BinAC2/Hardware and Architecture

Hardware and Architecture

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

Operating System and Software

• Operating System: Rocky Linux 9.5
• 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 three types of GPU nodes.

• 180 compute nodes
• 16 SMP node
• 32 GPU nodes (2xA30)
• 8 GPU nodes (4xA100)
• 4 GPU nodes (4xH200)
• plus several special purpose nodes for login, interactive jobs, etc.

Compute node specification:

	Standard	High-Mem	GPU (A30)	GPU (A100)	GPU (H200)
Quantity	180	14 / 2	32	8	4
Processors	2 x AMD EPYC Milan 7543	2 x AMD EPYC Milan 7443 / 2 x AMD EPYC Milan 75F3	2 x AMD EPYC Milan 7543	2 x AMD EPYC Milan 7543	2 x AMD EPYC Milan 9555
Processor Base Frequency (GHz)	2.80	2.85 / 2.95	2.80	2.80	3.20
Number of Physical Cores / Hypertreads	64 / 128	48 / 96 // 64 / 128	64 / 128	64 / 128	128 / 256
Working Memory (GB)	512	2048	512	512	1536
Local Disk (GiB)	450 (NVMe-SSD)	14000 (NVMe-SSD)	450 (NVMe-SSD)	14000 (NVMe-SSD)	28000 (NVMe-SSD)
Interconnect	HDR 100 IB (84 nodes) / 100GbE (96 nodes)	100GbE	100GbE	100GbE	HDR 200 IB + 100GbE
Coprocessors	-	-	2 x NVIDIA A30 (24 GB ECC HBM2, NVLink)	4 x NVIDIA A100 (80 GB ECC HBM2e)	4 x NVIDIA H200 NVL (141 GB ECC HBM3e, NVLink)

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 84 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.

File Systems

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	480 GB (compute nodes); 7.7 TB (GPU-A30 nodes); 16 TB (GPU-A100 and SMP nodes); 31 TB (GPU-H200 nodes)
Speed (read)	≈ 1 GB/s, shared by all nodes	max. 12 GB/s	≈ 145 GB/s peak, aggregated over 56 nodes, ideal striping	≈ 3 GB/s (compute)/ ≈5 GB/S (GPUA-30)/ ≈ 26 GB/s (GPU-A100 + SMP)/ ≈ 42 GB/s (GPU-H200) per node
Quotas	40 GB per user	not yet, maybe in the future	none	none
Backup	yes (nightly)	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

Please note that due to the large capacity of work and project and due to frequent file changes on these file systems, no backup can be provided. Backing up these file systems would require a redundant storage facility with multiple times the capacity of project. Furthermore, regular backups would significantly degrade the performance. Data is stored redundantly, i.e. immune against disk failures but not immune against catastrophic incidents like cyber attacks or a fire in the server room. Please consider to use on of the remote storage facilities like SDS@hd, bwSFS, LSFD Online Storage or the bwDataArchive to back up your valuable data.

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>.

Especially the SMP nodes and the GPU nodes are equipped with large and fast local disks that should be used for temporary data, scratch data or data staging for ML model training. The Lustre file system (WORK and PROJECT) is unsuited for repetitive random I/O, I/O sizes smaller than the Lustre and ZFS block size (1M) or I/O patterns where files are opened and closed in rapid succession. The XFS file system of the local scratch drives is better suited for typical scratch workloads and access patterns. Moreover, the local scratch drives offer a lower latency and a higher bandwidth than WORK.

SDS@hd

SDS@hd is mounted via NFS on login and compute nodes at /mnt/sds-hd.

To access your Speichervorhaben, the export to BinAC 2 must first be enabled by the SDS@hd-Team. Please contact SDS@hd support and provide the acronym of your Speichervorhaben, along with a request to enable the export to BinAC 2.

Once this has been done, you can access your Speichervorhaben as described in the SDS documentation.

$ kinit $USER
Password for <user>@BWSERVICES.UNI-HEIDELBERG.DE:

The Kerberos ticket store is shared across all nodes. Creating a single ticket is sufficient to access your Speichervorhaben on all nodes.