have an application specific buffer of pages cached from a large file, i.e. out-of-core execution using memory map.

Learn more:

Inaugural NAHOMCon19 Coming to San Diego February 14, 2019

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:

SUNDIALS 4.1.0 Released February 13, 2019

In this release:

  • Added an additional N_Vector implementation for Tpetra vector from Trilinos library (user docs and examples are updated to reflect this)
  • Fixed a bug where a nonlinear solver object could be freed twice in some use cases
  • Fixed a bug in ARKodeButcherTable_Write when printing a Butcher table without an embedding
  • Removed EXAMPLES_ENABLE_RAJA CMake option

Important notes:

  • The implementation header files (e.g., arkode_impl.h) are no longer installed. Users who are directly manipulating package memory structures will need to update their code to use the package’s public API.
  • Python is no longer required to run make test and make test_install.

Learn more:

ESGF Conference Caps a Productive Year February 12, 2019

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.

Charliecloud 0.9.7 Released February 12, 2019

Charliecloud provides user-defined software stacks (UDSS) for HPC centers. It uses Linux user namespaces to run containers with no privileged operations or daemons and minimal configuration changes on center resources.

This release includes:

  • Upgrade OpenMPI examples to 3.1.3
  • New example image build with skopeo and umoci
  • Re-mount images read-only reliably
  • Documentation improvements & miscellaneous bug fixes

Learn more:

LBANN 0.9 Released February 11, 2019

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.

v0.9 is LBANN’s initial release. The release notes linked below contain details about v0.9x iterations. Some deprecated features have been retired. At a high level, this release includes new development in these areas:

  • Support for new training algorithms (e.g., generative adversarial networks)
  • Support for new network structures
  • Support for new layers (e.g., learning, metrics, optimizers, activations)
  • Performance optimizations (e.g., GPU model-parallel softmax layer)
  • Model portability & usability
  • Support for an online, distributed data store
  • Overhauled I/O & data readers
  • Overhauled code base (see README_coding_style.txt)
  • New features & build system (e.g., support for convolutional and pooling layers, GPU acceleration of local Elemental GEMM operations)
  • and much more!

Learn more:

HiOp 0.2 Released February 01, 2019

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.

HiOp’s initial release occurred in December 2017. This v0.2 includes:

  • Implementation of various strategies to deal with fixed variables
  • Comprehensive testing and bug fixing for MacOS
  • Minor fixes of bugs found on various HPC platforms
  • Minor interface and options refinement required by the integration with MFEM mesh optimization interface

Learn more:

Aluminum 0.2 Released January 30, 2019

First released in September 2018, 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.

Improvements included in this release:

  • Host-transfer implementations of standard collectives in the MPI-CUDA backend
  • Experimental RMA Put/Get operations
  • Improved algorithm specification, point-to-point operations, testing, and benchmarks

Learn more:

CCT 1.0.4 Released January 25, 2019

The Coda Calibration Tool (CCT) calculates reliable moment magnitudes for small- to moderate-sized seismic events. The v1.0.4 release includes several performance and stability improvements along with a few new features:

  • Shared interaction between data plots and the map display
  • Data point selection highlights relevant elements on the map (events/stations) and vice-versa
  • Support for arbitrary user-defined lists of WMS 1.3.0-compliant map tile servers/layers for display on the map
  • Automatic display of context-sensitive information based on which tab the user is actively looking at

Learn more:

SUNDIALS 4.0.2 Released January 23, 2019

This release is a patch with many changes, including (but not limited to):

  • unified linear solver interfaces in all SUNDIALS packages
  • encapsulated nonlinear solvers in all SUNDIALS integrators
  • reorganization of ARKode to allow for the development of new integration methods
  • new ARKode stepper for two-rate explicit/explicit multirate infinitesimal step methods
  • Fortran 2003 interfaces to CVODE and several SUNDIALS modules
  • an OpenMP 4.5+ NVECTOR

Learn more:

New Repo: VisIt January 19, 2019

VisIt (Visualization and Data Analysis for Mesh-based Scientific Data) is an interactive, parallel visualization and graphical analysis tool for viewing scientific data on Unix and PC platforms. While this repo has been around for a while enjoying a robust developer community, it is newly housed on GitHub. Stay up to date with the latest release notes.

With VisIt, users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images for presentations.

VisIt contains a rich set of visualization features so that you can view your data in a variety of ways. It can be used to visualize scalar and vector fields defined on 2D and 3D structured and unstructured meshes. VisIt was designed to handle very large data set sizes in the peta-scale range, yet it can also handle small data sets in the kilobyte range.

Learn more:

RAJA 0.7.0 Released January 10, 2019

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 v0.7.0 release contains several major changes, new features, a variety of bug fixes, and expanded user documentation and accompanying example codes. Major changes include:

  • RAJA::forallN and RAJA::forall methods were marked deprecated in the v0.6.0 release and have been removed.
  • CUDA execution policies for use in RAJA::kernel policies have been significantly reworked and redefined to be much more flexible and provide improved run time performance.
  • Improved support for loop tiling algorithms, CPU cache blocking, CUDA GPU thread local data, and shared memory
  • Expanded documentation and example codes for the RAJA::kernel interface

Learn more:

New Repo: MemSurfer January 10, 2019

MemSurfer computes bilayer membrane surfaces found in a wide variety of large-scale molecular simulations. The tool works independent of the type of simulation, directly on the 3D point coordinates; as a result, it can handle a variety of membranes as well as atomic simulations.

Core functionality is written in Python and C++. Check out the GitHub repo for information about v0.1.

New Repo: Cardioid (Cardiac Simulation Toolkit) December 28, 2018

Cardioid is a cardiac multiscale simulation suite spanning from subcellular mechanisms up to simulations of organ-level clinical phenomena. The suite contains tools for simulating cardiac electrophysiology, cardiac mechanics, torso-ECGs, cardiac meshing, and fiber-generation tools.

This project’s history goes back a few years – it was a finalist for the 2012 Gordon Bell Prize – but only now is the code available as open source. Initially developed by a team of LLNL and IBM scientists, Cardioid divides the heart into a large number of manageable subdomains. This replicates the electrophysiology of the human heart, accurately simulating the activation of each heart muscle cell and cell-to-cell electric coupling.

SUNDIALS 4.0 Released December 20, 2018

This release includes unified linear solver interfaces in all SUNDIALS packages, encapsulated nonlinear solvers in all SUNDIALS integrators, a reorganization of ARKode to allow for the development of new integration methods, a new ARKode stepper for two-rate explicit/explicit multirate infinitesimal step methods, Fortran 2003 interfaces to CVODE and several SUNDIALS modules, an OpenMP 4.5+ NVECTOR, managed memory capabilities for the CUDA NVECTOR, and other improvements.

A patch release v4.0.1 was also released to fix a bug in ARKode where single precision builds would fail to compile.

Read more about v4.0.0 and the complete SUNDIALS release history. Downloads are available from the SUNDIALS website and GitHub.

ScrubJay: A Bird's-Eye View of Computing Performance December 10, 2018

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.

ESGF Installer 3.0 Beta Released December 06, 2018

The long-awaited Earth System Grid Federation (ESGF) installer software v3.0 beta release is here!

LLNL’s William Hill unveiled the beta at ESGF’s annual conference in Washington, DC. His slides can be downloaded here – look for the second link on Day 3.

v3.0 is a complete rewrite of the ESGF installation stack and includes a 2.x migration script to upgrade an existing node. This release addresses several long-standing problems such as a lack of error handling, lack of extensibility, and a complicated installation process. Note that the Conda environment must be activated to run this installer. Documentation is updated accordingly.

vCDAT 1.0 Released December 01, 2018

LLNL’s Community Data Analysis Tools (CDAT) provide a synergistic approach to climate modeling, allowing researchers to advance scientific visualization of large-scale climate data sets.

vCDAT is part of the CDAT suite. After beta testing, the new v1.0 is now available on GitHub. vCDAT is a desktop application that provides the graphical frontend for the CDAT package, using CDAT’s VCS and CDMS modules to render high-quality visualizations within a browser. Check out

With vCDAT you can export and import custom colormaps in multiple image formats. Tutorials and documentation are provided here. Installation requires Anaconda.

Stay tuned for v2.0, coming in spring 2019, which will leverage Jupyter Notebooks UI.

New Repo: UnifyCR November 26, 2018

Hierarchical storage systems are the wave of the future for HPC centers like LLNL’s Livermore Computing Complex. The Unify project aims to improve I/O performance by utilizing distributed, node-local storage systems. This design scales bandwidth and capacity according to the computer resources used by a given job. Furthermore, Unify avoids inter-job interference from parallel file systems or shared burst buffers.

Unify is a suite of specialized, flexible file systems – the first is available on GitHub with more on the way – that can be included in a user’s job allocations. A user can request which Unify file system(s) to be loaded and the respective mount points. Tests on LLNL’s Catalyst cluster show more than 2x improvement in write performance.

Like much of LLNL’s HPC performance improvement software, Unify is open source. The first Unify file system, UnifyCR (for checkpoint/restart workloads), is already available on GitHub. The team is working on another file system in the Unify “family” designed for machine learning workloads, in which large data sets need to be distributed quickly. Additional Unify file systems are in development.

DOE Machines Dominate Record-Breaking SC18 November 20, 2018

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:

  • Student program keynote from Bruce Hendrickson, associate director for Computing
  • Women in HPC workshop led by Elsa Gonsiorowski
  • Student technical program vice-chaired by Olga Pearce
  • Spack tutorial
  • Flux workshop
  • P3HPC (performance, portability, and productivity) workshop
  • Talks by LLNL experts at industry booths (e.g., Penguin Computing, NVIDIA)

New Repo: NLPVis November 19, 2018

Machine learning gurus, this one’s for you! NLPVis enables visualization of neural networks in natural-language ML models. Setup is straightforward and includes a pre-trained model.

New Computing Cluster Coming to LLNL November 13, 2018

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

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

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

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.

Audio/Video: Spotlight on Spack October 30, 2018

HPC developers build software from source code and optimize it for the targeted computer’s architecture. LLNL-developed Spack handles the process of downloading a tool and all the necessary dependencies – which can be tens or hundreds of other packages – and assembles those components and ensures they are properly linked and optimized for the machine. Todd Gamblin, Spack’s lead developer, talks with the Exascale Computing Project’s Exascale podcast. Both audio and video versions are available. Total runtime is 13:54.

Outline:

  • Spack: a US Department of Energy lab-developed app store for supercomputers (1:24)
  • Spack’s role in ECP (2:26)
  • The origins and evolution of Spack (5:23)
  • Spack’s benefits and advantages (7:42)
  • The use of Spack on Mac laptops and Linux machines (10:53)
  • The plans for Spack (11:18)

Flux and Spack Events Coming to Supercomputing '18 October 27, 2018

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!

Day Time Type Link
Sunday, November 11 10:55am –11:20am Workshop Flux: Overcoming Scheduling Challenges for Exascale Workflows
Monday, November 12 8:30am – 5:00pm Tutorial Managing HPC Software Complexity with Spack
Tuesday, November 13 12:15pm – 1:15pm BOF Spack Community

Read more about our past experiences and tips for first-timers. A complete list of LLNL-led sessions can be found on the LLNL Computing website. All times are listed in Central Standard Time.

Open-Source Developer Greg Becker Scales Projects and Mountains October 26, 2018

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.

Umpire 0.2.4 Released October 25, 2018

Umpire is a resource management library that allows the discovery, provision, and management of memory on next-generation architectures. It uses CMake and BLT to handle builds. New features in this version include:

  • Support for allocating “constant” memory on CUDA GPUs
  • A way of toggling introspection, to improve performance for allocators where you don’t need tracking

Fixes and enhancements:

  • Ability to deallocate nullptr
  • Fixed a bug when compiling with clang that would cause problems in the AllocationMap
  • Ensured all classes with virtual functions have virtual destructors

New Repo: ScrubJay October 15, 2018

ScrubJay is a framework for automatic and scalable data integration. Describe your datasets (files, formats, database tables), then describe the integrated dataset(s) you desire, and let ScrubJay derive it for you in a consistent and reproducible way.

ScrubJay is used at our HPC center to help analysts evaluate operations with data collected from every component. More news about this innovative project is on the way from LLNL’s science and technology magazine… stay tuned!

Sandia Open-Source Simulator Helps Solve the Mysteries of Metal Hardening October 08, 2018

HPC materials simulations at LLNL are revealing surprising insights into how metals behave under extreme pressure. Check out this research highlight on metal hardening from Science & Technology Review. Using Vulcan and Sequoia, two of our most powerful computers, a research team leveraged the LAMMPS (Large-Scale Atomic/Molecular Massively Parallel Simulator) molecular dynamics simulator to run simulations of a corrosion-resistant metal called tantalum. Developed by our colleagues at Sandia National Laboratories, LAMMPS is an open-source code that allows users to study the physical movement of atoms and molecules.

SUNDIALS 3.2 Released October 01, 2018

This latest release includes a constraint handling in CVODE/CVODES, hybrid MPI/CUDA support, and a number of bug fixes and build system updates. In addition, the SUNDIALS team has put out a development release, v4.0.0-dev.2, which includes encapsulated nonlinear solvers for all time integrators, streamlining of the linear solver interfaces in CVODE, ARKode, IDA, and KINSOL, and a reorganization of ARKode to allow for more time stepping options. The development release is another step toward a larger major release scheduled for the end of 2018. The full 4.0.0 release will also include the streamlined linear solver interfaces for CVODES and IDAS as well as a two-rate explicit/explicit integrator.

Read more about v3.2 and the complete SUNDIALS release history including v4.0.0-dev.2. Downloads are available from the SUNDIALS website and GitHub.

Second Annual Developer Day Continues to Build on Success September 20, 2018

On August 15, LLNL hosted Developer Day. The all-day event featured discussion panels, lightning talks, and deep dives intended to bring the LLNL developer community together. Many presentations featured open-source projects developed at the Lab, including:

XBraid Interweaves Timelines for Faster Solutions September 19, 2018

LLNL’s science and technology magazine highlights XBraid, homegrown open-source software that reduces the time to solution for HPC applications and simulations. XBraid provides a nonintrusive, powerful solution to the bottleneck posed by performing sequential time steps for problems involving thousands or millions of time steps. Fork XBraid on GitHub to start reducing your time to solution today.

Spack, a Lab-Developed App Store for Supercomputers, Becoming Standard-Bearer September 18, 2018

Spack has gone global! LLNL’s open-source package manager is making waves throughout the HPC community, including internationally, as evidenced by a recent tour of European HPC facilities by the tool’s developers. Everything you need to get started is available on the Spack website.

OSS Spotlight: Lawrence Livermore National Laboratory and ZFS on Linux September 04, 2018

This spotlight article on Medium explains the history of LLNL’s ZFS on Linux open-source project, which is now indexed by Code.gov. Follow @OpenZFSonLinux on Twitter and fork the code on GitHub.

SUNDIALS 3.1.2 Released July 31, 2018

SUNDIALs consists of six solvers and is implemented with the goal of providing robust time integrators and nonlinear solvers that can easily be incorporated into existing simulation codes. We have created a robust portal for users that includes documentation, usage notes, related publication, support information, and downloads. Detailed release history is available. Users can also fork the code on GitHub.

Video: How Open Source Supports the Largest Computers on the Planet July 26, 2018

Computer engineer Ian Lee presents a webinar for the Exascale Computing Project, describing LLNL’s engagement with the open-source community. Speaker’s notes are also available online.

The Case for Open Source Software July 12, 2018

LLNL computer engineer Ian Lee writes about the benefits of open-source software in this guest blog post for 18F, a tech agency within the U.S. General Services Administration.

PRUNERS: Providing Reproducibility for Uncovering Non-Deterministic Errors June 26, 2018

Non-deterministic software bugs are one of the most time-consuming and expensive problems to solve in software development. Furthermore, non-deterministic debugging of parallel applications running on large supercomputers, such as those at LLNL, presents even greater challenges. The PRUNERS toolset offers four novel debugging and testing tools to assist programmers with detecting, remediating, and preventing these errors in a coordinated manner.

Learn more on the LLNL Computing website, explore the toolset, and fork the code.

MFEM 3.4 Released May 29, 2018

Version 3.4 of MFEM, a lightweight, general, scalable C++ library for finite element methods, is now available at: http://mfem.org

The goal of MFEM is to enable high-performance scalable finite element discretization research and application development on a wide variety of platforms, ranging from laptops to exascale supercomputers.

It has many features, including:

  • 2D and 3D, arbitrary order H1, H(curl), H(div), L2, NURBS elements.
  • Parallel version scalable to hundreds of thousands of MPI cores.
  • Conforming/nonconforming adaptive mesh refinement (AMR), including anisotropic refinement, derefinement and parallel load balancing.
  • Galerkin, mixed, isogeometric, discontinuous Galerkin, hybridized, and DPG discretizations.
  • Support for triangular, quadrilateral, tetrahedral and hexahedral elements, including arbitrary order curvilinear meshes.
  • Scalable algebraic multigrid, time integrators, and eigensolvers.
  • Lightweight interactive OpenGL visualization with the MFEM-based GLVis tool.

Some of the new additions in version 3.4 are:

  • Significantly improved non-conforming unstructured AMR scalability.
  • Integration with PUMI, the Parallel Unstructured Mesh Infrastructure from RPI.
  • Block nonlinear operators and variable order NURBS.
  • Conduit Mesh Blueprint support
  • General “high-order”-to-“low-order refined” field transfer.
  • New specialized time integrators (symplectic, generalized-alpha).
  • Twelve new examples and miniapps.

MFEM is being developed in CASC, LLNL and is freely available under LGPL 2.1.

For more details, see the interactive documentation and the full CHANGELOG.

LLNL Magazine Cover Story & Video: Ambassadors of Code March 20, 2018

The January/February 2018 issue of Science & Technology Review features the Lab’s leadership in open-source software, with cover art showing an MFEM-generated simulation. Contributors to the article include LLNL developers Ian Lee, Brian Behlendorf, John Fisher, Todd Gamblin, Sei Jung Kim, Tzanio Kolev, Greg Pope, and Dan Quinlan.

Bruce Hendrickson, LLNL’s associate director for Computing, wrote the accompanying commentary, The High Value of Open-Source Software.

A video about the article, starring Lee, is available on the Lab’s YouTube channel.

Hackvideo March 13, 2018

As this video demonstrates, thrice-yearly hackathons at LLNL provide 24-hour opportunities to brainstorm, foster creativity, prototype, and explore. Participants work in groups or individually to learn new skills, languages, and tools. Many hackers use the time to use open-source tools and contribute to the open-source community.

MacPatch Keeps Thousands of LLNL Computers Running Smoothly February 26, 2018

Now in its third generation, LLNL-developed MacPatch handles software installation and patching for the Laboratory’s Mac computers. It’s open source, of course!

Conduit 0.3.1 Released February 26, 2018

Version 0.3.1 of Conduit is now available at: http://llnl-conduit.readthedocs.io/en/latest/releases.html

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

The 0.3.1 release includes:

  • New Node::diff and Node::diff_compatible methods
  • Updates to uberenv to use a newer Spack version and removed several custom packages
  • Changes to C++ Node::set methods to take const pointers for data
  • A Python version of basic tutorial
  • An expanded the Node Python Capsule API
  • Python API bug fixes
  • Fixes for API exports for static libs on Windows

For more details, see Conduit’s Release Notes.

Caliper: Application Introspection System December 12, 2017

Comprehensive understanding of performance behavior of large-scale simulations requires the ability to compile, analyze, and compare measurements and contexts from many independent sources. Caliper, a general-purpose application introspection system, makes that task easier by acting as the “glue” that connects various independent context annotations, measurement services, and data processing services.

Learn more on the LLNL Computing website, and download the software on GitHub.

SCR: Scalable Checkpoint/Restart for MPI November 27, 2017

Multilevel checkpointing allows HPC applications to take both frequent inexpensive checkpoints and less frequent, more resilient checkpoints, resulting in better efficiency and reduced load on the parallel file system. Accordingly, LLNL researchers developed the Scalable Checkpoint/Restart (SCR) library for the large-scale, production system context.

Learn more on the LLNL Computing website. Read the SCR user guide and fork the code on GitHub.

MFEM 3.3.2 Released November 10, 2017

Version 3.3.2 of MFEM, a lightweight, general, scalable C++ library for finite element methods, is now available at: http://mfem.org

The goal of MFEM is to enable high-performance scalable finite element discretization research and application development on a wide variety of platforms, ranging from laptops to exascale supercomputers.

MFEM has many features, including:

  • 2D and 3D, arbitrary order H1, H(curl), H(div), L2, NURBS elements.
  • Parallel version scalable to hundreds of thousands of MPI cores.
  • Conforming/nonconforming adaptive mesh refinement (AMR), including anisotropic refinement, derefinement and parallel load balancing.
  • Galerkin, mixed, isogeometric, discontinuous Galerkin, hybridized, and DPG discretizations.
  • Support for triangular, quadrilateral, tetrahedral and hexahedral elements, including arbitrary order curvilinear meshes.
  • Scalable algebraic multigrid, time integrators, and eigensolvers.
  • Lightweight interactive OpenGL visualization with the MFEM-based GLVis tool.

Some of the new additions in version 3.3.2 are:

  • Support for high-order mesh optimization based on the target-matrix optimization paradigm from the ETHOS project.
  • Implementation of the community policies in xSDK, the Extreme-scale Scientific Software Development Kit.
  • Integration with the STRUMPACK parallel sparse direct solver and preconditioner.
  • Several new linear interpolators, five new examples and miniapps.
  • Various memory, performance, discretization and solver improvements, including physical-to-reference space mapping capabilities.
  • Continuous integration testing on Linux, Mac and Windows.

MFEM is being developed in CASC, LLNL and is freely available under LGPL 2.1.

For more details, see the interactive documentation and the full CHANGELOG.

CHAI: Copy Hiding Application Interface August 07, 2017

LLNL’s Advanced Architecture Portability Specialists have developed a new abstraction model called CHAI, which automates the movement of data between main memory and other memory locations with minimal intrusion on the source code. This streamlined process provides productivity and efficiency boosts.

Learn more on the LLNL Computing website, and fork the software on GitHub.

Spack Featured in Podcast on Open Source and Supercomputers July 13, 2017

LLNL’s Todd Gamblin joins the “Request for Commits” podcast to talk about Spack, a versatile HPC package manager.

VisIt 2.12.3 Released June 30, 2017

Version 2.12.3 of VisIt is now available at: visit.llnl.gov

VisIt is an open source, cross platform, interactive, scalable, visualization and analysis tool for simulation data. VisIt 2.12.3 is primarily a bug fix release.

2.12.3 release highlights:

  • The ANSYS reader was improved to support more general kinds of NBLOCK format strings.
  • The GUI performance was improved on databases with large numbers of variables.
  • A bug was corrected with query-over-time where it would yield different results in certain instances than repeatedly changing the time state and querying the value.
  • A couple of bugs were corrected with the Silo reader.

For a complete list of changes see the 2.12.3 release notes

Video: PRUNERS: Warding Off Non-Deterministic Software Bugs at Scale May 16, 2017

This video introduces PRUNERS, a software toolset to fight non-deterministic bugs on supercomputers.

MFEM: Accelerating Simulation Software with Graphics Processing Units May 08, 2017

LLNL scientists are redesigning simulation software to leverage the capabilities of next-generation exascale computing. Read more about MFEM’s role in our transition to exascale technology.

NARAC Software Team Begins Modernization of GUI Framework March 30, 2017

As any computer systems professional knows, the “leading edge” is a moving target. When the system belongs to LLNL’s National Atmospheric Release Advisory Center (NARAC) — the DOE’s premier atmospheric transport and dispersion simulation facility — ensuring the reliability of core operational systems requires thoughtful consideration of new technology alongside evolving needs. NARAC’s software development team continually evaluates current capabilities and weighs appropriate solutions to meet NARAC’s critical national and international missions. The team is moving to a web-based technology stack, leveraging the stability of many open-source tools.

Spindle: Scalable Shared Library Loading March 16, 2017

Spindle is an LLNL-developed open-source tool for improving the library-loading performance of dynamically-linked HPC applications.

Learn more on the LLNL Computing website, and download v0.10 on GitHub.

MFEM 3.3 Released January 28, 2017

Version 3.3 of MFEM, a lightweight, general, scalable C++ library for finite element methods, is now available at: http://mfem.org

The goal of MFEM is to enable high-performance scalable finite element discretization research and application development on a wide variety of platforms, ranging from laptops to exascale supercomputers.

It has many features, including:

  • 2D and 3D, arbitrary order H1, H(curl), H(div), L2, NURBS elements.
  • Parallel version scalable to hundreds of thousands of MPI cores.
  • Conforming/nonconforming adaptive mesh refinement (AMR), including anisotropic refinement, derefinement and parallel load balancing.
  • Galerkin, mixed, isogeometric, discontinuous Galerkin, hybridized, and DPG discretizations.
  • Support for triangular, quadrilateral, tetrahedral and hexahedral elements, including arbitrary order curvilinear meshes.
  • Scalable algebraic multigrid, time integrators, and eigensolvers.
  • Lightweight interactive OpenGL visualization with the MFEM-based GLVis tool.

Some of the new additions in version 3.3 are:

  • Comprehensive support for the linear and nonlinear solvers, preconditioners, time integrators and other features from the PETSc and SUNDIALS suites.
  • Linear system interface for action-only linear operators including support for matrix-free preconditioning and low-order-refined spaces.
  • General quadrature and nodal finite element basis types.
  • Scalable parallel mesh format.
  • Thirty-six new integrators for common families of operators.
  • Sixteen new serial and parallel example codes.
  • Support for CMake, on-the-fly compression of file streams, and HDF5-based output following the Conduit mesh blueprint specification.

MFEM is being developed in CASC, LLNL and is freely available under LGPL 2.1.

For more details, see the interactive documentation and the full CHANGELOG.

Strawman 0.1.0 Released January 10, 2017

Strawman is an open source many-core capable lightweight in situ visualization and analysis infrastructure for multi-physics HPC simulations.

0.1.0, the first release of Strawman, is now available at: https://software.llnl.gov/strawman/Releases.html and on GitHub at https://github.com/llnl/strawman

For more details, see Strawman’s Documentation.

Conduit 0.2.1 Released January 06, 2017

Version 0.2.1 of Conduit is now available at: https://software.llnl.gov/conduit/releases.html

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

The 0.2.1 version is primarily a bug fix releases, which includes:

  • Fixes to support static builds, including on BGQ using xlc and gcc
  • Bug fixes for Blueprint verify routines.
  • The elimination of separate Fortran libs by moving Fortran symbols into their associated main libs

For more details, see Conduit’s Release Notes.

VisIt 2.12.0 Released November 10, 2016

Version 2.12.0 of VisIt is now available at: visit.llnl.gov

VisIt is an open source, cross platform, interactive, scalable, visualization and analysis tool for simulation data.

2.12.0 release highlights:

  • Improvements for rendering streamlines with the Pseudocolor Plot
  • Added gzstream support for ASCII-based database readers
  • Added experimental topological segmentation expressions (merge_tree,split_tree, and local_threshold)
  • Several bug fixes to VisIt and Libsim
  • Ship numpy with VisIt’s CLI

For a complete list of the changes see the 2.12.0 release notes.

Conduit 0.2.0 Released November 03, 2016

Version 0.2.0 of Conduit is now available at: http://software.llnl.gov/conduit/releases.html

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

The 0.2.0 release includes:

  • Changes to clarify concepts in the conduit::Node API
  • Added const access to conduit::Node’s children and a new NodeConstIterator
  • Added support for building on Windows
  • Added conduit::blueprint verify support and examples for the mcarray and mesh protocols
  • Added extensive HDF5 I/O support to conduit::relay for reading and writing between HDF5 files and conduit Node trees

For more details, see Conduit’s Release Notes.

How One National Lab is Opening Up Code without Compromising National Security September 14, 2016

In this FedSCoop article, LLNL Computer Engineer Ian Lee explains how he’s helping laboratory staff understand what they can develop in open source.

GridDyn Initial Release August 17, 2016

GridDyn is a power system simulator developed at Lawrence Livermore National Laboratory. The name is a concatenation of Grid Dynamics, and as such usually pronounced as “Grid Dine”. It was created to meet a research need for exploring coupling between transmission, distribution, and communications system simulations.

While good open source tools existed on the distribution side, the open source tools on the transmission side were limited in usability either in the language or platform or simulation capability, and commercial tools, while quite capable, simply did not allow the access to the internal components and data required to conduct the research. Thus, the decision was made to design a platform that met the needs of the research project. Building off of prior efforts in grid simulation, GridDyn was designed to meet the current and future research needs of the various power grid related research and computational efforts.

It is written in C++, making use of recent improvements in the C++ standards. It is intended to be cross platform with regard to operating system and machine scale. The design goals were for the software to be easy to couple with other simulations, and to be easy to modify and extend. It is very much still in development and as such, the interfaces and code are likely to change, in some cases significantly as more experience and testing is done. It is our expectation that the performance, reliability, capabilities, and flexibility will continue to improve as projects making use of the code continue and new ones develop. We expect there are still many issues so any bug reports or fixes are welcome. And hopefully even in its current state and as the software improves the broader power systems research community will find it useful.

GridDyn is Open Source software, publicly available on GitHub at: github.com/llnl/griddyn under a BSD License.

VisIt 2.10.3 Released July 21, 2016

Version 2.10.3 of VisIt, a cross platform Open Source, interactive, scalable, visualization, animation and analysis tool is now available at: visit.llnl.gov

VisIt 2.10.3 is primarily a bug fix release that resolves about twenty important issues.

For a complete list of the changes see the 2.10.3 release notes.

STAT: Discovering Supercomputers' Code Errors July 06, 2016

LLNL’s Stack Trace Analysis Tool (STAT) reduces the number of processes requiring more in-depth analysis by organizing processes within a parallel application based on behavioral patterns. This analytic tool was designed and developed by LLNL computer scientists with collaborators at the University of Wisconsin at Madison and the University of New Mexico. A video explains more.

Learn more on the LLNL Computing website, and download the software on GitHub.

MFEM 3.2 Released June 30, 2016

Version 3.2 of MFEM, a lightweight, general, scalable C++ library for finite element methods, is now available at: http://mfem.org

The goal of MFEM is to enable high-performance scalable finite element discretization research and application development. It has many features, including:

  • 2D and 3D, arbitrary order H1, H(curl), H(div), L2, NURBS elements.
  • Parallel version scalable to hundreds of thousands of MPI cores.
  • Conforming/nonconforming adaptive mesh refinement (AMR), including anisotropic refinement, derefinement and parallel load balancing.
  • Galerkin, mixed, isogeometric, discontinuous Galerkin, hybridized, and DPG discretizations.
  • Support for triangular, quadrilateral, tetrahedral and hexahedral elements, including arbitrary order curvilinear meshes.
  • Scalable algebraic multigrid, time integrators, and eigensolvers.
  • Lightweight interactive OpenGL visualization with the MFEM-based GLVis tool.

Some of the new additions in version 3.2 are:

  • Dynamic AMR with parallel load balancing, derefinement of non-conforming meshes.
  • Tensor-based high-performance finite element operator assembly and (matrix-free) evaluation.
  • Support for discontinuous Galerkin and hybridization methods on parallel non-conforming meshes.
  • Support for Gmsh and CUBIT meshes.
  • Secure socket communications in class socketstream based on GnuTLS.
  • Four new serial and parallel example codes.

MFEM is being developed in CASC, LLNL and is freely available under LGPL 2.1.

For more details, see the interactive documentation and the full CHANGELOG.

GLVis 3.2 Released June 30, 2016

Version 3.2 of GLVis, a lightweight OpenGL tool for accurate and flexible finite element visualization, is now available at: http://glvis.org.

The goal of GLVis is to enable quick but precise visualization of general finite element meshes and functions in a wide variety of applications. It has many features, including:

  • Support for arbitrary high-order and NURBS meshes.
  • Visualization of parallel meshes and solutions.
  • Accurate functional representation of many finite elements.
  • Server mode accepting multiple socket connections.

Some of the new additions in version 3.2 are:

  • Secure socket connections based on the GnuTLS library.
  • Optional plot caption support.
  • Various other small improvements and bug fixes.

GLVis being developed in CASC, LLNL and is freely available under LGPL 2.1.

For more details, see the full CHANGELOG.

Hypre 2.11.1 June 09, 2016

Congratulations to the Hypre team, that today released version 2.11.1, now available from their GitHub project page.

The notable changes from the CHANGELOG are:

  • Fixed one more bug related to SStructSetSharedPart and SetNeighborPart
  • Fixed a bug in PFMG red/black relaxation for 2D problems
  • Fixed various other bugs in ParCSR and the FEI
  • Fixed configure option --without-MLI and removed option --with-examples
  • Modified code to enable compilation with a C++ compiler.
  • Added several missing Fortran interface routines in Struct and BoomerAMG
  • Updated the AME and LOBPCG interfaces to work correctly with both absolute and relative tolerances.

Hypre is freely available under LGPL 2.1.

For the latest version, please visit the Hypre project on GitHub or on the LLNL Computing site.

XBraid: Parallel Time Integration with Multigrid May 23, 2016

LLNL scientists have developed an open-source, non-intrusive, and general purpose parallel-in-time code, XBraid. This tool solves for all time steps simultaneously with the help of a new multilevel algorithm and the massively parallel processing capabilities of current and future high-performance computers.

Learn more on the LLNL Computing website, and download the software on GitHub.

OpenZFS on Linux 0.6.5.6 March 22, 2016

Version 0.6.5.6 of OpenZFS on Linux, the native Linux kernel port of the ZFS filesystem, is now available at: http://zfsonlinux.org

Some notable improvements in version 0.6.5.6 are:

  • Bugs fixes for case-insensitive filesystem support. Users running Samba servers that export ZFS filesystems will benefit from this update.
  • Bug fixes and improved scalability for zvols. Support for asynchronous creation of device nodes. This fixes several hangs and allows pools with many zvols to be imported quickly.
  • Add -gLP to zpool subcommands to print vdev names as a GUID, a real path resolving all symbolic links, and as a full path. This change enables better ZFS integration in Ubuntu’s GRUB utilities.
  • Fix a corruption bug where, in certain circumstances, zfs send -i (incremental send) can produce a stream which will result in incorrect sparse file contents on the target.

For more details, check out the full changelog.

VisIt 2.10.1 Released March 09, 2016

Source code and prebuilt executables are available on the VisIt web site.

VisIt 2.10.1 contains the following enhancements:

  • VisIt now permits the -socket-bridge-host command line argument to override the host name passed to compute engines when VCL starts a socket bridge. This is useful for login nodes that are attached to multiple network interfaces such as on BlueGene/Q where compute nodes may need to attach to the socket bridge host (typically the LAC node) using an alias.
  • The PF3D database plugin was enhanced so that it reads the new multilevel file format.
  • The SPH Resample Operator now supports zone-centered data.
  • VTK’s higher order elements are now exposed via Libsim.
  • The Silo database plugin now supports all-empty multi-block objects.
  • The interpretation of “_meshtv_searchpath” and “_visit_searchpath” was changed in the Silo database plugin. If the search path is blank it will now be ignored instead of causing the plugin to ignore all variables located in subdirectories. The plugin will now ignore all variables located in subdirectories when the search path contains a path that doesn’t exist in the Silo file. This change in behavior was necessitated when we discovered that codes had been unintentionally outputting Silo files with blank search paths for years. Because the Silo plugin wasn’t handling a blank search path properly, this never caused a problem. When the behavior was fixed in VisIt 2.10, VisIt no longer displayed the variables in the subdirectories in its menus when it encountered such a file. Since we couldn’t fix all the existing files, we decided to change the interpretation of the search path in VisIt.
  • The pre-built Ubuntu distributions now contain support for reading ITAPS files.
  • The PDB Z File database plugin was enhanced to support marker meshes and variables.
  • The MFEM database plugin was updated to use MFEM 3.1, which provides support for MFEM AMR meshes. See http://mfem.org/ for more details.
  • The ADIOS database plugin was upgraded to use ADIOS 1.9.0.

As well as the following bug fixes:

  • The VisItAddPlot() function in Libsim was incorrectly using the global “Apply operators to all plots” setting when creating plots. The behavior for VisItAddPlot() has been changed so new plots are not created with previously applied operators to more closely match the operation of the VisIt CLI.
  • Large tecplot files can now be read on Windows.
  • A potential memory overwrite was fixed in the Fortran visitgetenv function in Libsim.
  • Fixed a bug where the QT4 include and archive files were missing after doing a ‘make install’.
  • Re-enabled adaptive csg discretization for Windows, which was inadvertently disabled for previous release.
  • Fixed a bug with the PF3D database plugin where the time and cycle were reported as zero for all the time states accessed after the initial time state accessed.
  • Fixed a bug preventing the reading of DOS-formatted .visit files on Linux.
  • Fixed bug whereby setting ‘ssh command’ would not work correctly on Windows. If the path to ssh contains spaces, the full path and command need to be surrounded in double-quotes, e.g., “C:\Program Files (x86)\Putty\plink.exe”. If manually adding this to an .xml host profile, the quotes and path-separators should be escaped: “"C:\Program Files (x86)\Putty\plink.exe"”.
  • Fixed a bug opening Silo files larger than 4 Gbytes on Windows.
  • Fixed the tensorVectorMult bug in the SPH Resample Operator found by Cody Raskin.
  • Fixed a bug that prevented the SPH Resample Operator from working with the Volume Plot.
  • Fixed handling of buggy mmesh_name member of multi-block objects in Silo files.

More information can be found on the Release Notes for VisIt 2.10.1 page.

A Flexible Package Manager for HPC Software February 19, 2016

Learn more about the origins of Spack, whose community of users and contributors continues to grow.

MFEM 3.1 Released February 16, 2016

Version 3.1 of MFEM, a lightweight, general, scalable C++ library for finite element methods, is now available at: http://mfem.org

The goal of MFEM is to enable research and development of scalable finite element discretization and solver algorithms through general finite element abstractions, accurate and flexible visualization, and tight integration with the hypre linear solvers library. It has many features, including:

  • 2D and 3D, arbitrary high-order H1, H(curl), H(div), L2 and NURBS elements.
  • Parallel version scalable to hundreds of thousands of MPI cores.
  • Conforming or nonconforming adaptive mesh refinement (AMR), including anisotropic refinement.
  • Galerkin, mixed, isogeometric, DG and DPG discretizations.
  • Support for triangular, quadrilateral, tetrahedral and hexahedral elements with curved boundaries.
  • Lightweight interactive OpenGL visualization with GLVis.

Some of the new additions in version 3.1 are:

  • Substantially improved non-conforming adaptive mesh refinement, which now works also in parallel.
  • General finite element spaces and solvers on surfaces and mesh skeletons.
  • Support for hybridization and static condensation, with a new FEM <-> linear system interface.
  • New eigensolvers and improved linear solvers and preconditioners.
  • Visualization of non-conforming meshes and grid functions, and vector fields on surface meshes.
  • Six new examples codes for parallel AMR, eigenvalue problems and DG diffusion.
  • Five new electromagnetic and meshing miniapps.

MFEM is freely available under LGPL 2.1.

For more details, see the interactive documentation and the full description of the changes.

GLVis 3.1 Released February 05, 2016

Version 3.1 of GLVis, a lightweight OpenGL tool for accurate and flexible finite element visualization, is now available at: http://glvis.org.

The goal of GLVis is to enable research and development of general finite element discretization algorithms through accurate OpenGL visualization, and tight integration with the MFEM library. It has many features, including:

  • Support for arbitrary high-order and NURBS meshes.
  • Visualization of parallel meshes and solutions.
  • Accurate functional representation of many finite elements.
  • Server mode accepting multiple socket connections.

Some of the new additions in version 3.1 are:

  • Support for visualization of non-conforming meshes and grid functions.
  • New visualization of vector fields on surface meshes.
  • Improved build system, command line options and PDF screenshots.

GLVis is freely available under LGPL 2.1.

For more details, see the full description of the changes.

Flux: Building a Framework for Resource Management February 01, 2016

Flux is a next-generation resource and job management framework that expands the scheduler’s view beyond the single dimension of “nodes.” Instead of simply developing a replacement for SLURM and Moab, Flux offers a framework that enables new resource types, schedulers, and framework services to be deployed as data centers continue to evolve. This approach is especially important for extremely large Linux clusters like those at LLNL.

Learn more on the LLNL Computing website and fork the code on GitHub.

SAMRAI: Structured Adaptive Mesh Refinement Application Infrastructure January 30, 2016

The SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure) library is LLNL’s code base for exploring application, numerical, parallel computing, and software issues associated with SAMR.

Learn more on the LLNL Computing website, which includes documentation and software downloads.

ROSE Compiler: Enabling Easy Access to Automated Compiler Technology January 11, 2016

ROSE is a compiler infrastructure with robust analysis, debugging, and optimization tool development capabilities developed by a group of LLNL computer scientists and external collaborators.

Learn more on the LLNL Computing website, and download the software on the ROSE website.

RAJA: Managing Application Portability for Next-Generation Platforms January 11, 2016

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. RAJA is designed to integrate with existing codes and provide a development model for new codes to be portable from inception.

Learn more on the LLNL Computing website and fork the code.

Qbox and Qb@ll: Computing Electronic Structures at the Quantum Level January 11, 2016

Qbox is a first-principles molecular dynamics code that is used to compute the electronic structure of atoms, molecules, solids, and liquids within the density functional theory formalism. LLNL’s version of Qbox is an extension called Qb@ll.

Learn more on the LLNL Computing website and fork the Qb@ll code.

GLVis: Finite Element Visualization January 07, 2016

GLVis is a lightweight OpenGL-based tool for accurate and flexible finite element visualization, based on MFEM.

Learn more on the LLNL Computing website, and visit the GLVis website.

High-Order Finite Element Library Provides Scientists with Access to Cutting-Edge Algorithms January 06, 2016

Learn more about the origins of MFEM, one of our flagship open-source projects.