DelftBluePhase1
Last updated on 16 June 2022
DelftBlue is the supercomputer at TU Delft. It is designed to meet researchers increasing need for extensive computing power to solve complex problems in physics, mechanics and dynamics. The system is characterized by flexibility, speed and user-friendliness. In its final phase it will offer 20,000 CPU cores in over 400 compute nodes. It incorporates a high-speed parallel storage subsystem, based on a BeeGFS. All the compute nodes and the storage system are interconnected with HDR100 InfiniBand technology for high-throughput low-latency inter-node communication.
Description of the DelftBlue system
The solution is built on Fujitsu hardware and makes use of processors with over 20,000 cores; the highest available memory throughput (2933Mhz); IB interconnect (HDR/HDR100) used for all nodes; and a high throughput IO subsystem.
Compute nodes
The compute nodes are built using the latest Intel Cascade Lake refresh processors offering high performance and power efficiency. The Rpeak for the system is 1.05 PFlops.
The cluster consists of three different types of compute nodes:
- Standard compute nodes
- Fat compute nodes (large memory) in 2 memory configurations
- Compute nodes with CPU's equipped with NVIDIA Tesla cards
Node Category | Number | Cores | CPU / GPU | Memory | SSD |
|---|---|---|---|---|---|
Standard | 218 | 48 | 2x Intel XEON E5-6248R 24C 3.0GHz | 192 GB | 480 GB |
Fat type-a | 6 | 48 | 2x Intel XEON E5-6248R 24C 3.0GHz | 768 GB | 480 GB |
Fat type-b | 4 | 48 | 2x Intel XEON E5-6248R 24C 3.0GHz | 1536 GB | 480 GB |
GPU | 10 | 48 | 2x AMD EPYC 7402 24C 2.80 GHz | 256 GB |
|
CPU total | Compute nodes | 238 |
GPU total | GPU nodes | 10 |
Front-end nodes
The Cluster uses a number of front-end nodes as the entry point to the cluster for end-users and administrators.
- Login nodes
- Interactive/visualization nodes equipped with NVIDIA Quadro RTX cards
Node Category | Number | Cores | CPU / GPU | Memory |
|---|---|---|---|---|
Login | 4 | 32 | 2x Intel XEON Gold E5-6226R 16C 2.9GHz | 384 GB |
Interactive/visualization | 2 | 32 | 2x Intel XEON Gold E5-6226R 16C 2.9GHz | 192 GB |
Highlights / Details:
- The login nodes are meant to be the main access point for all end-users of the system. It is expected they will have a high level of competition of user sessions and therefore they have been configured with 384GB or memory. In addition, these nodes are configured as HA pairs to ensure the effects of a single node failure does not stop user access to the cluster.
- The Interactive/visualization nodes can be used for running specific interactive tasks that need to utilize a high-end graphics card for visualization or for workloads that may not be suitable for running on the cluster. Quadro RTX 4000: with 2304 CUDA cores, 288 Tensor Cores, 36 RT cores and 8 GB GDDR6 memory.
- Two File Transfer nodes are specifically included in order to provide an optimal data flow between DelftBlue and the central research storage of the TU Delft. These nodes can be used as a pre-staging or post-staging job that runs just before or after a computational job.
Interconnect
HPC applications make frequent use of communication between nodes when calculating their computational results. To maintain application efficiency even when scaling over a large number of nodes, the interconnect must minimise overhead and enable high-speed message delivery. DelftBlue is equipped with a high performing InfiniBand network based on Mellanox InfiniBand products to build an efficient low-overhead transport fabric. This interconnect set-up not only enables efficient delivery of MPI based messages but also provides applications with high-speed access to the temporary storage area which is also accessible over the InfiniBand fabric.
Highlights/details:
- Mellanox InfiniBand HDR100/HDR interconnect configured in a Full Bisectional Bandwidth (FBB) non-blocking network fabric.
- Fat tree topology
- 100Gbps IB HDR100 HCA’s per server
Storage
To enable efficient I/O throughput for computational jobs, the configuration includes a high-speed file system with 696 TB usable storage space and a throughput of at least 20 GB/s. This storage subsystem consists of:
- 6x IO servers – 2 MetaData servers and 4 Storage Servers
- 1x NetApp All flash storage/controller shelf – MetaData storage
- 4x NetApp storage/controller shelves – File data storage
Highlights/details:
- NetApp All flash subsystem for managing the Meta Data requirements
- A set of NetApp High capacity, high throughput disk subsystems providing redundancy at all levels to avoid Single Point Of Failure conditions
- High speed connectivity
- Multiple HDR100 IB links per Storage server to the IB network
- Multiple high-speed FibreChannel 32 Gbps connections between the storage servers and storage devices
- File system built using the BeeGFS parallel file system
- Dynamic Job Parallel File System “BeeOND” is a facility, which lets a user build a parallel file system from the local disks of the nodes over which their job is running. Each node of the cluster incorporates a 480GB SSD device in addition to the OS boot device. This SSD can be used to build a local parallel file system.
HPC Management solution
Bright Cluster Manger (BCM) is used for deploying and managing the cluster and HPC software environment. It includes a complete set of HPC libraries, tools, management and reporting facilities.
Operating System
Red Hat Enterprise Linux 8
Job Management
DelftBlue is equipped with Slurm job resource manager, which will provide access to resources, based on the fair share principle.
End user Portal
Traditionally a HPC provides its users with SSH and FTP to access cluster resources. However, our goal is to encourage the use of the DHPC facilities by the use of a modern and easy to use portal. Therefore, DelftBlue is equipped with the Open OnDemand portal.