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Wouter Klijn

Publications and source records attributed to Wouter Klijn.

7 recordsLinked to original sources

Unifying von-Neumann HPC and Neuromorphic Acceleration via the EBRAINS Research Infrastructure: A Framework for High-Performance Workflows

Modern scientific workflows increasingly span diverse computing architectures, yet executing a single computational model across disparate systems often forces researchers to maintain fragmented, site-specific pipelines. In this paper, we address this challenge within the domain of computational neuroscience by presenting a unified, cloud-based workflow orchestrated via EBRAINS JupyterLab. This workflow enables users to transparently execute spiking neural networks on both von-Neumann supercomputers and neuromorphic hardware. Using a single federated identity, the system dispatches jobs to HPC sites (JUSUF, Galileo100) via PyUNICORE and to the SpiNNaker-1 neuromorphic system via the Neuromorphic Computing Platform Interface. To guarantee cross-site reproducibility and mitigate software version drift, we utilize a zero-installation execution mode that dynamically pulls PMIx-aware Apptainer containers to HPC compute nodes. Furthermore, we demonstrate genuine model-level portability using the NESTML domain-specific language, allowing custom neuron models to be written once and automatically compiled for either the NEST (C++) or sPyNNaker backends. Validated with a balanced random network case study, this work illustrates a practical, end-to-end path for hardware-agnostic workflows while highlighting the critical role of containerization and domain-specific languages in achieving true cross-platform reproducibility.

cs.DC

HPC Containers for EBRAINS: Towards Portable Cross-Domain Software Environment

Deploying complex, distributed scientific workflows across diverse HPC sites is often hindered by site-specific dependencies and complex build environments. This paper investigates the design and performance of portable HPC container images capable of encapsulating MPI- and CUDA-enabled software stacks without sacrificing bare-metal performance. This work is part of recent work performed within the EBRAINS Research Infrastructure, to evaluate the implementation of portable HPC (Apptainer-based) container images targeting the EBRAINS Software Distribution (ESD) -- a Spack-based software ecosystem comprising approximately 80 top-level packages (and 800 dependencies). We evaluate a hybrid, PMIx-based containerization strategy using Apptainer that seamlessly bypasses the need for site-specific builds by dynamically leveraging host-level specialized hardware, such as network interfaces and GPUs, on two production HPC clusters: Karolina and Jureca-DC. We demonstrate the feasibility of building portable, MPI- and CUDA-enabled scientific software into container images that correctly leverage site-installed drivers and hardware to reproduce bare-metal communication behavior. Using communication microbenchmarks (e.g., OSU and NCCL) alongside performance metrics of applications from neuroscience, we measure and verify their performance against bare-metal deployments. Crucially, our verification approach extends beyond top-level runtime measurements; we highlight the analysis of underlying debug logs to actively detect misbehavior and misconfigurations, such as suboptimal transport pathways. Ultimately, this investigation demonstrates the feasibility of a simple and reproducible methodology for decoupling software environments from underlying infrastructures, paving the way for automated pipelines that ensure optimized, performance-verified execution across varied HPC architectures.

cs.DC

Exploring hyper-parameter spaces of neuroscience models on high performance computers with Learning to Learn

Neuroscience models commonly have a high number of degrees of freedom and only specific regions within the parameter space are able to produce dynamics of interest. This makes the development of tools and strategies to efficiently find these regions of high importance to advance brain research. Exploring the high dimensional parameter space using numerical simulations has been a frequently used technique in the last years in many areas of computational neuroscience. High performance computing (HPC) can provide today a powerful infrastructure to speed up explorations and increase our general understanding of the model's behavior in reasonable times.

cs.NE

Brain Modelling as a Service: The Virtual Brain on EBRAINS

The Virtual Brain (TVB) is now available as open-source cloud ecosystem on EBRAINS, a shared digital research platform for brain science. It offers services for constructing, simulating and analysing brain network models (BNMs) including the TVB network simulator; magnetic resonance imaging (MRI) processing pipelines to extract structural and functional connectomes; multiscale co-simulation of spiking and large-scale networks; a domain specific language for automatic high-performance code generation from user-specified models; simulation-ready BNMs of patients and healthy volunteers; Bayesian inference of epilepsy spread; data and code for mouse brain simulation; and extensive educational material. TVB cloud services facilitate reproducible online collaboration and discovery of data assets, models, and software embedded in scalable and secure workflows, a precondition for research on large cohort data sets, better generalizability and clinical translation.

cs.CE

Performance Comparison for Neuroscience Application Benchmarks

Researchers within the Human Brain Project and related projects have in the last couple of years expanded their needs for high-performance computing infrastructures. The needs arise from a diverse set of science challenges that range from large-scale simulations of brain models to processing of extreme-scale experimental data sets. The ICEI project, which is in the process of creating a distributed infrastructure optimised for brain research, started to build-up a set of benchmarks that reflect the diversity of applications in this field. In this paper we analyse the performance of some selected benchmarks on an IBM POWER8 and Intel Skylake based systems with and without GPUs.

cs.PF

Staged deployment of interactive multi-application HPC workflows

Running scientific workflows on a supercomputer can be a daunting task for a scientific domain specialist. Workflow management solutions (WMS) are a standard method for reducing the complexity of application deployment on high performance computing (HPC) infrastructure. We introduce the design for a middleware system that extends and combines the functionality from existing solutions in order to create a high-level, staged user-centric operation/deployment model. This design addresses the requirements of several use cases in the life sciences, with a focus on neuroscience. In this manuscript we focus on two use cases: 1) three coupled neuronal simulators (for three different space/time scales) with in-transit visualization and 2) a closed-loop workflow optimized by machine learning, coupling a robot with a neural network simulation. We provide a detailed overview of the application-integrated monitoring in relationship with the HPC job. We present here a novel usage model for large scale interactive multi-application workflows running on HPC systems which aims at reducing the complexity of deployment and execution, thus enabling new science.

cs.DC

Arbor -- a morphologically-detailed neural network simulation library for contemporary high-performance computing architectures

We introduce Arbor, a performance portable library for simulation of large networks of multi-compartment neurons on HPC systems. Arbor is open source software, developed under the auspices of the HBP. The performance portability is by virtue of back-end specific optimizations for x86 multicore, Intel KNL, and NVIDIA GPUs. When coupled with low memory overheads, these optimizations make Arbor an order of magnitude faster than the most widely-used comparable simulation software. The single-node performance can be scaled out to run very large models at extreme scale with efficient weak scaling. HPC, GPU, neuroscience, neuron, software

q-bio.NC