arXiv subjects

Antonio J. Peña

Publications and source records attributed to Antonio J. Peña.

At least 19 recordsLinked to original sources

arXiv2026

Seamless Execution of Malleable Applications in Controlled and Production HPC Environments

Many large-scale scientific applications exhibit time-varying behavior, yet production HPC clusters still rely on rigid, fixed-size allocations, and most dynamic techniques remain confined to laboratory prototypes. This work presents a practical MPI malleability methodology that integrates with state-of-the-art high-performance computing (HPC) software stacks and operational practices. The methodology is implemented in the Dynamic Management of Resources (DMR) framework and is designed to ease adoption by existing applications without requiring intrusive code changes or scheduler modifications. We evaluate our approach by integrating the DMR API into two large-scale scientific applications and deploying them on three TOP500 supercomputers under realistic production configurations. Our non-invasive malleability solution achieves performance comparable to static baselines in controlled environments while substantially reducing node-hour consumption for identical workloads. These results show that malleability can be effectively exploited on production systems using vanilla resource managers, lowering the barrier to adoption of dynamic resource management in HPC.

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arXiv2026

Malleable Molecular Dynamics Simulations with GROMACS and DMR

Static resource allocations in high-performance computing (HPC) lead to inefficiencies for time-varying workloads, causing idle resources, queue delays, and higher node-hour costs. The Dynamic Management of Resources (DMR) middleware enables MPI process malleability in Slurm via a simple API decoupled from scheduler internals. In this work, we integrate DMR into the GROMACS molecular dynamics engine to obtain a malleable variant that can dynamically adapt its MPI process count by combining communication-efficiency-aware reconfiguration with GROMACS' native checkpoint/restart mechanism. We evaluate this design on the MareNostrum~5 supercomputer, comparing dynamic runs against static executions and quantifying reconfiguration overheads, time-to-solution, and node-hour savings for bursty GROMACS workloads.

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arXiv2026

HE-PIM: Demystifying Homomorphic Operations on a Real-world Processing-in-Memory System

Homomorphic encryption (HE) enables computation over encrypted data, offering strong privacy guarantees for untrusted computing environments. Practical adoption remains limited by high computational complexity, large ciphertext sizes, and substantial data movement. Processor-centric architectures (CPUs, GPUs, ASICs) hit fundamental bottlenecks on HE workloads because ciphertexts are large, data locality is low, and primitives such as relinearization and bootstrapping repeatedly access large auxiliary metadata. Processing-In-Memory (PIM) is a promising mitigation by computing near or inside memory. Prior PIM proposals for HE either do not target real-world PIM systems or cover only a narrow set of operations. We comprehensively characterize HE operations on a real-world, general-purpose PIM system. We implement a complete set of HE kernels used by emerging applications (databases, machine learning) on the UPMEM PIM system, evaluate performance and scalability, compare against CPU and GPU baselines, and discuss implications for future PIM hardware. Our results demonstrate four major findings. (1) HE-based applications expose distinct bottlenecks across execution stages: some kernels are compute-bound due to modular arithmetic, while others are memory-bound due to large ciphertexts and intermediate data. These bottlenecks are exacerbated by limited per-core compute and per-bank capacity, which force frequent data movement. (2) The dominant compute bottleneck is the lack of native 64-bit modular integer multiplication, a key HE primitive. (3) Limited per-bank memory capacity is the second major bottleneck, since HE ciphertexts and auxiliary metadata do not fit and require inter-bank movement. (4) Despite these limits, PIM can be a viable alternative to state-of-the-art CPU and GPU systems for HE when equipped with native modular multiplication and efficient inter-PIM data movement.

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arXiv2026

Towards the Democratization and Standardization of Dynamic Resources with MPI Spawning

This paper presents an efficient tool for managing dynamic resources in production high-performance computing (HPC) settings, focusing on flexibility, adaptability, and user-friendliness. We introduce a unified dynamic resource management application programming interface (API) that supports a wide range of HPC applications, allowing seamless integration without direct interaction with Dynamic Management of Resources (DMR). The DMR framework, evolved from the DMRlib structure, now supports various dynamic resource managers and includes the Proteo reconfiguration engine to enhance malleability strategies. This integration addresses previous limitations by allowing diverse reconfiguration methods without respawning all processes or lacking RMS support. The paper also showcases the solution's performance and coding productivity with the MPDATA (Multidimensional Positive Definite Advection Transport Algorithm) application. Key contributions include an enhanced modular DMR framework supporting different reconfiguration managers, upgraded DMRlib with the Proteo reconfiguration engine, offering extensive reconfiguration strategies, and a malleable version of the MPDATA solver.

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arXiv2026

A Test Taxonomy and Continuous Integration Ecosystem for Dynamic Resource Management in HPC

High-performance computing (HPC) systems are increasingly exploring dynamic resource management and malleable MPI applications to better adapt to heterogeneous architectures, fluctuating workloads, and energy constraints. However, the correctness of the libraries that support these techniques is often evaluated through ad hoc experiments that can be difficult to reproduce and maintain. This article introduces methodology for testing dynamic resource management frameworks that combines a taxonomy of tests for MPI malleable libraries with an HPC-oriented continuous integration (CI) ecosystem. The taxonomy structures functional and non-functional tests at both component-integration and system levels. The CI ecosystem instantiates this taxonomy in a containerized virtual cluster enabling automated validation. The approach is instantiated and evaluated using the Dynamic Management of Resources (DMR) framework as a representative case study. Results show that the proposed methodology improves early fault detection, simplifies maintenance under evolving dependencies, and transfers to other malleability solutions that expose analogous primitives for initialization, readiness checking, and reconfiguration.

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arXiv2026

DMRlib: Easy-coding and Efficient Resource Management for Job Malleability

Process malleability has proved to have a highly positive impact on the resource utilization and global productivity in data centers compared with the conventional static resource allocation policy. However, the non-negligible additional development effort this solution imposes has constrained its adoption by the scientific programming community. In this work, we present DMRlib, a library designed to offer the global advantages of process malleability while providing a minimalist MPI-like syntax. The library includes a series of predefined communication patterns that greatly ease the development of malleable applications. In addition, we deploy several scenarios to demonstrate the positive impact of process malleability featuring different scalability patterns. Concretely, we study two job submission modes (rigid and moldable) in order to identify the best-case scenarios for malleability using metrics such as resource allocation rate, completed jobs per second, and energy consumption. The experiments prove that our elastic approach may improve global throughput by a factor higher than 3x compared to the traditional workloads of non-malleable jobs.

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arXiv2026

Three ways to share a QPU: Scheduling strategies for hybrid Quantum-HPC applications

As quantum computing (QC) technologies mature, their integration into established high-performance computing (HPC) infrastructures is becoming a central objective for next-generation computing systems. However, unlocking the potential of hybrid platforms for computationally demanding workloads remains challenging. The mismatch between quantum and classical programming models, the limited maturity of quantum software stacks, and the scarcity of quantum processing units (QPUs) above all, necessitate scheduling strategies that go beyond standard HPC mechanisms to manage such heterogeneous and constrained resources. To address this issue, we investigate three distinct methodologies for HPC-QC resource scheduling: time-based multiplexing, dynamic resource management, and workflow decomposition. Experimental validation on production HPC clusters and real quantum hardware demonstrates the effectiveness of these approaches under different workload scenarios. Malleability and workflow strategies significantly optimize classical resource utilization, reducing consumption by up to 45.7% and 64% respectively, proving to be best fitted for hybrid jobs where quantum and classical workloads are evenly balanced. Conversely, time-multiplexing enhances QPU utilization and reduces execution time at the cluster level, making it the optimal strategy for the opposite context, which is characterized by high classical-quantum workload imbalances. These findings underscore the practical viability of tailored scheduling strategies for hybrid HPC-QC environments and highlight their complementarity in building efficient, scalable software stacks for next-generation quantum-accelerated facilities.

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arXiv2025

Dynamic Solutions for Hybrid Quantum-HPC Resource Allocation

The integration of quantum computers within classical High-Performance Computing (HPC) infrastructures is receiving increasing attention, with the former expected to serve as accelerators for specific computational tasks. However, combining HPC and quantum computers presents significant technical challenges, including resource allocation. This paper presents a novel malleability-based approach, alongside a workflow-based strategy, to optimize resource utilization in hybrid HPC-quantum workloads. With both these approaches, we can release classical resources when computations are offloaded to the quantum computer and reallocate them once quantum processing is complete. Our experiments with a hybrid HPC-quantum use case show the benefits of dynamic allocation, highlighting the potential of those solutions.

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arXiv2025

Resource Optimization with MPI Process Malleability for Dynamic Workloads in HPC Clusters

Dynamic resource management is essential for optimizing computational efficiency in modern high-performance computing (HPC) environments, particularly as systems scale. While research has demonstrated the benefits of malleability in resource management systems (RMS), the adoption of such techniques in production environments remains limited due to challenges in standardization, interoperability, and usability. Addressing these gaps, this paper extends our prior work on the Dynamic Management of Resources (DMR) framework, which provides a modular and user-friendly approach to dynamic resource allocation. Building upon the original DMRlib reconfiguration runtime, this work integrates new methodology from the Malleability Module (MaM) of the Proteo framework, further enhancing reconfiguration capabilities with new spawning strategies and data redistribution methods. In this paper, we explore new malleability strategies in HPC dynamic workloads, such as merging MPI communicators and asynchronous reconfigurations, which offer new opportunities for dramatically reducing memory overhead. The proposed enhancements are rigorously evaluated on a world-class supercomputer, demonstrating improved resource utilization and workload efficiency. Results show that dynamic resource management can reduce the workload completion time by 40% and increase the resource utilization by over 20%, compared to static resource allocation.

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arXiv2023

ACC Saturator: Automatic Kernel Optimization for Directive-Based GPU Code

Automatic code optimization is a complex process that typically involves the application of multiple discrete algorithms that modify the program structure irreversibly. However, the design of these algorithms is often monolithic, and they require repetitive implementation to perform similar analyses due to the lack of cooperation. To address this issue, modern optimization techniques, such as equality saturation, allow for exhaustive term rewriting at various levels of inputs, thereby simplifying compiler design. In this paper, we propose equality saturation to optimize sequential codes utilized in directive-based programming for GPUs. Our approach realizes less computation, less memory access, and high memory throughput simultaneously. Our fully-automated framework constructs single-assignment forms from inputs to be entirely rewritten while keeping dependencies and extracts optimal cases. Through practical benchmarks, we demonstrate a significant performance improvement on several compilers. Furthermore, we highlight the advantages of computational reordering and emphasize the significance of memory-access order for modern GPUs.

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arXiv2023

A Symbolic Emulator for Shuffle Synthesis on the NVIDIA PTX Code

Various kinds of applications take advantage of GPUs through automation tools that attempt to automatically exploit the available performance of the GPU's parallel architecture. Directive-based programming models, such as OpenACC, are one such method that easily enables parallel computing by just adhering code annotations to code loops. Such abstract models, however, often prevent programmers from making additional low-level optimizations to take advantage of the advanced architectural features of GPUs because the actual generated computation is hidden from the application developer. This paper describes and implements a novel flexible optimization technique that operates by inserting a code emulator phase to the tail-end of the compilation pipeline. Our tool emulates the generated code using symbolic analysis by substituting dynamic information and thus allowing for further low-level code optimizations to be applied. We implement our tool to support both CUDA and OpenACC directives as the frontend of the compilation pipeline, thus enabling low-level GPU optimizations for OpenACC that were not previously possible. We demonstrate the capabilities of our tool by automating warp-level shuffle instructions that are difficult to use by even advanced GPU programmers. Lastly, evaluating our tool with a benchmark suite and complex application code, we provide a detailed study to assess the benefits of shuffle instructions across four generations of GPU architectures.

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arXiv2021

JACC: An OpenACC Runtime Framework with Kernel-Level and Multi-GPU Parallelization

The rapid development in computing technology has paved the way for directive-based programming models towards a principal role in maintaining software portability of performance-critical applications. Efforts on such models involve a least engineering cost for enabling computational acceleration on multiple architectures while programmers are only required to add meta information upon sequential code. Optimizations for obtaining the best possible efficiency, however, are often challenging. The insertions of directives by the programmer can lead to side-effects that limit the available compiler optimization possible, which could result in performance degradation. This is exacerbated when targeting multi-GPU systems, as pragmas do not automatically adapt to such systems, and require expensive and time consuming code adjustment by programmers. This paper introduces JACC, an OpenACC runtime framework which enables the dynamic extension of OpenACC programs by serving as a transparent layer between the program and the compiler. We add a versatile code-translation method for multi-device utilization by which manually-optimized applications can be distributed automatically while keeping original code structure and parallelism. We show in some cases nearly linear scaling on the part of kernel execution with the NVIDIA V100 GPUs. While adaptively using multi-GPUs, the resulting performance improvements amortize the latency of GPU-to-GPU communications.

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arXiv2021

Particle-In-Cell Simulation using Asynchronous Tasking

Recently, task-based programming models have emerged as a prominent alternative among shared-memory parallel programming paradigms. Inherently asynchronous, these models provide native support for dynamic load balancing and incorporate data flow concepts to selectively synchronize the tasks. However, tasking models are yet to be widely adopted by the HPC community and their effective advantages when applied to non-trivial, real-world HPC applications are still not well comprehended. In this paper, we study the parallelization of a production electromagnetic particle-in-cell (EM-PIC) code for kinetic plasma simulations exploring different strategies using asynchronous task-based models. Our fully asynchronous implementation not only significantly outperforms a conventional, synchronous approach but also achieves near perfect scaling for 48 cores.

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arXiv2021

cuConv: A CUDA Implementation of Convolution for CNN Inference

Convolutions are the core operation of deep learning applications based on Convolutional Neural Networks (CNNs). Current GPU architectures are highly efficient for training and deploying deep CNNs, and hence, these are largely used in production for this purpose. State-of-the-art implementations, however, present a lack of efficiency for some commonly used network configurations. In this paper we propose a GPU-based implementation of the convolution operation for CNN inference that favors coalesced accesses, without requiring prior data transformations. Our experiments demonstrate that our proposal yields notable performance improvements in a range of common CNN forward propagation convolution configurations, with speedups of up to 2.29x with respect to the best implementation of convolution in cuDNN, hence covering a relevant region in currently existing approaches.

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arXiv2021

Enabling Homomorphically Encrypted Inference for Large DNN Models

The proliferation of machine learning services in the last few years has raised data privacy concerns. Homomorphic encryption (HE) enables inference using encrypted data but it incurs 100x-10,000x memory and runtime overheads. Secure deep neural network (DNN) inference using HE is currently limited by computing and memory resources, with frameworks requiring hundreds of gigabytes of DRAM to evaluate small models. To overcome these limitations, in this paper we explore the feasibility of leveraging hybrid memory systems comprised of DRAM and persistent memory. In particular, we explore the recently-released Intel Optane PMem technology and the Intel HE-Transformer nGraph to run large neural networks such as MobileNetV2 (in its largest variant) and ResNet-50 for the first time in the literature. We present an in-depth analysis of the efficiency of the executions with different hardware and software configurations. Our results conclude that DNN inference using HE incurs on friendly access patterns for this memory configuration, yielding efficient executions.

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arXiv2020

MPI+OpenMP Tasking Scalability for Multi-Morphology Simulations of the Human Brain

The simulation of the behavior of the human brain is one of the most ambitious challenges today with a non-end of important applications. We can find many different initiatives in the USA, Europe and Japan which attempt to achieve such a challenging target. In this work, we focus on the most important European initiative (the Human Brain Project) and on one of the models developed in this project. This tool simulates the spikes triggered in a neural network by computing the voltage capacitance on the neurons' morphology, being one of the most precise simulators today. In the present work, we have evaluated the use of MPI+OpenMP tasking on top of this framework. We prove that this approach is able to achieve a good scaling even when computing a relatively low workload (number of neurons) per node. One of our targets consists of achieving not only a highly scalable implementation, but also to develop a tool with a high degree of abstraction without losing control and performance by using \emph{MPI+OpenMP} tasking. The main motivation of this work is the evaluation of this cutting-edge simulation on multi-morphology neural networks. The simulation of a high number of neurons, which are completely different among them, is an important challenge. In fact, in the multi-morphology simulations, we find an important unbalancing between the nodes, mainly due to the differences in the neurons, which causes an important under-utilization of the available resources. In this work, the authors present and evaluate mechanisms to deal with this and reduce the time of this kind of simulations considerably.

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arXiv2020

Understanding Memory Access Patterns Using the BSC Performance Tools

The growing gap between processor and memory speeds results in complex memory hierarchies as processors evolve to mitigate such divergence by taking advantage of the locality of reference. In this direction, the BSC performance analysis tools have been recently extended to provide insight relative to the application memory accesses depicting their temporal and spatial characteristics, correlating with the source-code and the achieved performance simultaneously. These extensions rely on the Precise Event-Based Sampling (PEBS) mechanism available in recent Intel processors to capture information regarding the application memory accesses. The sampled information is later combined with the Folding technique to represent a detailed temporal evolution of the memory accesses and in conjunction with the achieved performance and the source-code counterpart. The results obtained from the combination of these tools help not only application developers but also processor architects to understand better how the application behaves and how the system performs. In this paper, we describe a tighter integration of the sampling mechanism into the monitoring package. We also demonstrate the value of the complete workflow by exploring already optimized state--of--the--art benchmarks, providing detailed insight of their memory access behavior. We have taken advantage of this insight to apply small modifications that improve the applications' performance.

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arXiv2020

DMR API: Improving cluster productivity by turning applications into malleable

Adaptive workloads can change on--the--fly the configuration of their jobs, in terms of number of processes. In order to carry out these job reconfigurations, we have designed a methodology which enables a job to communicate with the resource manager and, through the runtime, to change its number of MPI ranks. The collaboration between both the workload manager---aware of the queue of jobs and the resource allocation---and the parallel runtime---able to transparently handle the processes and the program data---is crucial for our throughput-aware malleability methodology. Hence, when a job triggers a reconfiguration, the resource manager will check the cluster status and return an action: an expansion, if there are spare resources; a shrink, if queued jobs can be initiated; or none, if no change can improve the global productivity. In this paper, we describe the internals of our framework and how it is capable of reducing the global workload completion time along with providing a smarter usage of the underlying resources. For this purpose, we present a thorough study of the adaptive workloads processing by showing the detailed behavior of our framework in representative experiments and the low overhead that our reconfiguration involves.

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