Probing the Applicability of Polarizable Force-Field Molecular Dynamics for Parallel Architectures: A Comparison of Digital MPI with LAM-MPI and MPICH2 Export

@incollection{citeulike:2531014, abstract = {Polarizable Force Fields have a great potential in improving the quality of Molecular Dynamics simulations. Especially for the description of solvents such kind of simulations are greatly appreciated because of the important role solvation plays in all kind of biomedical research. The open source package TINKER is taken for parallelization of a routine made for the proper usage of Polarizable Force Fields. Profiling with the GNU tool gprof identifies the relevant target subroutines to parallelize. MPI is used for the parallelization. Several different parallel platforms and several different versions of MPI are tested and compared. Parallel scalability with reasonable amounts of parallel operating CPUs seems to be limited beyond a factor of 2.5. Appraisal of the present MPI-implementation of the TINKER Molecular Dynamics program using Polarizable Force Fields for large scale computation will heavily depend on the relative availability of computing resources within a given production environment. Keywords: MPI, Polarizable Force Fields, Molecular Dynamics, MPICH2, LAM-MPI.}, author = {Almeida, Benjamin and Mahajan, Reema and Kranzlm\"{u}ller, Dieter and Volkert, Jens and H\"{o}finger, Siegfried}, citeulike-article-id = {2531014}, citeulike-linkout-0 = {http://dx.doi.org/10.1007/11557265_55}, doi = {10.1007/11557265_55}, journal = {Recent Advances in Parallel Virtual Machine and Message Passing Interface}, keywords = {case\_study, high-performance\_computing, molecular\_dynamics, mpi, parallel\_algorithms, performance\_analysis}, pages = {433--440}, posted-at = {2008-03-14 08:14:18}, priority = {2}, title = {Probing the Applicability of Polarizable Force-Field Molecular Dynamics for Parallel Architectures: A Comparison of Digital MPI with LAM-MPI and MPICH2}, url = {http://dx.doi.org/10.1007/11557265_55}, year = {2005} }

TY - CHAP ID - citeulike:2531014 L3 - citeulike-article-id:2531014 N2 - Polarizable Force Fields have a great potential in improving the quality of Molecular Dynamics simulations. Especially for the description of solvents such kind of simulations are greatly appreciated because of the important role solvation plays in all kind of biomedical research. The open source package TINKER is taken for parallelization of a routine made for the proper usage of Polarizable Force Fields. Profiling with the GNU tool gprof identifies the relevant target subroutines to parallelize. MPI is used for the parallelization. Several different parallel platforms and several different versions of MPI are tested and compared. Parallel scalability with reasonable amounts of parallel operating CPUs seems to be limited beyond a factor of 2.5. Appraisal of the present MPI-implementation of the TINKER Molecular Dynamics program using Polarizable Force Fields for large scale computation will heavily depend on the relative availability of computing resources within a given production environment. Keywords: MPI, Polarizable Force Fields, Molecular Dynamics, MPICH2, LAM-MPI. JF - Recent Advances in Parallel Virtual Machine and Message Passing Interface EP - 440 TI - Probing the Applicability of Polarizable Force-Field Molecular Dynamics for Parallel Architectures: A Comparison of Digital MPI with LAM-MPI and MPICH2 SP - 433 KW - case_study KW - high-performance_computing KW - molecular_dynamics KW - mpi KW - parallel_algorithms KW - performance_analysis AU - Almeida, Benjamin AU - Mahajan, Reema AU - Kranzlmüller, Dieter AU - Volkert, Jens AU - Höfinger, Siegfried PY - 2005/// UR - http://dx.doi.org/10.1007/11557265_55 ER -