"Crystal structure prediction (CSP) is becoming a standard procedure in drug R&D. Our partners place great trust in its accuracy and reliability as it offers valuable insights that accelerate key steps of drug development while also bolstering the safety and intellectual property (IP) protection of new medicines. Crystal structure comparison, an essential application within the computationally intensive CSP, necessitates a significant amount of computational power. This poses a significant challenge as we continually refine and optimize our CSP process. By utilizing Intel® toolkits (Intel® oneAPI DPC++/C++ Compiler, Intel® oneAPI Math Kernel Library, Intel® Integrated Performance Primitives, and Intel® VTune™ Profiler) and employing techniques such as instruction set optimization and function substitution, we have significantly improved the performance of crystal structure comparison tool. This enhancement accelerates the drug R&D process for our customers, providing faster execution and numerous benefits. Additionally, it allows us to better exploit the hardware's potential, resulting in increased return on investment for the R&D project."
— Xiaolu Lin, senior algorithm engineer, XtalPi
Resources
Using the components of the Intel toolkits, XtalPi could significantly accelerate Ilum, its C++ application that's designed for biopharmaceutical drug discovery. The online version of this application achieves an impressive 2.32x speedup. These performance enhancements helped expedite the drug research and development (R&D) process with faster running and several other advantages, inspiring XtalPi to explore more optimization opportunities:
- Up to 41% better performance using Intel oneAPI DPC++/C++ Compiler as compared to the baseline GNU Compiler Collection (GCC)* v12.1 (with O3 optimization)
- Up to 28% performance improvement in calculating Euclidean distance using Intel oneAPI Math Kernel Library (oneMKL)
- Up to 38% performance improvement for the sorting function using Intel Integrated Performance Primitives (Intel IPP)