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Data Management for Molecule Simulation : A Throughput-Oriented Approach

分子模拟的数据管理：一种面向吞吐量的方法

基本信息

批准号：
10799206
负责人：
Yicheng Tu
金额：
$ 19.09万
依托单位：
UNIVERSITY OF SOUTH FLORIDA
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-09-22 至 2025-08-31
项目状态：
未结题

项目摘要

Project Summary This is an administrative supplement to the parent R01 project GM140316 titled “Data Management for Molecule Sim- ulation: A Throughput-Oriented Approach." The main objective is to acquire a parallel computing server that hosts 4 NVidia H100 GPU cards, two Intel Xeon Platinum 8480+ 28-core CPUs, 2TB of DDR5 system memory, and 64TB of NVMe M.2 internal storage. We believe this will be an essential component that leads to the success of the proposed research tasks in the parent grant. Speciﬁcally, the new server will provide the following capabilities that are not found in existing computing facilities the project team has access to: (1) and Memory Capacity: With 37-64 petaFLOPs of to- tal in-core computing power, 320GB of GPU memory with a bandwidth of 3.35TB/s, the server can signiﬁcantly improve Speciﬁc Aim 2 tasks by reducing the time for processing analytical queries against molecular dynamics (MD) simula- tion data; (2) Storage Capacity: we propose to use NVMe devices with 64TB of space to store datasets and associated metadata, with 1.2 million IOPS and 48GBps of total bandwidth. This will allow low latency access to large datasets for processing, which is required by tasks in Speciﬁc Aim 3; (3) Data Communication: the H100 GPUs are connected by NVidia's 4th-generation NVLink buses, allowing non-blocking bidirectional communication between GPUs with a total bandwidth of 900GB/s. This will speed up large-scale MD simulations by releasing the GPU-to-GPU data transmission bottleneck, affecting Speciﬁc Aim 4 of the parent project.

项目摘要这是对父R 01项目GM 140316的管理补充，标题为“分子模拟的数据管理”。评估：一种以产出为导向的方法。“主要目标是获得一个并行计算服务器， NVidia H100 GPU卡，两个Intel Xeon Platinum 8480+ 28核CPU，2 TB DDR5系统内存，64 TB NVMe M.2内部存储。我们认为，这将是使拟议的《联合国宪章》获得成功的一个重要组成部分。家长补助金中的研究任务。具体而言，新服务器将提供以下功能，这些功能在在现有的计算设施中，项目团队可以访问：（1）和内存容量：37-64 petaFLOPs的到- 谈到核心计算能力，320 GB的GPU内存，带宽为3.35TB/s，服务器可以显著提高通过减少针对分子动力学（MD）模拟处理分析查询的时间，（2）存储容量：我们建议使用具有64 TB空间的NVMe设备来存储数据集和相关的数据集。元数据，具有120万IOPS和48 GBps的总带宽。这将允许低延迟访问大型数据集，（3）数据通信：H100 GPU通过以下方式连接： NVidia的第四代NVLink总线，允许GPU之间的无阻塞双向通信，带宽为900 GB/s。这将通过释放GPU到GPU的数据传输来加快大规模MD模拟瓶颈，影响父项目的具体目标4。