Computer simulation of liquids
Computer simulation of liquids
Computer simulation using particles
Computer simulation using particles
Pfortran: a parallel dialect of Fortran
ACM SIGPLAN Fortran Forum
Molecular dynamics on a distributed-memory multiprocessor
Journal of Computational Chemistry
Fast parallel algorithms for short-range molecular dynamics
Journal of Computational Physics
PVM: Parallel virtual machine: a users' guide and tutorial for networked parallel computing
PVM: Parallel virtual machine: a users' guide and tutorial for networked parallel computing
Parallel programming with guarded objects
Parallel programming with guarded objects
ISCA '95 Proceedings of the 22nd annual international symposium on Computer architecture
The parallel fast multipole method in molecular dynamics
The parallel fast multipole method in molecular dynamics
Experiences in data-parallel programming
Scientific Programming - Special issue: High Performance Fortran comes of age
Compiler support for machine-independent parallelization of irregular problems
Compiler support for machine-independent parallelization of irregular problems
Parallel molecular dynamics: implications for massively parallel machines
Journal of Parallel and Distributed Computing
Efficient run-time support for irregular block-structured applications
Journal of Parallel and Distributed Computing - Special issue on irregular problems in supercomputing applications
NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Compiler Analysis for Irregular Problems in Fortran D
Proceedings of the 5th International Workshop on Languages and Compilers for Parallel Computing
Writing a Multigrid Solver Using Co-array Fortran
PARA '98 Proceedings of the 4th International Workshop on Applied Parallel Computing, Large Scale Scientific and Industrial Problems
Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis
ACM SIGMETRICS Performance Evaluation Review
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After at least a decade of parallel tool development, parallelization of scientific applications remains a significant undertaking. Typically parallelization is a specialized activity supported only partially by the programming tool set, with the programmer involved with parallel issues in addition to sequential ones. The details of concern range from algorithm design down to low-level data movement details. The aim of parallel programming tools is to automate the latter without sacrificing performance and portability, allowing the programmer to focus on algorithm specification and development. We present our use of two similar parallelization tools, Pfortran and Cray's Co-Array Fortran, in the parallelization of the GROMOS96 molecular dynamics module. Our parallelization started from the GROMOS96 distribution's shared-memory implementation of the replicated algorithm, but used little of that existing parallel structure. Consequently, our parallelization was close to starting with the sequential version. We found the intuitive extensions to Pfortran and Co-Array Fortran helpful in the rapid parallelization of the project. We present performance figures for both the Pfortran and Co-Array Fortran parallelizations showing linear speedup within the range expected by these parallelization methods.