High-performance Computing

Context

A high-performance computing (HPC) system or environment is made up of a single computer system with many CPUs, or a cluster of multiple computer clusters. It can handle a large amount of data and perform high-performance computing that would be rather difficult for PCs. HPC has ultra-high capability in floating-point computation and can be used for compute-intensive and data-intensive fields, such as industrial design, bioscience, energy exploration, image rendering, and heterogeneous computing. Different scenarios put different requirements on general-purpose file systems:

Industrial design: In automobile manufacturing, CAE and CAD simulation software is widely used. When the software is operating, compute nodes need to communicate with each other closely, which requires general-purpose file systems that can provide high bandwidth and low latency.
Bioscience: General-purpose file systems should have high bandwidth and large storage, and be easy to expand.
- Bioinformatics: To sequence, stitch, and compare genes.
- Molecular dynamics: To simulate the changes of proteins at molecular and atomic levels.
- New drug R&D: To complete high-throughput screening (HTS) to shorten the R&D cycle and reduce the investment.
Energy exploration: Field operations, geologic prospecting, geological data processing and interpretation, and identification of oil and gas reservoirs all require general-purpose file systems to provide large memory and high bandwidth.
Image rendering: Image processing, 3D rendering, and frequent processing of small files require high read/write performance, large capacity, and high bandwidth of general-purpose file systems.
Heterogeneous computing: Compute elements may have different instruction set architectures, requiring general-purpose file systems to provide high bandwidth and low latency.

SFS is a shared storage service based on general-purpose file systems. It features high-speed data sharing, dynamic storage tiering, as well as on-demand, smooth, and online resizing. These outstanding features empower SFS to meet the demanding requirements of HPC on storage capacity, throughput, IOPS, and latency.

A biological company needs to perform plenty of gene sequencing using software. However, due to the trivial steps, slow deployment, complex process, and low efficiency, self-built clusters are reluctant to keep abreast of business development. Things are getting better since the company resorted to professional HPC service process management software. With massive compute and storage resource of the cloud platform, the initial investment cost and O&M cost are greatly reduced, the service rollout time is shortened, and efficiency is boosted.

Configuration Process

Prepare the files of DNA sequencing to be uploaded.
Log in to the SFS console and create a general-purpose file system to store the prepared files.
Log in to the cloud servers that function as the head node and compute node, and mount the general-purpose file system on them.
On the head node, upload the files to the general-purpose file system.
On the compute node, edit the files.

Prerequisites

A VPC has been created.
Cloud servers that function as the head node and compute node have been created and are in the created VPC.
SFS has been enabled.

Example Configuration

Log in to the SFS console.
In the upper right corner of the page, click Create File System.
On the page for creating a general-purpose file system, configure parameters as instructed.
After the configuration is complete, click Create Now.

For how to mount a file system to Linux ECSs, see Mounting a General-Purpose File System to Linux ECSs.
Log in to the head node and upload the files to the general-purpose file system.
Start gene sequencing. The compute node obtains the gene sequencing file from the mounted general-purpose file system for calculation.