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Published December 30, 2014 | Version v1
Working paper Open

Memory Optimization for the Octopus Scientific Code

  • 1. Nano-Bio Spectroscopy Group and European Theoretical Spectroscopy Facility (ETSF); Department of Computer Architecture and Technology University of the Basque Country UPV/EHU, Donostia, Spain
  • 1. Nano-Bio Spectroscopy Group and European Theoretical Spectroscopy Facility (ETSF) University of the Basque Country UPV/EHU, Donostia, Spain;Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany Departamento de Física de Materiales, Centro de Física de Materiales CSIC-UPV/EHU-MPC and DIPC, University of the Basque Country UPV/EHU, Donostia, Spain
  • 2. Dep. Physique, Université of Liège
  • 3. Greek Research and Technology Network, Athens, Greece; Scientific Computing Center, Aristotle University of Thessaloniki, Greece

Description

Octopus is a software package for density-functional theory (DFT), and its time-dependent (TDDFT) variant. Linear Combination of the Atomic Orbitals (LCAO) is performed previous to the actual DFT run. LCAO is used to get an initial guess of densities, and therefore, to start with the Self Consistent Field (SCF) of the Ground-State (GS). System initialization and LCAO steps consume a large amount of memory and do not demonstrate good performance. In this study, extensive profiling has been performed, in order to identify large matrices and scaling behaviour of initialization and LCAO. Alternative implementations of LCAO in Octopus have been investigated in order to optimize memory usage and performance of LCAO approach. Use of ScaLAPACK library led to significant improvement of memory allocation and performance. Benchmark tests have been performed on MareNostrum III HPC system using various combinations of atomic  systems’ sizes and numbers of CPU cores.

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Funding

PRACE-3IP – PRACE - Third Implementation Phase Project 312763
European Commission