Memory Optimization for the Octopus Scientific Code

Alberdi-Rodriguez, J.; Rubio, A.; Oliveira, M.; Charalampidou, A.; Folias, D.

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Memory Optimization for the Octopus Scientific Code

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Rubio, A.
Theory Department, Max Planck Institute for the Structure and Dynamics of Matter, Max Planck Society;
Theory, Fritz Haber Institute, Max Planck Society;
Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Departamento de F;

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Alberdi-Rodriguez__2015_1022-1.pdf
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Citation

Alberdi-Rodriguez, J., Rubio, A., Oliveira, M., Charalampidou, A., & Folias, D. (in preparation). Memory Optimization for the Octopus Scientific Code.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0024-C453-4

Abstract

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.