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At least 37 records · Page 2

DEDUPKV: A Space-Efficient and High-Performance Key-Value Store via Fine-Grained Deduplication

Log-Structured Merge Tree (LSM-tree) based key-value stores excel in write-intensive environments but suffer from data duplication, consuming up to 49% of storage space in LSM-tree-based key-value store deployments. Traditional solutions like compression and coarse-grained file system-level deduplication introduce overhead or have limited effectiveness. In this study, we propose DedupKV, a fine-grained deduplication framework tailored for LSM-tree, maximizing data reduction efficiency while minimizing write stalls and read overheads. DedupKV features three key innovations: (1) FLUSH-integrated inline deduplication, which removes duplicates during memory-to-storage writes; (2) WAL file-based offline deduplication, repurposing write-ahead logs to avoid double writes; and (3) elastic execution, dynamically balancing inline and offline deduplication based on memory pressure and workload intensity. Additionally, dynamic granularity management reduces deduplication metadata overhead. We implemented these four ideas in RocksDB for the first time and conducted experiments in a Linux environment. Our evaluation shows that WAL file-based offline deduplication and DedupKV outperform BlobDB by 33% and 23%, respectively, in write-heavy workloads, while reducing write amplification by 1.2 ×, 2 ×, and 1.6 × for real KV datasets.

Jamil, Safdar [Sogang University]

Accessible Content Optimization for Research Needs (ACORN)

ACORN employs a set of automated processes for informing and/or enforcing defined content schemas to create standardized and highly structured data. Because of its standardized data source, ACORN easily applies computer automation to generate communication assets such as PDFs, Powerpoint presentations, and web pages. Built using the memory-safe Rust programming language, ACORN is portable and accessible for use on any Windows, Mac, or Linux machine.

Wohlgemuth, JasonHoward [Oak Ridge National Labora

t9p

A lightweight 9P2000.L client and file system driver for RTEMS and Linux. t9p is designed to operate on performance constrained systems with as little as 16MB of memory and a single core.

Lorelli, Jeremy [SLAC National Accelerator Laborat

pseudopod

Pseudopod is a software tool that makes it easier and safer to build and run Linux containers without needing additional system privileges. It is designed to work with the open-soruce Podman container runtime. Pseudopod also provides and implements small library named libpseudo that provides the core functionality for tracking and emulating identity related system calls with low performance overhead. This allows complex tools, such as package managers and build systems, to run in a familiar way within a container while preserving the security of the host system and networks.

Green, ElenaN [Lawrence Livermore National Laborat

static-subid: Deterministic subordinate UID/GID assignment for unprivileged containers

static-subid calculates predictable subordinate UID and GID ranges for Linux users based on their UID, ensuring consistent ID mappings across multiple systems. Unlike shadow-utils' sequential allocation (which depends on creation order), static-subid uses a deterministic formula that guarantees the same user UID always receives the same subordinate ID range. Subordinate IDs enable user namespaces for unprivileged container runtimes (Podman, Docker rootless mode, LXC) by mapping container UIDs/GIDs to host subordinate IDs without requiring root privileges.

Riehecky, Pat [Fermi National Accelerator Laborato

Scientific Core Library Stack (SCLS) v2026

SCLS (Scientific Core Library Stack) is an opinionated build and packaging system for scientific computing libraries developed at Lawrence Berkeley National Laboratory. It produces a coherent, reproducible stack of numerical libraries — including BLAS/LAPACK, MPI, sparse direct and iterative solvers, graph partitioners, and parallel I/O libraries (e.g., PETSc, SLEPc, HDF5, NetCDF, MUMPS, OpenBLAS) — that work together without manual repair by downstream scientific software. From a single recipe-and-flavor model, SCLS produces native RPM packages for RHEL-family Linux, DEB packages for Debian/Ubuntu, direct Unix-style prefix installs for HPC and locked-down environments, and native macOS builds. Multiple build "flavors" (e.g., GCC+OpenBLAS, GCC+MKL, Intel+MKL, debug) coexist in distinct prefixes on the same host. Compared to general-purpose meta-build frameworks, SCLS is deliberately curated rather than infinitely configurable. It enforces deterministic, audit-friendly behavior: explicit build dependencies, no silent feature autodetection, a clear open-source license policy, and rpath-based runtime linkage so installs integrate cleanly with standard package-manager workflows.

Messe, Christian [Lawrence Berkeley National Labor

slac-epics/devLinuxAdc

EPICS device support for ADCs using the Linux industrial IO (IIO) subsystem

Lorelli, Jeremy [SLAC National Accelerator Laborat

UMap: An application-oriented user level memory mapping library

Exploiting the prominent role of complex memories in exascale node architecture, the UMap page fault handler offers new capabilities to access large memory-mapped data sets directly. UMap provides flexible configuration options to customize page handling to each application, including analysis of massive observational and simulation data sets. The high-performance design features I/O decoupling, dynamic load balancing, and application-level controls. Page faults triggered by application threads and processes accessing data mapped to a UMapp’ed region are handled via the Linux userfaultfd protocol, an asynchronous message-oriented kernel-user communication mechanism that avoids the context switch penalty of traditional signal fault handlers. UMap is fully open source. In this paper, we give an overview of the UMap library architecture, its extensible plugin architecture, and the use/performance of UMap in emerging heterogeneous memory hierarchies such as near-node Non-volatile Memory (NVM) and network attached memories. We highlight new capabilities in two pagefault management plugins, the NetworkStore and SparseStore. We demonstrate the integration between UMap and multiple ECP products including Caliper, Metall, ZFP, Mochi, and Ripples.

97 MATHEMATICS AND COMPUTING

From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture

Background Characterizing the physical organization of the genome is essential for understanding long-range gene regulation, chromatin compartmentalization, and epigenetic accessibility. Hi-C experiments generate two-dimensional (2D) genome-wide contact maps of chromatin interactions by capturing the spatial proximity between genomic loci, which reveal interaction frequencies but lack the spatial resolution needed to interpret the three-dimensional (3D) genome structure(s). Emerging evidence suggests that epigenetic regulation is closely linked to 3D genome architecture, and that structural changes over time (4D) drive key biological processes in development, disease, and environmental response. Thus, integrating 3D structure with functional data is critical for a more complete understanding of genome regulation. Previous work, most notably the 4DHiC chromosome modeling framework, has shown that physical multi-dimensional modeling approaches rooted in polymer physics and molecular dynamics can resolve these structures at biologically meaningful resolutions by integrating temporal Hi-C data with physical constraints to uncover dynamic chromosome reorganization. Thus, molecular dynamics simulations, constrained by Hi-C contact matrices, can resolve fine-scale structural changes and reveal functionally significant transitions in chromatin conformation. Results Herein, we present the 4D Genome Browser Workflow (4DGBWorkflow) and the 4D Genome Browser (4DGB). The algorithm is based on the 4DHiC method, and the containerized tool is an end-to-end workflow that can transform, filter, and view 4D epigenomics and chromatin datasets, allowing non-specialists to apply three-dimensional modeling principles to diverse datasets and experimental conditions. The software executes on a laptop running macOS, Linux or Windows. From input Hi-C files (.hic), the 4DGBWorkflow produces 3D reconstructions of chromosomes, integrates the reconstruction with track data (e.g., epigenetic marks, transcriptome profiles), and provides comparative visualization of the results in a single workflow. Conclusions The 4DGBWorkflow and 4D Genome Browser are open-source tools for comparative analysis and visualization of 4D chromosome datasets, including chromatin architecture and epigenomic signals. Automatic integration of Hi-C data with molecular dynamics democratizes the construction of time resolved 3D genome structures, simplifying complex simulations and data integration schemes.

3D Genome Browser

FTS3 Summer Container Integration Project

SLATE is discontinuing the previously used FTS3 container images so this project focuses on migrating these images, updating them from Scientific Linux 7 (SL7) to AlmaLinux 9, building a continuous integration (CI) pipeline, and executing self-hosted CI runners. This allows FNAL to no longer rely on the SLATE images.

Nnaji, Victoria C.

Mu2e otsdaq Documentation and Online Reconstruction Analytics

This report outlines the results of the DOE-funded SULI (Science Undergraduate Laboratory Internship) research completed over the summer 2024 on site at Fermilab. The project focused on the \textit{otsdaq} software responsible for data acquisition. The project included drafting updated documentation for new users including new procedures relevant for the Alma-Linux 9 operating system update, and the UPS package managing system replacement with spack (scientific software package manager). A new \textit{art} module (ReadTriggerCounts) to track trigger rates was created, with compatibility to be displayed via a Grafana server. The author also assisted in calorimeter cable installation in the detector hall.

Saarinen, Talia

Docker Containers for MCNP ® Development

Containers are a revolutionary technology in software development and deployment that provides a lightweight, portable environment for ensuring consistency across multiple computing environments. In anticipation of the MCNP 6.3.1 release, two Docker container images have been released on DockerHub for general use. The MCNP source code is not included in the images, and users are still required to obtain it through RSICC. The images produced by Docker are compliant with the OCI (Open Container Initiative) standards, ensuring compatibility with other container engines such as Podman or Kubernetes’ CRI-O. Initially, the images are stored under the author’s personal space on DockerHub (docker.io/azukaitis), but they will be relocated to a dedicated MCNP group space once approved. In the future, they will also be available through the registry feature of the https://github.com/lanl/mcnp-containers project. The use of Docker provides a pre-configured environment for building and running MCNP, ensuring reproducibility of results across various host architectures. This significantly improves consistency when running MCNP on different systems. Notably, executables and installers from the Docker images have successfully passed the MCNP development branch testing suite on x86-64 architectures, including Windows, macOS, and Linux operating systems. Furthermore, testing has demonstrated compatibility with macOS Docker in emulation mode on the latest Apple Mac M2 Ultra hardware, ensuring robust support even on the latest platforms. In this document, we will provide a step-by-step guide to using the Docker images across multiple platforms. Additionally, we will present performance numbers for building and running the MCNP test suite.

97 MATHEMATICS AND COMPUTING

Decode the Workload: Training Deep Learning Models for Efficient Compute Cluster Representation

Monitoring the status of a high throughput computing cluster running computationally intensive production jobs is a crucial yet challenging system administration task due to the complexity of such systems. To this end, we train autoencoders using the Linux kernel CPU metrics of the cluster. Additionally, we explore assisting these models with graph neural networks to share information across threads within a compute node. The models are compared in terms of their ability to: 1) Produce a compressed latent representation that captures the salient features of the input, 2) Detect anomalous activity, and 3) Make distinction between different kinds of jobs run at Jefferson Lab. The goal is to have a robust encoder whose compressed embeddings are used for several downstream tasks. We extend this study further by deploying these models in a human-in-the-loop production-based setting for the anomaly detection task and discuss the associated implementation aspects such as continual learning and the criterion to generate alarms. This study represents a first step in the endeavor towards building self-supervised large-scale foundation models for computing centers.

Mohammed, Ahmed

Best of Both Worlds: Integrating Slurm with Kubernetes in a Kubernetes Native Way

We present K-Foundry, a framework that enables the integration of Simple Linux Utility for Resource Management (SLURM) with Kubernetes (K8s) via a Kubernetes-like Control Plane (KCP). Our implementation seamlessly enables a unified communication and scheduling layer for a fleet of multiple diverse computing platforms. While SLURM and K8s traditionally support distinct scheduling models, they have recently started aligning their objectives by moving towards a more converged execution environment.

Beltre, Angel Manuel

Experiences with SYCL on AMD GPUs with Kokkos

With the recent diversification of the hardware landscape in the high-performance computing (HPC) community, performance-portability solutions are becoming more and more important. One of the most popular choices is Kokkos, which recently became a Linux Foundation project. Most of its development is supported by the US Department of Energy and the French Alternative Energies and Atomic Energy Commission. Kokkos is implemented as a C++ library with multiple backends to support CPUs as well as various GPU architectures. These backends include OpenMP, CUDA, HIP, and also SCYL. This approach enables users to leverage the preferred vendor toolchain for the respective platform (e.g. CUDA, ROCm, OneAPI). The SYCL backend is used to target Intel GPUs, in particular to support the Aurora exascale supercomputer. However, SYCL itself also offers a large degree of portability, and in fact Kokkos’ CI for SYCL has been running on NVIDIA hardware due to a lack of access to Intel GPUs. In this report, we describe our experience with using Kokkos SYCL backend on AMD GPUs targeting the Frontier supercomputer at Oak Ridge National Laboratory. The two major SYCL implementations are DPC++ and AdaptiveCpp. While the Kokkos SYCL backend has been implemented using the former, the latter was the first implementation to target AMD GPUs. We will discuss the experience with both of these SYCL implementations in terms of functionality and performance. Using Kokkos to evaluate SYCL toolchains has a number of benefits. Kokkos’ use of SYCL is fairly complex, exercising features such as graphs, relocatable device functions, atomics – including for non-arithmetic types, as well as pinned and page migratable memory allocations. Kokkos also needs to implement capabilities such as Kokkos’ hierarchical parallelism that are not a straight-forward mapping to SYCL capabilities. Furthermore, a large number of libraries and applications that represent diverse use cases are implemented in Kokkos, providing readily available test cases for a toolchain evaluation. Preliminary results show that support for AMD GPUs in DPC++ is much less mature than for NVIDIA GPUs or Intel GPUs. While the situation has improved significantly over the last year, we still encounter many runtime failures, dispatching problems, and code generation issues. With AdaptiveCpp the challenges arise even earlier in the evaluation process. Since Kokkos’ SYCL implementation is largely focused on supporting Intel GPUs, we opted to leverage SYCL extensions which are available in DPC++ but not in AdaptiveCpp. Furthermore, AdaptiveCpp appears to be less conformant with the SYCL2020 standard which Kokkos relies on. In some cases, we are able to work around the lack of feature support, in other cases we have to disable certain Kokkos capabilities to evaluate the toolchain. Our evaluation will leverage Kokkos’ unit tests to establish basic functionality and feature completeness. We then use simple benchmarks for components of a CG implementation as a measure of usability and performance of the SYCL toolchains.

97 MATHEMATICS AND COMPUTING

Establishing Data Analysis Pipeline for Bulk ATAC-Seq Datasets

We developed an analysis pipeline for transposase-accessible chromatin sequencing (ATAC-Seq) data derived from bulk samples, which brings together publicly available R packages in addition to command-line tools designed for analysis of bulk ATAC-Seq data and can be run on any computer running a Linux-like operating system such as Ubuntu or Apple OSX.

97 MATHEMATICS AND COMPUTING

FAST-1.2.2: A Computer Code for Thermal-Mechanical Nuclear Fuel Analysis under Steady-state and Transients

Fuel Analysis under Steady-state and Transients (FAST) is the U.S. Nuclear Regulatory Commission (NRC)’s computer code that calculates the steady-state and transient response of nuclear reactor fuel rods during long-term in-reactor burnup, anticipated operational occurrences (AOOs), design basis accidents (DBAs), and dry storage conditions. The code calculates the temperature, pressure, and deformation of a fuel rod as functions of time-dependent fuel rod power and coolant boundary conditions. The phenomena modeled by the code include heat conduction through the fuel and other materials, heat transfer from the cladding-to-coolant, cladding elastic and plastic deformation (including creep), fuel-cladding mechanical interaction, fission gas release from the fuel, rod internal pressure, void volume, and cladding oxidation. The code contains necessary material and coolant properties, as well as clad-to-coolant heat transfer correlations, for normal operation through postulated accidents and AOOs for today’s U.S.-based light water reactor (LWR) fuel designs. FAST-1.2.2 also contains preliminary materials and models for new LWR fuel concepts, such as accident tolerant fuel (ATF), and non-LWR fuel concepts such as metallic fuels for sodium fast reactors (SFRs). FAST has been developed for use on Windows and Linux operating systems. This document describes FAST-1.2.2 and is one of a series of documents on the code; the other documents detail the material properties used by FAST as well as its integral assessment to experiments and commercial data.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS

Graphical User Interface for a Biasing Board for the PSEC6

The PSEC6 is an application-specific integrated circuit (ASIC) designed for a readout system for a large area picosecond photodetector (LAPPD). The PSEC6 is currently in fabrication and pending testing. The testing system for the PSEC5, the previous iteration of the ASIC, required expensive and non-portable equipment, because the ASIC needs twelve adjustable reference voltages. The new testing system consists of an low-cost, open-source, cross-platform graphical user interface (GUI), a digital system, and a biasing board. The digital system is the interface between the GUI and biasing board, and can be implemented on a microcontroller or field-programmable gate array (FPGA). The biasing board contains twelve digital-to-analog converters (DACs) that are configurable via the GUI, which gives users the ability to write voltage values to all or specific DACs. The GUI was developed in C on Linux using the widget library GTK4 and cross-compiled for Windows compatibility. I2C and SPI protocols were implemented on an Adafruit Feather ESP32-S3 microcontroller to write commands to the DACs and PSEC6. A hardware implementation of the I2C protocol is in development on an FPGA. Since LAPPDs will be used by the Accelerator Neutrino Neutron Interaction Experiment (ANNIE) at Fermilab, the PSEC6 testing system in this internship project can potentially benefit future neutrino research. The project is relevant to the Department of Energy’s microelectronics mission, because the PSEC6 is an ASIC that will handle fast time signals arriving from the detector for readout. It also provided experience with building a cross-platform user interface, practicing digital design and implementation in hardware description language (HDL), and using simulations to inform new design iterations.

Guerrero, Sasha Camila [North Central Coll.]