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Publications of SPCL
|T. Hoefler and S. Gottlieb:|
|Parallel Zero-Copy Algorithms for Fast Fourier Transform and Conjugate Gradient using MPI Datatypes|
(Vol LNCS 6305, Nr. , In Recent Advances in the Message Passing Interface (EuroMPI'10), presented in Stuttgart, Germany, pages 132--141, Springer, ISSN: 0302-9743, ISBN: 078-3-642-15645-8, Sep. 2010, )
AbstractMany parallel applications need to communicate non-contiguous data. Most applications manually copy (pack/unpack) data before communications even though MPI allows a zero-copy specification. In this work, we study two complex use-cases: (1) Fast Fourier Transformation where we express a local memory transpose as part of the datatype, and (2) a conjugate gradient solver with a checkerboard layout that requires multiple nested datatypes. We demonstrate significant speedups up to a factor of 3.8 and 18%, respectively, in both cases. Our work can be used as a template to utilize datatypes for application developers. For MPI implementers, we show two practically relevant access patterns that deserve special optimization.