BinAC2/Hardware and Architecture

Hardware and Architecture

The bwForCluster BinAC 2 supports researchers from the broader fields of Bioinformatics, Astrophysics, and Geosciences.

Operating System and Software

• Operating System: Rocky Linux 9.4
• Queuing System: Slurm (see BinAC2/Slurm for help)
• (Scientific) Libraries and Software: Environment Modules

Compute Nodes

BinAC 2 offers compute nodes, high-mem nodes, and two types of GPU nodes.

• 180 compute nodes
• 14 SMP node
• 32 GPU nodes (A30)
• 8 GPU nodes (A100)
• plus several special purpose nodes for login, interactive jobs, etc.

Compute node specification:

	Standard	High-Mem	GPU (A30)	GPU (A100)
Quantity	180	14	32	8
Processors	2 x AMD EPYC Milan 7543	2 x AMD EPYC Milan 7443	2 x AMD EPYC Milan 7543	2 x AMD EPYC Milan 7543
Processor Frequency (GHz)	2.80	2.85	2.80	2.80
Number of Cores	64	48	64	64
Working Memory (GB)	512	2048	512	512
Local Disk (GB)	512 (SSD)	1920 (SSD)	512 (SSD)	512 (SSD)
Interconnect	HDR IB (80 nodes) / 100GbE	HDR	HDR	HDR
Coprocessors	-	-	2 x NVIDIA A30 (24 GB ECC HBM2, NVLink	4 x NVIDIA A100 (80 GB ECC HBM2e)

Network

The compute nodes and the parallel file system are connected via 100GbE ethernet
In contrast to BinAC 1 not all compute nodes are connected via Infiniband, but there are 80 standard compute nodes connected via HDR Infiniband (100 GbE). In order to get your jobs onto the Infiniband nodes, submit your job with --constraint=ib.

Storage

The bwForCluster BinAC 2 consists of two separate storage systems, one for the user's home directory $HOME and one serving as a project/work space. The home directory is limited in space and parallel access but offers snapshots of your files and backup.

The project/work is a parallel file system (PFS) which offers fast and parallel file access and a bigger capacity than the home directory. It is mounted at /pfs/10 on the login and compute nodes. This storage is based on Lustre and can be accessed parallel from many nodes. The PFS contains the project and the work directory. Each compute project has its own directory at /pfs/10/project that is accessible for all members of the compute project. Each user can create workspaces under /pfs/10/work using the workspace tools. These directories are only accessible for the user who created the workspace.

Additionally, each compute node provides high-speed temporary storage (SSD) on the node-local solid state disk via the $TMPDIR environment variable.

	$HOME	project	work	$TMPDIR
Visibility	global	global	global	node local
Lifetime	permanent	permanent	work space lifetime (max. 30 days, max. 5 extensions)	batch job walltime
Capacity	-	8.1 PB	1000 TB	512 GB per node; 1920 GB on high-mem nodes
Speed	...	...	...	...
Quotas	40 GB per user	not yet, maybe in the future	none	none
Backup	yes	no	no	no

 global             : all nodes access the same file system
 local              : each node has its own file system
 permanent          : files are stored permanently
 batch job walltime : files are removed at end of the batch job

Home

Home directories are meant for permanent file storage of files that are keep being used like source codes, configuration files, executable programs etc.; the content of home directories will be backed up on a regular basis. Because the backup space is limited we enforce a quota of 40GB on the home directories.

NOTE: Compute jobs on nodes must not write temporary data to $HOME. Instead they should use the local $TMPDIR directory for I/O-heavy use cases and work spaces for less I/O intense multinode-jobs.

Project

Each compute project has its own project directory at /pfs/10/project.

$ ls -lh /pfs/10/project/
drwxrwx---. 2 root bw16f003 33K Dec 12 16:46 bw16f003
[...]

As you can see the directory is owned by a group representing your compute project (here bw16f003) and the directory is accessible by all group members. It is upon your group to decide how to use the space inside this directory: shared data folders, personal directories for each project member, software containers, etc.

The data is stored on HDDs. The primary focus of /pfs/10/project is pure capacity, not speed.

Work

The data at /pfs/10/work is stored on SSDs. The primary focus is speed, not capacity. In contrast to BinAC 1 we will enforce work space lifetime, as the capacity is limited. We ask you to only store data you actively use for computations on /pfs/10/work. Please move data to /pfs/10/project when you don't need it on the fast storage any more.

Each user can create workspaces at /pfs/10/work through the workspace tools To create a work space you'll need to supply a name for your work space area and a lifetime in days. For more information read the corresponding help, e.g: ws_allocate -h.

Command	Action
ws_allocate mywork 30	Allocate a work space named "mywork" for 30 days.
ws_allocate myotherwork	Allocate a work space named "myotherwork" with maximum lifetime.
ws_list -a	List all your work spaces.
ws_find mywork	Get absolute path of work space "mywork".
ws_extend mywork 30	Extend life me of work space mywork by 30 days from now.
ws_release mywork	Manually erase your work space "mywork". Please remove directory content first.

Scratch

Please use the fast local scratch space for storing temporary data during your jobs.

For each job a scratch directory will be created on the compute nodes. It is available via the environment variable $TMPDIR, which points to /scratch/<jobID>.