arXiv subjects

Eve Le Guillou

Publications and source records attributed to Eve Le Guillou.

2 recordsLinked to original sources

arXiv2025

Distributed Discrete Morse Sandwich: Efficient Computation of Persistence Diagrams for Massive Scalar Data

The persistence diagram, which describes the topological features of a dataset, is a key descriptor in Topological Data Analysis. The "Discrete Morse Sandwich" (DMS) method has been reported to be the most efficient algorithm for computing persistence diagrams of 3D scalar fields on a single node, using shared-memory parallelism. In this work, we extend DMS to distributed-memory parallelism for the efficient and scalable computation of persistence diagrams for massive datasets across multiple compute nodes. On the one hand, we can leverage the embarrassingly parallel procedure of the first and most time-consuming step of DMS (namely the discrete gradient computation). On the other hand, the efficient distributed computations of the subsequent DMS steps are much more challenging. To address this, we have extensively revised the DMS routines by contributing a new self-correcting distributed pairing algorithm, redesigning key data structures and introducing computation tokens to coordinate distributed computations. We have also introduced a dedicated communication thread to overlap communication and computation. Detailed performance analyses show the scalability of our hybrid MPI+thread approach for strong and weak scaling using up to 16 nodes of 32 cores (512 cores total). Our algorithm outperforms DIPHA, a reference method for the distributed computation of persistence diagrams, with an average speedup of x8 on 512 cores. We show the practical capabilities of our approach by computing the persistence diagram of a public 3D scalar field of 6 billion vertices in 174 seconds on 512 cores. Finally, we provide a usage example of our open-source implementation at https://github.com/eve-le-guillou/DDMS-example.

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arXiv2024

TTK is Getting MPI-Ready

This system paper documents the technical foundations for the extension of the Topology ToolKit (TTK) to distributed-memory parallelism with the Message Passing Interface (MPI). While several recent papers introduced topology-based approaches for distributed-memory environments, these were reporting experiments obtained with tailored, mono-algorithm implementations. In contrast, we describe in this paper a versatile approach (supporting both triangulated domains and regular grids) for the support of topological analysis pipelines, i.e. a sequence of topological algorithms interacting together. While developing this extension, we faced several algorithmic and software engineering challenges, which we document in this paper. We describe an MPI extension of TTK's data structure for triangulation representation and traversal, a central component to the global performance and generality of TTK's topological implementations. We also introduce an intermediate interface between TTK and MPI, both at the global pipeline level, and at the fine-grain algorithmic level. We provide a taxonomy for the distributed-memory topological algorithms supported by TTK, depending on their communication needs and provide examples of hybrid MPI+thread parallelizations. Performance analyses show that parallel efficiencies range from 20% to 80% (depending on the algorithms), and that the MPI-specific preconditioning introduced by our framework induces a negligible computation time overhead. We illustrate the new distributed-memory capabilities of TTK with an example of advanced analysis pipeline, combining multiple algorithms, run on the largest publicly available dataset we have found (120 billion vertices) on a cluster with 64 nodes (for a total of 1536 cores). Finally, we provide a roadmap for the completion of TTK's MPI extension, along with generic recommendations for each algorithm communication category.

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