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Hybrid MPI/OpenMP parallelization of the effective fragment potential method in the libefp software library
Ilya A Kaliman1, Lyudmila V Slipchenko
1Department of Chemistry, Purdue University, West Lafayette, Indiana, 47907.
Journal of Computational Chemistry
|November 14, 2014
Summary
A new hybrid parallelization scheme for the Effective Fragment Potential (EFP) method shows excellent performance. This advancement in computational chemistry expands the reach of EFP and QM/EFP methods to larger scales.
Area of Science:
- Computational Chemistry
- High-Performance Computing
Background:
- The Effective Fragment Potential (EFP) method is a powerful tool for molecular modeling.
- Scaling EFP calculations to larger systems and longer timescales is computationally demanding.
Purpose of the Study:
- To introduce a novel hybrid MPI/OpenMP parallelization scheme for the EFP method.
- To enhance the performance and scalability of the libefp software library.
Main Methods:
- Implementation of a hybrid Message Passing Interface (MPI) and Open Multi-Processing (OpenMP) parallelization.
- Utilizing a dynamic load balancing algorithm with a master/slave model.
- Adherence to the MPI-1 standard for enhanced portability.
Main Results:
- Demonstrated excellent parallel scaling of the EFP method up to hundreds of CPU-cores across multiple nodes.
- The new implementation maintains portability due to its reliance on the MPI-1 standard.
- Significantly expanded the attainable time- and length-scales for EFP and QM/EFP calculations.
Conclusions:
- The new parallel EFP implementation offers substantial performance gains.
- This advancement broadens the applicability of EFP and QM/EFP methods in computational chemistry.
- The use of standard MPI functions ensures ease of use and portability.
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