arXiv subjects

Gerald Mathias

Publications and source records attributed to Gerald Mathias.

5 recordsLinked to original sources

arXiv2026

Node-Level Performance and Energy Characterization of Flagship Science Applications on SuperMUC-NG Phase 2

We present a systematic performance and energy-efficiency characterization of five flagship scientific workloads on SuperMUC-NG phase 2, the 28 PetaFLOPs system at the Leibniz Supercomputing Center (LRZ) equipped with Intel Xeon Platinum 8480+ and Intel Data Center GPU Max 1550 (Ponte Vecchio, PVC) accelerators. The selected codes span molecular dynamics (gromacs, lammps), astrophysics and cosmology (OpenGadget3, AthenaK), and finite-element PDE solvers from the dealii-X Center of Excellence. For each code we measure throughput and energy efficiency expressed as compute-elements per wall-clock second (or per Joule of consumed energy) on a single compute node, comparing CPU-only (SPR) against combined CPU+GPU (SPR+PVC) configurations where available. Energy measurements rely on lightweight code instrumentation with p3em, or the Energy Aware Runtime (EAR) present on the system. Our results show that GPU offload yields $4-12\times$ higher throughput and up to $15\times$ better energy efficiency compared to CPU-only execution, with lammps and AthenaK benefiting most. However, both throughput and energy gains are sensitive to problem granularity: insufficient work per GPU tile erodes the accelerator advantage, as clearly observed in AthenaK at small mesh-block sizes. The power-budget utilization is systematically lower for CPUs than it is for GPUs, indicating that even at peak useful-work rate, most applications running on CPUs leave a significant fraction of the node's thermal envelope unused.

cs.DC↗

arXiv2021

Pandemic Drugs at Pandemic Speed: Infrastructure for Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers

The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. There is a major bottleneck screening the vast number of potential small molecules to shortlist lead compounds for antiviral drug development. New opportunities to accelerate drug discovery lie at the interface between machine learning methods, in this case developed for linear accelerators, and physics-based methods. The two in silico methods, each have their own advantages and limitations which, interestingly, complement each other. Here, we present an innovative infrastructural development that combines both approaches to accelerate drug discovery. The scale of the potential resulting workflow is such that it is dependent on supercomputing to achieve extremely high throughput. We have demonstrated the viability of this workflow for the study of inhibitors for four COVID-19 target proteins and our ability to perform the required large-scale calculations to identify lead antiviral compounds through repurposing on a variety of supercomputers.

cs.DC↗

arXiv2020

IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads

The drug discovery process currently employed in the pharmaceutical industry typically requires about 10 years and $2-3 billion to deliver one new drug. This is both too expensive and too slow, especially in emergencies like the COVID-19 pandemic. In silicomethodologies need to be improved to better select lead compounds that can proceed to later stages of the drug discovery protocol accelerating the entire process. No single methodological approach can achieve the necessary accuracy with required efficiency. Here we describe multiple algorithmic innovations to overcome this fundamental limitation, development and deployment of computational infrastructure at scale integrates multiple artificial intelligence and simulation-based approaches. Three measures of performance are:(i) throughput, the number of ligands per unit time; (ii) scientific performance, the number of effective ligands sampled per unit time and (iii) peak performance, in flop/s. The capabilities outlined here have been used in production for several months as the workhorse of the computational infrastructure to support the capabilities of the US-DOE National Virtual Biotechnology Laboratory in combination with resources from the EU Centre of Excellence in Computational Biomedicine.

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arXiv2020

Integrating State of the Art Compute, Communication, and Autotuning Strategies to Multiply the Performance of the Application Programm CPMD for Ab Initio Molecular Dynamics Simulations

We present our recent code modernizations of the of the ab initio molecular dynamics program CPMD (www.cpmd.org) with a special focus on the ultra-soft pseudopotential (USPP) code path. Following the internal instrumentation of CPMD, all time critical routines have been revised to maximize the computational throughput and to minimize the communication overhead for optimal performance. Throughout the program missing hybrid MPI+OpenMP parallelization has been added to optimize scaling. For communication intensive routines, as the multiple distributed 3d FFTs of the electronic states and distributed matrix-matrix multiplications related to the $\beta$-projectors of the pseudopotentials, this MPI+OpenMP parallelization now overlaps computation and communication. The necessary partitioning of the workload is optimized by an auto-tuning algorithm. In addition, the largest global MPI_Allreduce operation has been replaced by highly tuned node-local parallelized operations using MPI shared-memory windows to avoid inter-node communication. A batched algorithm for the multiple 3d FFTs improves the throughput of the MPI_Alltoall communication and, thus, the scalability of the implementation, both for USPP and for the frequently used norm-conserving pseudopotential code path. The enhanced performance and scalability is demonstrated on a mid-sized benchmark system of 256 water molecules and further water systems of from 32 up to 2048 molecules.

physics.comp-ph↗

arXiv2016

Extreme Scale-out SuperMUC Phase 2 - lessons learned

In spring 2015, the Leibniz Supercomputing Centre (Leibniz-Rechenzentrum, LRZ), installed their new Peta-Scale System SuperMUC Phase2. Selected users were invited for a 28 day extreme scale-out block operation during which they were allowed to use the full system for their applications. The following projects participated in the extreme scale-out workshop: BQCD (Quantum Physics), SeisSol (Geophysics, Seismics), GPI-2/GASPI (Toolkit for HPC), Seven-League Hydro (Astrophysics), ILBDC (Lattice Boltzmann CFD), Iphigenie (Molecular Dynamic), FLASH (Astrophysics), GADGET (Cosmological Dynamics), PSC (Plasma Physics), waLBerla (Lattice Boltzmann CFD), Musubi (Lattice Boltzmann CFD), Vertex3D (Stellar Astrophysics), CIAO (Combustion CFD), and LS1-Mardyn (Material Science). The projects were allowed to use the machine exclusively during the 28 day period, which corresponds to a total of 63.4 million core-hours, of which 43.8 million core-hours were used by the applications, resulting in a utilization of 69%. The top 3 users were using 15.2, 6.4, and 4.7 million core-hours, respectively.

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