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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:

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:

Some other new additions in version 4.0 are:

The MFEM library has many more features, including:

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:

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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.

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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:

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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 publicaiton 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:

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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.

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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:

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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:

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

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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.

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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:

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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.

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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 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.

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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:

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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.

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