A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation (Articolo in rivista)

Type

• Articolo in rivista (Classe)
• Prodotto della ricerca (Classe)

Label

• A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation (Articolo in rivista) (literal)

Anno

• 2014-01-01T00:00:00+01:00 (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi

• 10.1155/2014/560987 (literal)

Alternative label

• Colmenares J.; Galizia A.; Ortiz J.; Clematis A.; Rocchia W. (2014)
  A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation
  in BioMed Research International
  (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori

• Colmenares J.; Galizia A.; Ortiz J.; Clematis A.; Rocchia W. (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#url

• http://www.scopus.com/inward/record.url?eid=2-s2.0-84903648275&partnerID=q2rCbXpz (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroVolume

• 2014 (literal)

Rivista

• BioMed Research International (Rivista)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#pagineTotali

• 12 (literal)

Note

• Google Scholar (literal)
• ISI Web of Science (WOS) (literal)
• Scopu (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni

• Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy; Department of Geosciences, University of Padova, 35131 Padova, Italy; IMATI, CNR, 16149 Genova, Italy; Department of Advanced Robotics, Italian Institute of Technology, 16163 Genova, Italy (literal)

Titolo

• A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation (literal)

Abstract

• 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. © 2014 José Colmenares et al. (literal)

Prodotto di

• Istituto di matematica applicata e tecnologie informatiche \"Enrico Magenes\" (IMATI) (Istituto)
• Metodologie, algoritmi ed applicazioni per Grid di collaborazione (ICT.P09.004.002) (Modulo)

Autore CNR

• ANTONELLA GALIZIA (Unità di personale interno)
• ANDREA CLEMATIS (Persona)

Incoming links:

Autore CNR di

• ANDREA CLEMATIS (Persona)
• ANTONELLA GALIZIA (Unità di personale interno)

Prodotto

• Istituto di matematica applicata e tecnologie informatiche \"Enrico Magenes\" (IMATI) (Istituto)
• Metodologie, algoritmi ed applicazioni per Grid di collaborazione (ICT.P09.004.002) (Modulo)
• http://www.cnr.it/ontology/cnr/individuo/modulo/ID8873

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#rivistaDi

• BioMed Research International (Rivista)