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Mohammad Atif

Publications and source records attributed to Mohammad Atif.

15 recordsLinked to original sources

CelloAI Benchmarks: Toward Repeatable Evaluation of AI Assistants

Large Language Models (LLM) are increasingly used for software development, yet existing benchmarks for LLM-based coding assistance do not reflect the constraints of High Energy Physics (HEP) and High Performance Computing (HPC) software. Code correctness must respect science constraints and changes must integrate into large, performance-critical codebases with complex dependencies and build systems. The primary contribution of this paper is the development of practical, repeatable benchmarks that quantify LLM performance on HEP/HPC-relevant tasks. We introduce three evaluation tracks -- code documentation benchmarks measure the ability of an LLM to generate Doxygen-style comments, code generation benchmarks evaluate end-to-end usability on representative GPU kernels, and graphical data analysis benchmarks evaluate vision-enabled LLMs. These benchmarks provide a unified framework for measuring progress in scientific coding assistance across documentation quality, code generation robustness, and multimodal validation analysis. By emphasizing repeatability, automated scoring, and domain-relevant failure modes, the suite enables fair comparisons of models and settings while supporting future work on methods that improve reliability for HEP/HPC software development.

hep-ex

Building an AI-native Research Ecosystem for Experimental Particle Physics: A Community Vision

Experimental particle physics seeks to understand the universe by probing its fundamental particles and forces and exploring how they govern the large-scale processes that shape cosmic evolution. This whitepaper presents a vision for how Artificial Intelligence (AI) can accelerate discovery in this field. We outline grand challenges that must be addressed to enable transformative breakthroughs and describe how current and planned experimental facilities can implement this vision to advance our understanding of the vast and complex physical world from the smallest to the largest scales. We show how facilities currently under construction, such as the HL-LHC, DUNE and soon EIC, can both benefit from and serve as proving grounds for this vision, while also enabling a longer-term goal for how future experiments -- like FCC-ee at CERN, IceCube-Gen2, a Muon Collider in the U.S., and smaller to mid-scale projects -- can be fully AI-native. We describe how a truly national-scale collaboration, jointly managed across large funding partners, and involving both DOE laboratories and universities, can make this happen.

hep-ex

Evaluating Application Characteristics for GPU Portability Layer Selection

GPUs have become the dominant source of computing power for high performance computing and are increasingly being used across the High Energy Physics computing landscape for a wide variety of tasks. Though NVIDIA is currently the main provider of GPUs, AMD and Intel are rapidly increasing their market share. As a result, programming using a vendor-specific language such as CUDA can significantly reduce deployment choices. There are a number of portability layers such as Kokkos, Alpaka, SYCL, OpenMP and std::par that permit execution on a broad range of GPU and CPU architectures, significantly increasing the flexibility of application programmers. However, each of these portability layers has its own characteristics, performing better at some tasks and worse at others, or placing limitations on aspects of the application. In this presentation, we report on a study of application and kernel characteristics that can influence the choice of a portability layer and show how each layer handles these characteristics. We have analyzed representative heterogeneous applications from CMS (patatrack and p2r), DUNE (Wire-Cell Toolkit), and ATLAS (FastCaloSim) to identify key application characteristics that have different behaviors for the various portability technologies. Using these results, developers can make more informed decisions on which GPU portability technology is best suited to their application.

hep-ex

CelloAI: Leveraging Large Language Models for HPC Software Development in High Energy Physics

Next-generation High Energy Physics (HEP) experiments will generate unprecedented data volumes, necessitating High Performance Computing (HPC) integration alongside traditional high-throughput computing. However, HPC adoption in HEP is hindered by the challenge of porting legacy software to heterogeneous architectures and the sparse documentation of these complex scientific codebases. We present CelloAI, a locally hosted coding assistant that leverages Large Language Models (LLMs) with retrieval-augmented generation (RAG) to support HEP code documentation and generation. This local deployment ensures data privacy, eliminates recurring costs and provides access to large context windows without external dependencies. CelloAI addresses two primary use cases, code documentation and code generation, through specialized components. For code documentation, the assistant provides: (a) Doxygen style comment generation for all functions and classes by retrieving relevant information from RAG sources (papers, posters, presentations), (b) file-level summary generation, and (c) an interactive chatbot for code comprehension queries. For code generation, CelloAI employs syntax-aware chunking strategies that preserve syntactic boundaries during embedding, improving retrieval accuracy in large codebases. The system integrates callgraph knowledge to maintain dependency awareness during code modifications and provides AI-generated suggestions for performance optimization and accurate refactoring. We evaluate CelloAI using real-world HEP applications from ATLAS, CMS, and DUNE experiments, comparing different embedding models for code retrieval effectiveness. Our results demonstrate the AI assistant's capability to enhance code understanding and support reliable code generation while maintaining the transparency and safety requirements essential for scientific computing environments.

cs.SE

AI-Powered Assistant for Long-Term Access to RHIC Knowledge

As the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory concludes 25 years of operation, preserving not only its vast data holdings ($\sim$1 ExaByte) but also the embedded scientific knowledge becomes a critical priority. The RHIC Data and Analysis Preservation Plan (DAPP) introduces an AI-powered assistant system that provides natural language access to documentation, workflows, and software, with the aim of supporting reproducibility, education, and future discovery. Built upon Large Language Models using Retrieval-Augmented Generation and the Model Context Protocol, this assistant indexes structured and unstructured content from RHIC experiments and enables domain-adapted interaction. We report on the deployment, computational performance, ongoing multi-experiment integration, and architectural features designed for a sustainable and explainable long-term AI access. Our experience illustrates how modern AI/ML tools can transform the usability and discoverability of scientific legacy data.

cs.IR

Packaging HEP Heterogeneous Mini-apps for Portable Benchmarking and Facility Evaluation on Modern HPCs

High Energy Physics (HEP) experiments are making increasing use of GPUs and GPU dominated High Performance Computer facilities. Both the software and hardware of these systems are rapidly evolving, creating challenges for experiments to make informed decisions as to where they wish to devote resources. In its first phase, the High Energy Physics Center for Computational Excellence (HEP-CCE) produced portable versions of a number of heterogeneous HEP mini-apps, such as \ptor, FastCaloSim, Patatrack and the WireCell Toolkit, that exercise a broad range of GPU characteristics, enabling cross platform and facility benchmarking and evaluation. However, these mini-apps still require a significant amount of manual intervention to deploy on a new facility. We present our work in developing turn-key deployments of these mini-apps, where by means of containerization and automated configuration and build techniques such as Spack, we are able to quickly test new hardware, software, environments and entire facilities with minimal user intervention, and then track performance metrics over time.

hep-ex

A Microbenchmark Framework for Performance Evaluation of OpenMP Target Offloading

We present a framework based on Catch2 to evaluate performance of OpenMP's target offload model via micro-benchmarks. The compilers supporting OpenMP's target offload model for heterogeneous architectures are currently undergoing rapid development. These developments influence performance of various complex applications in different ways. This framework can be employed to track the impact of compiler upgrades and compare their performance with the native programming models. We use the framework to benchmark performance of a few commonly used operations on leadership class supercomputers such as Perlmutter at National Energy Research Scientific Computing (NERSC) Center and Frontier at Oak Ridge Leadership Computing Facility (OLCF). Such a framework will be useful for compiler developers to gain insights into the overall impact of many small changes, as well as for users to decide which compilers and versions are expected to yield best performance for their applications.

cs.PF

Fourier neural operators for spatiotemporal dynamics in two-dimensional turbulence

High-fidelity direct numerical simulation of turbulent flows for most real-world applications remains an outstanding computational challenge. Several machine learning approaches have recently been proposed to alleviate the computational cost even though they become unstable or unphysical for long time predictions. We identify that the Fourier neural operator (FNO) based models combined with a partial differential equation (PDE) solver can accelerate fluid dynamic simulations and thus address computational expense of large-scale turbulence simulations. We treat the FNO model on the same footing as a PDE solver and answer important questions about the volume and temporal resolution of data required to build pre-trained models for turbulence. We also discuss the pitfalls of purely data-driven approaches that need to be avoided by the machine learning models to become viable and competitive tools for long time simulations of turbulence.

physics.flu-dyn

Towards Accelerating Particle-Resolved Direct Numerical Simulation with Neural Operators

We present our ongoing work aimed at accelerating a particle-resolved direct numerical simulation model designed to study aerosol-cloud-turbulence interactions. The dynamical model consists of two main components - a set of fluid dynamics equations for air velocity, temperature, and humidity, coupled with a set of equations for particle (i.e., cloud droplet) tracing. Rather than attempting to replace the original numerical solution method in its entirety with a machine learning (ML) method, we consider developing a hybrid approach. We exploit the potential of neural operator learning to yield fast and accurate surrogate models and, in this study, develop such surrogates for the velocity and vorticity fields. We discuss results from numerical experiments designed to assess the performance of ML architectures under consideration as well as their suitability for capturing the behavior of relevant dynamical systems.

physics.flu-dyn

Evaluating Portable Parallelization Strategies for Heterogeneous Architectures in High Energy Physics

High-energy physics (HEP) experiments have developed millions of lines of code over decades that are optimized to run on traditional x86 CPU systems. However, we are seeing a rapidly increasing fraction of floating point computing power in leadership-class computing facilities and traditional data centers coming from new accelerator architectures, such as GPUs. HEP experiments are now faced with the untenable prospect of rewriting millions of lines of x86 CPU code, for the increasingly dominant architectures found in these computational accelerators. This task is made more challenging by the architecture-specific languages and APIs promoted by manufacturers such as NVIDIA, Intel and AMD. Producing multiple, architecture-specific implementations is not a viable scenario, given the available person power and code maintenance issues. The Portable Parallelization Strategies team of the HEP Center for Computational Excellence is investigating the use of Kokkos, SYCL, OpenMP, std::execution::parallel and alpaka as potential portability solutions that promise to execute on multiple architectures from the same source code, using representative use cases from major HEP experiments, including the DUNE experiment of the Long Baseline Neutrino Facility, and the ATLAS and CMS experiments of the Large Hadron Collider. This cross-cutting evaluation of portability solutions using real applications will help inform and guide the HEP community when choosing their software and hardware suites for the next generation of experimental frameworks. We present the outcomes of our studies, including performance metrics, porting challenges, API evaluations, and build system integration.

hep-ex

Portable Programming Model Exploration for LArTPC Simulation in a Heterogeneous Computing Environment: OpenMP vs. SYCL

The evolution of the computing landscape has resulted in the proliferation of diverse hardware architectures, with different flavors of GPUs and other compute accelerators becoming more widely available. To facilitate the efficient use of these architectures in a heterogeneous computing environment, several programming models are available to enable portability and performance across different computing systems, such as Kokkos, SYCL, OpenMP and others. As part of the High Energy Physics Center for Computational Excellence (HEP-CCE) project, we investigate if and how these different programming models may be suitable for experimental HEP workflows through a few representative use cases. One of such use cases is the Liquid Argon Time Projection Chamber (LArTPC) simulation which is essential for LArTPC detector design, validation and data analysis. Following up on our previous investigations of using Kokkos to port LArTPC simulation in the Wire-Cell Toolkit (WCT) to GPUs, we have explored OpenMP and SYCL as potential portable programming models for WCT, with the goal to make diverse computing resources accessible to the LArTPC simulations. In this work, we describe how we utilize relevant features of OpenMP and SYCL for the LArTPC simulation module in WCT. We also show performance benchmark results on multi-core CPUs, NVIDIA and AMD GPUs for both the OpenMP and the SYCL implementations. Comparisons with different compilers will also be given where appropriate.

hep-ex

Effect of outer cylinder rotation on the radially heated Taylor-Couette flow

A Taylor-Couette setup with radial heating is considered where a Boussinesq fluid is sheared in the annular region between two concentric, independently rotating cylinders maintained at different temperatures. Linear stability analysis is performed to determine the Taylor number for the onset of instability. Two radius ratios corresponding to wide and thin gaps with several rotation rate ratios are considered. The rotation of the outer cylinder is found to have a general stabilizing effect on the stability threshold as compared to pure inner-cylinder rotation, with a few exceptions. The radial heating sets up an axial flow which breaks the reflection symmetry of isothermal Taylor-Couette flow in the axial coordinate. This symmetry breaking separates linear stability thresholds and we find fastest growing modes with both positive and negative azimuthal numbers for different parameters. Another important finding of the current study is the discovery of unstable modes in the Rayleigh-stable regime. Furthermore, closed disconnected neutral curves (CDNCs) are observed for both wide and thin gaps which can separate from or merge into open neutral-stability curves. Alternatively, CDNCs can also morph into open neutral stability curves as the rotation rate ratio is changed. CDNCs are observed to be sensitive to changes in control parameters and their appearance/disappearance is shown to induce discontinuous jumps in the critical Taylor number. For both wide and thin gaps, the fastest-growing modes found in the pure corotation case are shown to have their origins in the instability islands at smaller values of rotation rate ratios.

physics.flu-dyn

Essentially entropic lattice Boltzmann model: Theory and simulations

We present a detailed description of the essentially entropic lattice Boltzmann model. The entropic lattice Boltzmann model guarantees unconditional numerical stability by iteratively solving the nonlinear entropy evolution equation. In this paper we explain the construction of closed-form analytic solutions to this equation. We demonstrate that near equilibrium this exact solution reduces to the standard lattice Boltzmann model. We consider a few test cases to show that the exact solution does not exhibit any significant deviation from the iterative solution. We also extend the analytical solution for the ES-BGK model to remove the limitation on the Prandtl number for heat transfer problems. The simplicity of the exact solution removes the computational overhead and algorithmic complexity associated with the entropic lattice Boltzmann models.

cond-mat.stat-mech

Reduced kinetic model of polyatomic gases

Kinetic models of polyatomic gas typically account for the internal degrees of freedom at the level of the two-particle distribution function. However, close to the hydrodynamic limit, the internal (rotational) degrees of freedom tend to be well represented just by rotational kinetic energy density. We account for the rotational energy by augmenting the Ellipsoidal-statistical BGK (ES-BGK) model, an extension of the Bhatnagar-Gross- Krook (BGK) model, at the level of the single-particle distribution function with an advection-diffusion-relaxation equation for the rotational energy. This reduced model respects the H theorem and recovers the compressible hydrodynamics for polyatomic gases as its macroscopic limit. As required for a polyatomic gas model, this extension of the ES-BGK model has not only correct specific heat ratio but also allows for three independent tunable transport coefficients: thermal conductivity, shear viscosity, and bulk viscosity. We illustrate the effectiveness of the model via a lattice Boltzmann method implementation.

physics.flu-dyn

Lattice Boltzmann model for weakly compressible flows

We present an energy conserving lattice Boltzmann model based on a crystallographic lattice for simulation of weakly compressible flows. The theoretical requirements and the methodology to construct such a model are discussed. We demonstrate that the model recovers the isentropic sound speed in addition to the effects of viscous heating and heat flux dynamics. Several test cases for acoustics, thermal and thermoacoustic flows are simulated to show the accuracy of the proposed model.

physics.comp-ph