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Persistent URL http://purl.org/net/epubs/work/49558
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Record Id 49558
Title Is MPI-2 suitable for Quantum Chemistry? Performance of passive target one-sided communications
Abstract Quantum chemistry calculations have a compelling requirement for one-sided communication given their irregular data access patterns and irregular task sizes. Hence the MPI-2 passive target one-sided communications seem attractive as a standards based foundation for the implementation of the main algorithms in the field. For successful deployment it is important that good performance can be achieved reliably across a wide variety of platforms. We have tested this performance using a simple shared counter kernel across a number of machines and MPI implementations, including both open source MPI implementations - OpenMPI and MPICH2 - and those on the current and previous generation of the UK’s national academic supercomputers, HECToR and HPCx. We find that the performance varies greatly with the MPI implementation in question. The speed with which communications are progressed was found to vary up to 4 orders of magnitude in the kernel program depending on the MPI library used. As a result the “time to solution” for the kernel could vary by as much as about a factor 2, although greater impacts are anticipated for more complex algorithms such as Fock-builders. This spread in performance relates to two aspects of the MPI-2 standard. The first is whether the MPI implementation takes a minimalistic approach to satisfy rule 11.7.2 on the progress of one-sided communications or goes beyond that. Secondly, does the MPI library implement full multi-threading support, as specified in section 12.4, or not. Overall, we find that the MPI-2 standard is not strong enough to guarantee that MPI libraries provide acceptable performance characteristics to use one-sided communications effectively. We suggest that the standard be strengthened to address these performance issues – without this it seems unlikely that the MPI-2 one-sided communications will be useful for real world applications.
Organisation CSE , CSE-CCG , CSE-HEC , STFC
Keywords shared counter , Chemistry , performance , MPI-2 , one-sided communications
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Language English (EN)
Type Details URI(s) Local file(s) Year
Report HPCx Technical Reports-HPCxTR0807. 2008. http://www.hpcx.a…ports/HPCxTR0807.pdf HPCxTR0807.pdf 2008
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