• closedAccess   A fast band–Krylov eigensolver for macromolecular functional motion simulation on multicore architectures and graphics processors 

      Aliaga Estellés, José Ignacio; Alonso-Jordá, Pedro; Badía, José; Chacón, Pablo; Davidovic, Davor; López Blanco, José R.; Quintana-Orti, Enrique S. Elsevier (2016-03-15)
      We introduce a new iterative Krylov subspace-based eigensolver for the simulation of macromolecular motions on desktop multithreaded platforms equipped with multicore processors and, possibly, a graphics accelerator (GPU). ...
    • openAccess   Adapting concurrency throttling and voltage–frequency scaling for dense eigensolvers 

      Aliaga Estellés, José Ignacio; Barreda Vayá, Maria; Castaño Álvarez, María Asunción; Dolz, Manuel F.; Quintana-Orti, Enrique S. Springer Verlag (2015)
      We analyze power dissipation and energy consumption during the execution of high-performance dense linear algebra kernels on multi-core processors. On top of this analysis, we propose and evaluate several strategies to ...
    • closedAccess   Exploring large macromolecular functional motions on clusters of multicore processors 

      López Blanco, José R.; Reyes, Ruymán; Aliaga Estellés, José Ignacio; Badía Sala, Rosa María; Chacón, Pablo; Quintana-Orti, Enrique S. Elsevier (2013-08)
      Normal modes in internal coordinates (IC) furnish an excellent way to model functional collective motions of macromolecular machines, but exhibit a high computational cost when applied to large-sized macromolecules. In ...
    • closedAccess   Out-of-core macromolecular simulations on multithreaded architectures 

      Aliaga Estellés, José Ignacio; Badía, José; Castillo Catalán, María Isabel; Davidovic, Davor; Mayo, Rafael; Quintana-Orti, Enrique S. Wiley (2015)
      We address the solution of large-scale eigenvalue problems that appear in the motion simulation o f com- plex macromolecules on multithreaded platforms, consisting of multicore processors and possibly a graphics processor ...
    • closedAccess   Two-sided orthogonal reductions to condensed forms on asymmetric multicore processors 

      Alonso-Jordá, Pedro; Catalán, Sandra; Herrero, José R.; Quintana-Orti, Enrique S.; Rodríguez Sánchez, Rafael Elsevier (2018)
      We investigate how to leverage the heterogeneous resources of an Asymmetric Multicore Processor (AMP) in order to deliver high performance in the reduction to condensed forms for the solution of dense eigenvalue and ...