UNRES-GPU 用于基于物理的生物时间和大小尺度的蛋白质体系的粗粒化模拟。
UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales.
机构信息
Centre of Informatics Tricity Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk 80-233, Poland.
Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk 80-309, Poland.
出版信息
Bioinformatics. 2023 Jun 1;39(6). doi: 10.1093/bioinformatics/btad391.
SUMMARY
The UNited RESisdue (UNRES) package for coarse-grained simulations, which has recently been optimized to treat large protein systems, has been implemented on Graphical Processor Units (GPUs). An over 100-time speed-up of the GPU code (run on an NVIDIA A100) with respect to the sequential code and an 8.5 speed-up with respect to the parallel Open Multi-Processing (OpenMP) code (run on 32 cores of 2 AMD EPYC 7313 Central Processor Units (CPUs)) has been achieved for large proteins (with size over 10 000 residues). Due to the averaging over the fine-grain degrees of freedom, 1 time unit of UNRES simulations is equivalent to about 1000 time units of laboratory time; therefore, millisecond time scale of large protein systems can be reached with the UNRES-GPU code.
AVAILABILITY AND IMPLEMENTATION
The source code of UNRES-GPU along with the benchmarks used for tests is available at https://projects.task.gda.pl/eurohpcpl-public/unres.
摘要
最近，针对大型蛋白质系统进行了优化的粗粒度模拟的 UNited RESidue（UNRES）包已在图形处理单元（GPU）上实现。与顺序代码相比，GPU 代码（在 NVIDIA A100 上运行）的速度提高了 100 多倍，与并行 Open Multi-Processing（OpenMP）代码（在 2 个 AMD EPYC 7313 中央处理器（CPU）的 32 个内核上运行）相比，速度提高了 8.5 倍，可用于大型蛋白质（大小超过 10,000 个残基）。由于细粒度自由度的平均化，UNRES 模拟的 1 个时间单位相当于大约 1000 个实验室时间单位；因此，使用 UNRES-GPU 代码可以达到毫秒时间尺度的大型蛋白质系统。
可用性和实现
UNRES-GPU 的源代码以及用于测试的基准测试可在 https://projects.task.gda.pl/eurohpcpl-public/unres 上获得。
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