论文标题
Tomocupy:具有异步数据处理的有效基于GPU的层析成像重建
TomocuPy: efficient GPU-based tomographic reconstruction with asynchronous data processing
论文作者
论文摘要
通过更改环境条件或采集参数的快速3D数据分析和层析成像实验的转向需要快速,接近实时的大型数据量的3D重建。在这里,我们提出了一个高度优化的Tomocupy软件包,作为用于层析成像重建的常用CPU的Tomopy软件包的GPU替代品。 Tomocupy利用现代硬件功能来组织3D异步重建,涉及带有存储驱动器,CPU-GPU数据传输和GPU计算的并行读取工具。在异步重建中,所有操作都及时重叠以几乎完全隐藏所有数据管理时间。由于大多数摄像机的数字输出不到16位,因此我们通过使用16位浮点算术算术来优化内存使用速度和处理速度。结果,Tomocupy的3D重建比其多线Readed CPU等效速度快20-30倍。 2048x2048x2048层析成像量的完整重建(包括读取工具和方法初始化)在单个NVIDIA TESLA A100和PCIE 4.0 NVME SSD上所需的时间少于7〜s,并且几乎线性地增加了数据大小。为了简化同步梁上的操作,TomoCupy提供了易于使用的命令行界面。在多孔样品中的气体水合物形成的层析成像实验中证明了该包装的功效,其中将转向选项作为改变镜头的机制,以放大感兴趣的区域。
Fast 3D data analysis and steering of a tomographic experiment by changing environmental conditions or acquisition parameters require fast, close to real-time, 3D reconstruction of large data volumes. Here we present a performance-optimized TomocuPy package as a GPU alternative to the commonly-used CPU-based TomoPy package for tomographic reconstruction. TomocuPy utilizes modern hardware capabilities to organize a 3D asynchronous reconstruction involving parallel read-write operations with storage drives, CPU-GPU data transfers, and GPU computations. In the asynchronous reconstruction, all the operations are timely overlapped to almost fully hide all data management time. Since most cameras work with less than 16-bit digital output, we furthermore optimize the memory usage and processing speed by using 16-bit floating-point arithmetic. As a result, 3D reconstruction with TomocuPy became 20-30 times faster than its multithreaded CPU equivalent. Full reconstruction (including read-write operations and methods initialization) of a 2048x2048x2048 tomographic volume takes less than 7~s on a single Nvidia Tesla A100 and PCIe 4.0 NVMe SSD, and scales almost linearly increasing the data size. To simplify operation at synchrotron beamlines, TomocuPy provides an easy-to-use command-line interface. Efficacy of the package was demonstrated during a tomographic experiment on gas-hydrate formation in porous samples, where a steering option was implemented as a lens-changing mechanism for zooming to regions of interest.