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Accelerating the Pace of Protein Functional Annotation With Intel Xeon Phi Coprocessors
IEEE Transactions on Nanobioscience
|March 14, 2015
Summary
Parallelizing the eFindSite algorithm for Intel Xeon Phi accelerators significantly boosts protein ligand-binding site prediction performance. This optimization achieves substantial speedups, making complex bioinformatics research more efficient.
Area of Science:
- Computational biology
- Bioinformatics
- High-performance computing
Background:
- Intel Xeon Phi offers powerful parallel acceleration for scientific research.
- Limited availability of optimized scientific codes for this platform.
- eFindSite is a structural bioinformatics algorithm for predicting ligand-binding sites in proteins.
Purpose of the Study:
- To develop and benchmark a parallel version of the eFindSite algorithm for the Intel Xeon Phi platform.
- To evaluate the performance improvements and scalability of the parallelized algorithm.
- To assess the feasibility of porting scientific codes to the Intel Xeon Phi architecture.
Main Methods:
- Parallelization of the structure alignment component of eFindSite using pragma-based OpenMP.
- Benchmarking the parallel code on the Intel Xeon Phi CPU and coprocessor.
- Comparison of execution times against a serial version and performance with simultaneous resource utilization.
Main Results:
- The parallel eFindSite code achieved speedups of 11.8x on the CPU and 10.1x on the coprocessor.
- Simultaneous utilization of both resources resulted in a 17.6x speedup.
- Ligand-binding predictions for 501 proteins were completed in 2.1 hours on a Xeon Phi-equipped node, compared to 3.1 hours without and 36.8 hours for the serial version.
Conclusions:
- The parallelized eFindSite demonstrates significant performance improvements on the Intel Xeon Phi.
- Porting scientific codes to the Intel Xeon Phi architecture is feasible with short development times.
- The parallel version of eFindSite is available for academic use, promoting its adoption in computational research.
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