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Marcin Copik

Publications and source records attributed to Marcin Copik.

At least 19 recordsLinked to original sources

ADELIA: Automatic Differentiation for Efficient Laplace Inference Approximations

Spatio-temporal Bayesian inference drives environmental and health sciences using latent Gaussian models. Integrated Nested Laplace Approximations (INLA) enable inference for these models at HPC scale but rely on derivative-based optimization over $d$ hyperparameters. State-of-the-art INLA implementations approximate derivatives via central finite differences (FD), requiring $2d{+}1$ evaluations. These evaluations are embarrassingly parallel, but total work and energy grow with $d$, limiting time-to-solution under fixed budgets. Reverse-mode automatic differentiation (AD) computes exact gradients independently of $d$, but its efficient application to INLA's structured-sparse kernels is an open challenge. We present ADELIA, the first AD-enabled INLA implementation with a structure-exploiting multi-GPU backward pass leveraging model sparsity. We evaluate ADELIA on ten benchmark models, including real-world air-pollution monitoring. We achieve $4.2$--$7.9\times$ per-gradient speedups and reliable convergence on production-scale models with up to 1.9M latent variables, where FD struggles. Even when scaled to 16--32 GPUs to match ADELIA's wall-clock time, FD consumes $5$--$8\times$ more energy.

cs.DC

Computing the Full Earth System at 1 km Resolution

We present the first-ever global simulation of the full Earth system at 1.25 km grid spacing, achieving highest time compression with an unseen number of degrees of freedom. Our model captures the flow of energy, water, and carbon through key components of the Earth system: atmosphere, ocean, and land. To achieve this landmark simulation, we harness the power of 8192 GPUs on Alps and 20480 GPUs on JUPITER, two of the world's largest GH200 superchip installations. We use both the Grace CPUs and Hopper GPUs by carefully balancing Earth's components in a heterogeneous setup and optimizing acceleration techniques available in ICON's codebase. We show how separation of concerns can reduce the code complexity by half while increasing performance and portability. Our achieved time compression of 145.7 simulated days per day enables long studies including full interactions in the Earth system and even outperforms earlier atmosphere-only simulations at a similar resolution.

physics.ao-ph

Hazel: Secure and Efficient Disaggregated Storage

Disaggregated storage with NVMe-over-Fabrics (NVMe-oF) has emerged as the standard solution in modern supercomputers and data center clusters, achieving superior performance, resource utilization, and power efficiency. Simultaneously, confidential computing (CC) is becoming the de facto security paradigm, enforcing stronger isolation and protection for sensitive workloads. However, securing state-of-the-art storage with traditional CC methods struggles to scale and compromises performance or security. To address these issues, we introduce Hazel, a storage management system that extends the NVMe-oF protocol capabilities and adheres to the CC threat model, providing confidentiality, integrity, and freshness guarantees. Hazel offers an appropriate control path with novel concepts such as counter-leasing. Hazel also optimizes data path performance by leveraging NVMe metadata and introducing a new disaggregated Hazel Merkle Tree (HMT), all while remaining compatible with NVMe-oF. For additional efficiency, Hazel also supports offloading to CC-capable smart NIC accelerators. We prototype Hazel on an NVIDIA BlueField-3 and demonstrate that it can achieve as little as 1-2% performance degradation for synthetic patterns, AI training, IO500, and YCSB.

cs.CR

Confidential LLM Inference: Performance and Cost Across CPU and GPU TEEs

Large Language Models (LLMs) are increasingly deployed on converged Cloud and High-Performance Computing (HPC) infrastructure. However, as LLMs handle confidential inputs and are fine-tuned on costly, proprietary datasets, their heightened security requirements slow adoption in privacy-sensitive sectors such as healthcare and finance. We investigate methods to address this gap and propose Trusted Execution Environments (TEEs) as a solution for securing end-to-end LLM inference. We validate their practicality by evaluating these compute-intensive workloads entirely within CPU and GPU TEEs. On the CPU side, we conduct an in-depth study running full Llama2 inference pipelines (7B, 13B, 70B) inside Intel's TDX and SGX, accelerated by Advanced Matrix Extensions (AMX). We derive 12 insights, including that across various data types, batch sizes, and input lengths, CPU TEEs impose under 10% throughput and 20% latency overheads, further reduced by AMX. We run LLM inference on NVIDIA H100 Confidential Compute GPUs, contextualizing our CPU findings and observing throughput penalties of 4-8% that diminish as batch and input sizes grow. By comparing performance, cost, and security trade-offs, we show how CPU TEEs can be more cost-effective or secure than their GPU counterparts. To our knowledge, our work is the first to comprehensively demonstrate the performance and practicality of modern TEEs across both CPUs and GPUs for enabling confidential LLMs (cLLMs).

cs.PF

XaaS Containers: Performance-Portable Representation With Source and IR Containers

High-performance computing (HPC) systems and cloud data centers are converging, and containers are becoming the default method of portable software deployment. Yet, while containers simplify software management, they face significant performance challenges in HPC environments as they must sacrifice hardware-specific optimizations to achieve portability. Although HPC containers can use runtime hooks to access optimized MPI libraries and GPU devices, they are limited by application binary interface (ABI) compatibility and cannot overcome the effects of early-stage compilation decisions. Acceleration as a Service (XaaS) proposes a vision of performance-portable containers, where a containerized application should achieve peak performance across all HPC systems. We present a practical realization of this vision through Source and Intermediate Representation (IR) containers, where we delay performance-critical decisions until the target system specification is known. We analyze specialization mechanisms in HPC software and propose a new LLM-assisted method for automatic discovery of specializations. By examining the compilation pipeline, we develop a methodology to build containers optimized for target architectures at deployment time. Our prototype demonstrates that new XaaS containers combine the convenience of containerization with the performance benefits of system-specialized builds.

cs.DC

AI Factories: It's time to rethink the Cloud-HPC divide

The strategic importance of artificial intelligence is driving a global push toward Sovereign AI initiatives. Nationwide governments are increasingly developing dedicated infrastructures, called AI Factories (AIF), to achieve technological autonomy and secure the resources necessary to sustain robust local digital ecosystems. In Europe, the EuroHPC Joint Undertaking is investing hundreds of millions of euros into several AI Factories, built atop existing high-performance computing (HPC) supercomputers. However, while HPC systems excel in raw performance, they are not inherently designed for usability, accessibility, or serving as public-facing platforms for AI services such as inference or agentic applications. In contrast, AI practitioners are accustomed to cloud-native technologies like Kubernetes and object storage, tools that are often difficult to integrate within traditional HPC environments. This article advocates for a dual-stack approach within supercomputers: integrating both HPC and cloud-native technologies. Our goal is to bridge the divide between HPC and cloud computing by combining high performance and hardware acceleration with ease of use and service-oriented front-ends. This convergence allows each paradigm to amplify the other. To this end, we will study the cloud challenges of HPC (Serverless HPC) and the HPC challenges of cloud technologies (High-performance Cloud).

cs.DC

DaCe AD: Unifying High-Performance Automatic Differentiation for Machine Learning and Scientific Computing

Automatic differentiation (AD) is a set of techniques that systematically applies the chain rule to compute the gradients of functions without requiring human intervention. Although the fundamentals of this technology were established decades ago, it is experiencing a renaissance as it plays a key role in efficiently computing gradients for backpropagation in machine learning algorithms. AD is also crucial for many applications in scientific computing domains, particularly emerging techniques that integrate machine learning models within scientific simulations and schemes. Existing AD frameworks have four main limitations: limited support of programming languages, requiring code modifications for AD compatibility, limited performance on scientific computing codes, and a naive store-all solution for forward-pass data required for gradient calculations. These limitations force domain scientists to manually compute the gradients for large problems. This work presents DaCe AD, a general, efficient automatic differentiation engine that requires no code modifications. DaCe AD uses a novel ILP-based algorithm to optimize the trade-off between storing and recomputing to achieve maximum performance within a given memory constraint. We showcase the generality of our method by applying it to NPBench, a suite of HPC benchmarks with diverse scientific computing patterns, where we outperform JAX, a Python framework with state-of-the-art general AD capabilities, by more than 92 times on average without requiring any code changes.

cs.LG

Higher-Order Graph Databases

Recent advances in graph databases (GDBs) have been driving interest in large-scale analytics, yet current systems fail to support higher-order (HO) interactions beyond first-order (one-hop) relations, which are crucial for tasks such as subgraph counting, polyadic modeling, and HO graph learning. We address this by introducing a new class of systems, higher-order graph databases (HO-GDBs) that use lifting and lowering paradigms to seamlessly extend traditional GDBs with HO. We provide a theoretical analysis of OLTP and OLAP queries, ensuring correctness, scalability, and ACID compliance. We implement a lightweight, modular, and parallelizable HO-GDB prototype that offers native support for hypergraphs, node-tuples, subgraphs, and other HO structures under a unified API. The prototype scales to large HO OLTP & OLAP workloads and shows how HO improves analytical tasks, for example enhancing accuracy of graph neural networks within a GDB by 44%. Our work ensures low latency and high query throughput, and generalizes both ACID-compliant and eventually consistent systems.

cs.DB

Affordable AI Assistants with Knowledge Graph of Thoughts

Large Language Models (LLMs) are revolutionizing the development of AI assistants capable of performing diverse tasks across domains. However, current state-of-the-art LLM-driven agents face significant challenges, including high operational costs and limited success rates on complex benchmarks like GAIA. To address these issues, we propose Knowledge Graph of Thoughts (KGoT), an innovative AI assistant architecture that integrates LLM reasoning with dynamically constructed knowledge graphs (KGs). KGoT extracts and structures task-relevant knowledge into a dynamic KG representation, iteratively enhanced through external tools such as math solvers, web crawlers, and Python scripts. Such structured representation of task-relevant knowledge enables low-cost models to solve complex tasks effectively while also minimizing bias and noise. For example, KGoT achieves a 29% improvement in task success rates on the GAIA benchmark compared to Hugging Face Agents with GPT-4o mini. Moreover, harnessing a smaller model dramatically reduces operational costs by over 36x compared to GPT-4o. Improvements for other models (e.g., Qwen2.5-32B and Deepseek-R1-70B) and benchmarks (e.g., SimpleQA) are similar. KGoT offers a scalable, affordable, versatile, and high-performing solution for AI assistants.

cs.AI

Reasoning Language Models: A Blueprint

Reasoning language models (RLMs), also known as Large Reasoning Models (LRMs), such as OpenAI's o1 and o3, DeepSeek-R1, and Alibaba's QwQ, have redefined AI's problem-solving capabilities by extending LLMs with advanced reasoning mechanisms. Yet, their high costs, proprietary nature, and complex architectures - uniquely combining reinforcement learning (RL), search heuristics, and LLMs - present accessibility and scalability challenges. To address these, we propose a comprehensive blueprint that organizes RLM components into a modular framework, based on a survey and analysis of all RLM works. This blueprint incorporates diverse reasoning structures (chains, trees, graphs, and nested forms), reasoning strategies (e.g., Monte Carlo Tree Search, Beam Search), RL concepts (policy, value models and others), supervision schemes (Outcome-Based and Process-Based Supervision), and other related concepts (e.g., Test-Time Compute, Retrieval-Augmented Generation, agent tools). We also provide detailed mathematical formulations and algorithmic specifications to simplify RLM implementation. By showing how schemes like LLaMA-Berry, QwQ, Journey Learning, and Graph of Thoughts fit as special cases, we demonstrate the blueprint's versatility and unifying potential. To illustrate its utility, we introduce x1, a modular implementation for rapid RLM prototyping and experimentation. Using x1 and a literature review, we provide key insights, such as multi-phase training for policy and value models, and the importance of familiar training distributions. Finally, we discuss scalable RLM cloud deployments and we outline how RLMs can integrate with a broader LLM ecosystem. Our work demystifies RLM construction, democratizes advanced reasoning capabilities, and fosters innovation, aiming to mitigate the gap between "rich AI" and "poor AI" by lowering barriers to RLM design and experimentation.

cs.AI

Core Hours and Carbon Credits: Incentivizing Sustainability in HPC

Realizing a shared responsibility between providers and consumers is critical to manage the sustainability of HPC. However, while cost may motivate efficiency improvements by infrastructure operators, broader progress is impeded by a lack of user incentives. We conduct a survey of HPC users that reveals fewer than 30 percent are aware of their energy consumption, and that energy efficiency is among users' lowest priority concerns. One explanation is that existing pricing models may encourage users to prioritize performance over energy efficiency. We propose two transparent multi-resource pricing schemes, Energy- and Carbon-Based Accounting, that seek to change this paradigm by incentivizing more efficient user behavior. These two schemes charge for computations based on their energy consumption or carbon footprint, respectively, rewarding users who leverage efficient hardware and software. We evaluate these two pricing schemes via simulation, in a prototype, and a user study.

cs.DC

A Priori Loop Nest Normalization: Automatic Loop Scheduling in Complex Applications

The same computations are often expressed differently across software projects and programming languages. In particular, how computations involving loops are expressed varies due to the many possibilities to permute and compose loops. Since each variant may have unique performance properties, automatic approaches to loop scheduling must support many different optimization recipes. In this paper, we propose a priori loop nest normalization to align loop nests and reduce the variation before the optimization. Specifically, we define and apply normalization criteria, mapping loop nests with different memory access patterns to the same canonical form. Since the memory access pattern is susceptible to loop variations and critical for performance, this normalization allows many loop nests to be optimized by the same optimization recipe. To evaluate our approach, we apply the normalization with optimizations designed for only the canonical form, improving the performance of many different loop nest variants. Across multiple implementations of 15 benchmarks using different languages, we outperform a baseline compiler in C on average by a factor of $21.13$, state-of-the-art auto-schedulers such as Polly and the Tiramisu auto-scheduler by $2.31$ and $2.89$, as well as performance-oriented Python-based frameworks such as NumPy, Numba, and DaCe by $9.04$, $3.92$, and $1.47$. Furthermore, we apply the concept to the CLOUDSC cloud microphysics scheme, an actively used component of the Integrated Forecasting System, achieving a 10% speedup over the highly-tuned Fortran code.

cs.PF

SeBS-Flow: Benchmarking Serverless Cloud Function Workflows

Serverless computing has emerged as a prominent paradigm, with a significant adoption rate among cloud customers. While this model offers advantages such as abstraction from the deployment and resource scheduling, it also poses limitations in handling complex use cases due to the restricted nature of individual functions. Serverless workflows address this limitation by orchestrating multiple functions into a cohesive application. However, existing serverless workflow platforms exhibit significant differences in their programming models and infrastructure, making fair and consistent performance evaluations difficult in practice. To address this gap, we propose the first serverless workflow benchmarking suite SeBS-Flow, providing a platform-agnostic workflow model that enables consistent benchmarking across various platforms. SeBS-Flow includes six real-world application benchmarks and four microbenchmarks representing different computational patterns. We conduct comprehensive evaluations on three major cloud platforms, assessing performance, cost, scalability, and runtime deviations. We make our benchmark suite open-source, enabling rigorous and comparable evaluations of serverless workflows over time.

cs.DC

CheckEmbed: Effective Verification of LLM Solutions to Open-Ended Tasks

Large Language Models (LLMs) are transforming a wide range of domains, yet verifying their outputs remains a significant challenge, especially for complex open-ended tasks such as consolidation, summarization, and knowledge extraction. To address this, we introduce CheckEmbed (CE): a simple, scalable, and accurate verification method. CE reduces each LLM answer to a single embedding vector using powerful modern embedding LLM models like SFR-Embedding-Mistral. Prior methods such as BERTScore and SelfCheckGPT relied on weaker encoders like BERT, forcing them to operate at token or sentence granularity. In contrast, CE performs fast, semantically rich comparisons directly at the whole-answer level, overcoming key limitations in both accuracy and scalability. We conduct a comprehensive design and time complexity analysis across 13 verification baselines, including classical text scorers (e.g., BLEU), stability-based methods (e.g., SelfCheckGPT), and generative evaluators (e.g., LLM-as-a-Judge), which highlights the effectiveness, efficiency, versatility, and simplicity of CE. Empirical results show that CE reliably detects hallucinations in both closed and open-ended tasks. We further present evidence that CE generalizes beyond text to other modalities such as vision, establishing it as a practical and versatile verification framework.

cs.CL

Demystifying Chains, Trees, and Graphs of Thoughts

The field of natural language processing (NLP) has witnessed significant progress in recent years, with a notable focus on improving large language models' (LLM) performance through innovative prompting techniques. Among these, prompt engineering coupled with structures has emerged as a promising paradigm, with designs such as Chain-of-Thought, Tree of Thoughts, or Graph of Thoughts, in which the overall LLM reasoning is guided by a structure such as a graph. As illustrated with numerous examples, this paradigm significantly enhances the LLM's capability to solve numerous tasks, ranging from logical or mathematical reasoning to planning or creative writing. To facilitate the understanding of this growing field and pave the way for future developments, we devise a general blueprint for effective and efficient LLM reasoning schemes. For this, we conduct an in-depth analysis of the prompt execution pipeline, clarifying and clearly defining different concepts. We then build the first taxonomy of structure-enhanced LLM reasoning schemes. We focus on identifying fundamental classes of harnessed structures, and we analyze the representations of these structures, algorithms executed with these structures, and many others. We refer to these structures as reasoning topologies, because their representation becomes to a degree spatial, as they are contained within the LLM context. Our study compares existing prompting schemes using the proposed taxonomy, discussing how certain design choices lead to different patterns in performance and cost. We also outline theoretical underpinnings, relationships between prompting and other parts of the LLM ecosystem such as knowledge bases, and the associated research challenges. Our work will help to advance future prompt engineering techniques.

cs.CL

Software Resource Disaggregation for HPC with Serverless Computing

Aggregated HPC resources have rigid allocation systems and programming models which struggle to adapt to diverse and changing workloads. Consequently, HPC systems fail to efficiently use the large pools of unused memory and increase the utilization of idle computing resources. Prior work attempted to increase the throughput and efficiency of supercomputing systems through workload co-location and resource disaggregation. However, these methods fall short of providing a solution that can be applied to existing systems without major hardware modifications and performance losses. In this paper, we improve the utilization of supercomputers by employing the new cloud paradigm of serverless computing. We show how serverless functions provide fine-grained access to the resources of batch-managed cluster nodes. We present an HPC-oriented Function-as-a-Service (FaaS) that satisfies the requirements of high-performance applications. We demonstrate a software resource disaggregation approach where placing functions on unallocated and underutilized nodes allows idle cores and accelerators to be utilized while retaining near-native performance.

cs.DC

Cppless: Single-Source and High-Performance Serverless Programming in C++

The rise of serverless computing introduced a new class of scalable, elastic and widely available parallel workers in the cloud. Many systems and applications benefit from offloading computations and parallel tasks to dynamically allocated resources. However, the developers of C++ applications find it difficult to integrate functions due to complex deployment, lack of compatibility between client and cloud environments, and loosely typed input and output data. To enable single-source and efficient serverless acceleration in C++, we introduce Cppless, an end-to-end framework for implementing remote functions which handles the creation, deployment, and invocation of serverless functions. Cppless is built on top of LLVM and requires only two compiler extensions to automatically extract C++ function objects and deploy them to the cloud. We demonstrate that offloading parallel computations, such as from a C++ application to serverless workers, can provide up to 59x speedup with minimal cost increase while requiring only minor code modifications.

cs.DC

XaaS: Acceleration as a Service to Enable Productive High-Performance Cloud Computing

HPC and Cloud have evolved independently, specializing their innovations into performance or productivity. Acceleration as a Service (XaaS) is a recipe to empower both fields with a shared execution platform that provides transparent access to computing resources, regardless of the underlying cloud or HPC service provider. Bridging HPC and cloud advancements, XaaS presents a unified architecture built on performance-portable containers. Our converged model concentrates on low-overhead, high-performance communication and computing, targeting resource-intensive workloads from climate simulations to machine learning. XaaS lifts the restricted allocation model of Function-as-a-Service (FaaS), allowing users to benefit from the flexibility and efficient resource utilization of serverless while supporting long-running and performance-sensitive workloads from HPC.

cs.DC