In recent years, high performance computing and powerful supercomputers are becoming a staple in many areas of academia and industry. The author introduces the concepts of shared memory programming in the context of s...
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In recent years, high performance computing and powerful supercomputers are becoming a staple in many areas of academia and industry. The author introduces the concepts of shared memory programming in the context of solving the heat equation, which will allow the exploration of several finite difference and parallelization schemes.
Supervised learning of Convolutional Neural Networks (CNNs), also known as supervised Deep Learning, is a computationally demanding process. To find the most suitable parameters of a network for a given application, n...
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ISBN:
(纸本)9781479989379
Supervised learning of Convolutional Neural Networks (CNNs), also known as supervised Deep Learning, is a computationally demanding process. To find the most suitable parameters of a network for a given application, numerous training sessions are required. Therefore, reducing the training time per session is essential to fully utilize CNNs in practice. While numerous research groups have addressed the training of CNNs using GPUs, so far not much attention has been paid to the Intel Xeon Phi coprocessor. In this paper we investigate empirically and theoretically the potential of the Intel Xeon Phi for supervised learning of CNNs. We design and implement a parallelization scheme named CHAOS that exploits both the thread-and SIMD-parallelism of the coprocessor. Our approach is evaluated on the Intel Xeon Phi 7120P using the MNIST dataset of handwritten digits for various thread counts and CNN architectures. Results show a 103.5x speed up when training our large network for 15 epochs using 244 threads, compared to one thread on the coprocessor. Moreover, we develop a performance model and use it to assess our implementation and answer what-if questions.
Background: Small-molecule docking is an important tool in studying receptor-ligand interactions and in identifying potential drug candidates. Previously, we developed a software tool (DOVIS) to perform large-scale vi...
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Background: Small-molecule docking is an important tool in studying receptor-ligand interactions and in identifying potential drug candidates. Previously, we developed a software tool (DOVIS) to perform large-scale virtual screening of small molecules in parallel on Linux clusters, using AutoDock 3.05 as the docking engine. DOVIS enables the seamless screening of millions of compounds on high-performance computing platforms. In this paper, we report significant advances in the software implementation of DOVIS 2.0, including enhanced screening capability, improved file system efficiency, and extended usability. Implementation: To keep DOVIS up-to-date, we upgraded the software's docking engine to the more accurate AutoDock 4.0 code. We developed a new parallelization scheme to improve runtime efficiency and modified the AutoDock code to reduce excessive file operations during large-scale virtual screening jobs. We also implemented an algorithm to output docked ligands in an industry standard format, sd-file format, which can be easily interfaced with other modeling programs. Finally, we constructed a wrapper-script interface to enable automatic rescoring of docked ligands by arbitrarily selected third-party scoring programs. Conclusion: The significance of the new DOVIS 2.0 software compared with the previous version lies in its improved performance and usability. The new version makes the computation highly efficient by automating load balancing, significantly reducing excessive file operations by more than 95%, providing outputs that conform to industry standard sd-file format, and providing a general wrapper-script interface for rescoring of docked ligands. The new DOVIS 2.0 package is freely available to the public under the GNU General Public License.
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