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A Combined MPI-CUDA Parallel Solution of Linear and Nonlinear Poisson-Boltzmann Equation
Joint Authors
Clematis, Andrea
Colmenares, José
Galizia, Antonella
Ortiz, Jesús
Rocchia, Walter
Source
Issue
Vol. 2014, Issue 2014 (31 Dec. 2014), pp.1-12, 12 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2014-06-12
Country of Publication
Egypt
No. of Pages
12
Main Subjects
Abstract EN
The Poisson-Boltzmann equation models the electrostatic potential generated by fixed charges on a polarizable solute immersed in an ionic solution.
This approach is often used in computational structural biology to estimate the electrostatic energetic component of the assembly of molecular biological systems.
In the last decades, the amount of data concerning proteins and other biological macromolecules has remarkably increased.
To fruitfully exploit these data, a huge computational power is needed as well as software tools capable of exploiting it.
It is therefore necessary to move towards high performance computing and to develop proper parallel implementations of already existing and of novel algorithms.
Nowadays, workstations can provide an amazing computational power: up to 10 TFLOPS on a single machine equipped with multiple CPUs and accelerators such as Intel Xeon Phi or GPU devices.
The actual obstacle to the full exploitation of modern heterogeneous resources is efficient parallel coding and porting of software on such architectures.
In this paper, we propose the implementation of a full Poisson-Boltzmann solver based on a finite-difference scheme using different and combined parallel schemes and in particular a mixed MPI-CUDA implementation.
Results show great speedups when using the two schemes, achieving an 18.9x speedup using three GPUs.
American Psychological Association (APA)
Colmenares, José& Galizia, Antonella& Ortiz, Jesús& Clematis, Andrea& Rocchia, Walter. 2014. A Combined MPI-CUDA Parallel Solution of Linear and Nonlinear Poisson-Boltzmann Equation. BioMed Research International،Vol. 2014, no. 2014, pp.1-12.
https://search.emarefa.net/detail/BIM-480830
Modern Language Association (MLA)
Colmenares, José…[et al.]. A Combined MPI-CUDA Parallel Solution of Linear and Nonlinear Poisson-Boltzmann Equation. BioMed Research International No. 2014 (2014), pp.1-12.
https://search.emarefa.net/detail/BIM-480830
American Medical Association (AMA)
Colmenares, José& Galizia, Antonella& Ortiz, Jesús& Clematis, Andrea& Rocchia, Walter. A Combined MPI-CUDA Parallel Solution of Linear and Nonlinear Poisson-Boltzmann Equation. BioMed Research International. 2014. Vol. 2014, no. 2014, pp.1-12.
https://search.emarefa.net/detail/BIM-480830
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-480830