Enabling Large-Molecule Simulations of Biological Interest through LSDALTON's DFT Method
Creators
- 1. National Supercomputing Centre, Linköping University, 581 83 Linköping, Sweden
Contributors
Others:
- 1. Centre for Theoretical and Computational Chemistry, Department of Chemistry, Oslo University, Postbox 1033, Blindern, 0315, Oslo , Norway
- 2. gLEAP – Center for Theoretical Chemistry, Department of Chemistry , Aarhus University , Langelandsgade 140, Aarhus C , 8000 , Denmark
Description
In this paper, we present the performance of LSDALTON's DFT method in large molecular simulations of biological interest. We primarily focus on evaluating the performance gain by applying the density fitting (DF) scheme and the auxiliary density matrix method (ADMM). The enabling effort is put towards finding the right build environment (composition of the compiler, an MPI and extra libraries) which generates a full 64-bit integer-based binary. Using three biological molecules varying in size, we verify that the DF and the ADMM schemes provide much gain in the performance of the DFT code, at the cost of large memory consumption to store extra matrices and a little change on scalability characteristics with the ADMM calculation. In the insulin simulation, the parallel region of the code accelerates by 30 percent with the DF calculation and 56 percent in the case of the DF-ADMM calculations.
Files
WP169.pdf
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