In recent years, the traditional structure based design method has gradually reached its limit, making the capital expenditure for drug research and discovery increase exponentially. Therefore, for the field of drug design, the motion based drug design scheme, namely molecular dynamics simulation, can be regarded as one of the most exciting and innovative advances in the industry. The realization of molecular dynamics simulation requires high computational power.

In the past, only large supercomputers were able to provide enough computing power for molecular dynamics calculations. However, snow lake technology, which is committed to providing “special supercomputing” solutions, hopes to break this bottleneck and develop a solution with higher performance, lower cost and higher energy efficiency than traditional supercomputers.

Special engine for molecular dynamics based on FPGA

As mentioned above, in order to promote the development of medicine, drug research and development has progressed to the molecular level. At this level, scientists can better understand the role of molecular and biological processes and unlock the mysteries of their movement.

Dr. Sheng Nan, chief scientist of life science computing of Xuehu technology, said: “just as it is easier to capture the details of the crime when ‘watching the surveillance video’ than ‘looking at the scene photos’ when solving the case, molecular dynamics simulation allows drug designers to’ see ‘the whole effective process of drug molecules more directly, thus greatly improving the success rate of new drug research and development.”

Founded in 2017, Shanghai Xuehu Technology Co., Ltd. is an innovative enterprise dedicated to the research and development of high-performance computing products and solutions. The company mainly provides innovative and dedicated high-performance computing solutions and products for life sciences, oil and gas exploration, autonomous driving, distributed storage and other related fields.

“Yaddle MD” designed and developed by Xuehu technology is a special molecular dynamics engine based on FPGA. This is a kind of ™ The special solution for molecular dynamics calculation implemented on the accelerator provides compatibility support for commonly used molecular dynamics software and other analysis plug-ins through the special API for molecular dynamics with the help of Xilinx runtime library (XRT).

Figure 1 – molecular dynamics calculations used in drug research and discovery

In terms of performance, the Yaddle MD FPGA molecular dynamics special engine of Xuehu technology runs on the alveo accelerator card, which is nearly 50 times higher than the molecular dynamics software scheme using CPU only, and twice higher than the molecular dynamics software scheme using GPU acceleration, as shown in Figure 2. At the same time, the power consumption of FPGA is only 2/3 of that of CPU and 2/9 of that of GPU. Therefore, the analog quantity provided by Yaddle MD per kilowatt hour is nearly 100 times that of CPU and 10 times that of GPU.

Figure 2 – Yaddle MD FPGA molecular dynamics special engine of Xuehu technology has higher performance and lower energy consumption compared with competitive solutions

The value of adaptive alveo accelerator cards

Because the evolution speed of complex algorithms has far exceeded the design cycle of the chip, GPU and ASIC devices with fixed functions can not keep up with the pace of development. Based on Xilinx 16nm ultrascale ™ The Xilinx alveo accelerator card based on the architecture is designed to meet the rapidly changing needs of modern data centers. It is oriented to common workloads such as machine learning inference, video transcoding, database search and analysis, and can provide up to 90 times the performance of CPU.

Alveo U200 accelerator card

Alveo accelerator card provides a unique reconfigurable acceleration function for Yaddle MD, which can not only support the continuous optimization of its flexible adaptive algorithm, but also reduce the total cost of ownership while supporting any type of workload.

Yadde MD has realized an ultra-high performance FPGA molecular dynamics algorithm with the help of alveo U200 accelerator card, which can perform very complex calculations. Based on a single alveo card, Yaddle MD can achieve higher performance than using CPU and GPU processors, and provide the powerful computing power previously only provided by supercomputers, thus greatly accelerating the dynamic simulation speed of biomolecules.

With yadde MD, help users achieve:

·Complete molecular dynamics calculation is realized on a single FPGA, thus releasing a large amount of CPU resources

·Realize distributed pipeline computing of atomic interaction, and significantly improve computing performance

·Encode the bonding information between atoms and decode it during real-time calculation

·Provide compatibility support for common molecular dynamics software and other analysis tools (including format conversion) through the tool set

Dr. Sheng Nan said: “high performance is the key to ensure the efficiency and accuracy of molecular dynamics calculation. Xuehu technology’s high-performance molecular dynamics special engine based on alveo can not only save customers a lot of time and cost, but also make the dynamics based drug design from impossible to possible”.

At present, Yaddle MD engine of snow lake technology has started to provide MD acceleration service through Alibaba cloud, and its acceleration scheme based on alveo card is also under small-scale external development and testing. At the same time, the innovation pace of snow lake science and technology continues. It plans to continue to expand the simulation capability through the combination of multiple alveo devices in the future, further speed up the application of molecular dynamics computing and expand the throughput.

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