Unified Code Generation for the Parallel Computation of Pairwise Interactions using Partial Evaluation

Schmitt, Jonas; Köstler, Harald; Eitzinger, Jan; Membarth, Richard

The evaluation of pairwise interactions is fundamental for the simulation of most molecular processes. Their efficient computation is therefore crucial for the overall performance of these simulations on modern computer architectures. We show how code for computing pairwise interactions on parallel and heterogeneous platforms can be generated from a unified base through partial evaluation of higher-order functions. For this purpose, we introduce a complete implementation of the neighbor list algorithm based on the AnyDSL framework, from which we are able to generate executables for both CPU and GPU through compile-time specialization. Furthermore, we discuss the advantages and disadvantages of our approach and compare it with the miniMD simulation package from the Mantevo project, which is implemented in the C++ programming language and uses a similar computational core as the widely used molecular dynamics package LAMMPS. Finally, we assess the performance of our implementation in a number of test cases on modern CPU and GPU hardware.

In Proceedings of the 17th International Symposium on Parallel and Distributed Computing (ISPDC), pp. 1-8, Geneva, Switzerland, June 25-28, 2018

@inproceedings{schmitt2018unifiedmd,
    author          = {Schmitt, Jonas and Köstler, Harald and Eitzinger, Jan and Membarth, Richard},
    address         = {Geneva, Switzerland},
    booktitle       = {Proceedings of the 17th International Symposium on Parallel and Distributed Computing (ISPDC)},
    title           = {{Unified Code Generation for the Parallel Computation of Pairwise Interactions using Partial Evaluation}},
    pages           = {1--8},
    year            = 2018,
    month           = jun,
    date            = {2018-06-25/2018-06-28},
    doi             = {},
    organization    = {IEEE}
}