BinAC2/Hardware and Architecture and BinAC2: Difference between pages

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{| style="width: 100%; border-spacing: 5px;"
= Hardware and Architecture =
| style="text-align:center; color:#000;vertical-align:middle;font-size:75%;" |
[[File:BinAC2_Logo_RGB_subtitel.svg|center|500px||]]
|-
|
|}


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


{| style=" background:#ffa833; width:100%;"
== Operating System and Software ==
| style="padding:8px; background:#f80; font-size:120%; font-weight:bold; text-align:left" | BinAC 1 -> BinAC 2 Migration
|-
|
* Still using BinAC 1: '''[[BinAC|Go To BinAC 1 Legacy Wiki]]'''
* '''Users of BinAC 1 must''' [[Registration/bwForCluster/BinAC2|'''re-register for BinAC 2''']] (only step C necessary). You keep your existing projects (Rechenvorhaben).
* '''[[BinAC2/Migrate BinAC 1 workspaces to BinAC 2 workspaces|Migrate BinAC 1 workspaces to BinAC 2 workspaces]]'''
* '''[[BinAC2/Migrate Moab to Slurm jobs|Migrate Moab/Torque to Slurm jobs]]'''
|}


* Operating System: Rocky Linux 9.5
* Queuing System: [https://slurm.schedmd.com/documentation.html Slurm] (see [[BinAC2/Slurm]] for help)
* (Scientific) Libraries and Software: [[Environment Modules]]


{| style=" background:#FEF4AB; width:100%;"
== Compute Nodes ==
| style="padding:8px; background:#FFE856; font-size:120%; font-weight:bold; text-align:left" | News and Events

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:
{| class="wikitable"
|-
! style="width:10%"|
! style="width:10%"| Standard
! style="width:10%"| High-Mem
! style="width:10%"| GPU (A30)
! style="width:10%"| GPU (A100)
! style="width:10%"| GPU (H200)
|-
|-
|
!scope="column"| Quantity
* [https://uni-tuebingen.de/de/274923 11th bwHPC Symposium - September 23rd, Tübingen]
| 180
<!--TODO* [http://vis01.binac.uni-tuebingen.de/ Cluster Status and Usage]-->
| 14 / 2
| 32
| 8
| 4
|-
!scope="column" | Processors
| 2 x [https://www.amd.com/de/products/processors/server/epyc/7003-series/amd-epyc-7543.html AMD EPYC Milan 7543]
| 2 x [https://www.amd.com/de/products/processors/server/epyc/7003-series/amd-epyc-7443.html AMD EPYC Milan 7443] / 2 x [https://www.amd.com/en/products/processors/server/epyc/7003-series/amd-epyc-75f3.html AMD EPYC Milan 75F3]
| 2 x [https://www.amd.com/de/products/processors/server/epyc/7003-series/amd-epyc-7543.html AMD EPYC Milan 7543]
| 2 x [https://www.amd.com/de/products/processors/server/epyc/7003-series/amd-epyc-7543.html AMD EPYC Milan 7543]
| 2 x [https://www.amd.com/de/products/processors/server/epyc/9005-series/amd-epyc-9555.html AMD EPYC Milan 9555]
|-
!scope="column" | Processor Base Frequency (GHz)
| 2.80
| 2.85 / 2.95
| 2.80
| 2.80
| 3.20
|-
!scope="column" | Number of Physical Cores / Hypertreads
| 64 / 128
| 48 / 96 // 64 / 128
| 64 / 128
| 64 / 128
| 128 / 256
|-
!scope="column" | Working Memory (GB)
| 512
| 2048
| 512
| 512
| 1536
|-
!scope="column" | Local Disk (GiB)
| 450 (NVMe-SSD)
| 14000 (NVMe-SSD)
| 450 (NVMe-SSD)
| 14000 (NVMe-SSD)
| 28000 (NVMe-SSD)
|-
!scope="column" | Interconnect
| HDR 100 IB (84 nodes) / 100GbE (96 nodes)
| 100GbE
| 100GbE
| 100GbE
| HDR 200 IB + 100GbE
|-
!scope="column" | Coprocessors
| -
| -
| 2 x [https://www.nvidia.com/de-de/data-center/products/a30-gpu/ NVIDIA A30 (24 GB ECC HBM2, NVLink)]
| 4 x [https://www.nvidia.com/de-de/data-center/a100/ NVIDIA A100 (80 GB ECC HBM2e)]
| 4 x [https://www.nvidia.com/de-de/data-center/h200/ NVIDIA H200 NVL (141 GB ECC HBM3e, NVLink)]
|}
|}


{| style=" background:#eeeefe; width:100%;"
= Network =
| style="padding:8px; background:#dedefe; font-size:120%; font-weight:bold; text-align:left" | Training & Support

The compute nodes and the parallel file system are connected via 100GbE ethernet</br>
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 <code>--constraint=ib</code>.

= 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 <code>/pfs/10</code> 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 <code>/pfs/10/project</code> that is accessible for all members of the compute project.
Each user can create workspaces under <code>/pfs/10/work</code> 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.

{| class="wikitable"
|-
! style="width:10%"|
! style="width:10%"| <tt>$HOME</tt>
! style="width:10%"| project
! style="width:10%"| work
! style="width:10%"| <tt>$TMPDIR</tt>
|-
|-
|
!scope="column" | Visibility
* [[BinAC2/Getting_Started|Getting Started]]
| global
* [https://training.bwhpc.de E-Learning Courses]
| global
* [[BinAC2/Support|Contact and Support]]
| global
* Send [[Feedback|Feedback]] about Wiki pages
| node local
|-
!scope="column" | Lifetime
| permanent
| permanent
| work space lifetime (max. 30 days, max. 5 extensions)
| batch job walltime
|-
!scope="column" | 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)
|-
!scope="column" | 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
|-
!scope="column" | [https://en.wikipedia.org/wiki/Disk_quota#Quotas Quotas]
| 40 GB per user
| not yet, maybe in the future
| none
| none
|-
!scope="column" | Backup
| yes (nightly)
| '''no'''
| '''no'''
| '''no'''
|}
|}


{| style=" background:#deffee; width:100%;"
global : all nodes access the same file system
| style="padding:8px; background:#cef2e0; font-size:120%; font-weight:bold; text-align:left" | User Documentation
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

{| class="wikitable" style="color:red; background-color:#ffffcc;" cellpadding="10"
|
|
* [[Registration/bwForCluster|Registration]]
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.</br>
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.</br>
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.</br>
Please consider to use on of the remote storage facilities like [https://wiki.bwhpc.de/e/SDS@hd SDS@hd], [https://uni-tuebingen.de/einrichtungen/zentrum-fuer-datenverarbeitung/projekte/laufende-projekte/bwsfs bwSFS], [https://www.scc.kit.edu/en/services/lsdf.php LSFD Online Storage] or the [https://www.rda.kit.edu/english/ bwDataArchive] to back up your valuable data.
|}


* [[BinAC2/Login|Login]]


* [[BinAC2/Hardware_and_Architecture|Hardware and Architecture]]
=== Home ===
** [[BinAC2/Hardware_and_Architecture#Compute_Nodes|Node Specifications]]
** [[BinAC2/Hardware_and_Architecture#File_Systems|File Systems and Workspaces]]
* Usage of [[BinAC2/Software|Software]] on BinAC 2
** For available Software Modules see [https://www.bwhpc.de/software.php bwhpc.de Software Search] (select bwForCluster BinAC 2)
** Create Software Environments with [[Development/Conda|Conda]]
** Use [[BinAC2/Software/Nextflow|nf-core Nextflow pipelines]]
** See [[Development]] for info about compiler and parallelization


* [[BinAC2/Slurm|Batch System (SLURM)]]
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.
** [[BinAC2/SLURM_Partitions|SLURM Partitions]]
Because the backup space is limited we enforce a quota of 40GB on the home directories.


|}
'''NOTE:'''
{| style=" background:#e6e9eb; width:100%;"
Compute jobs on nodes must not write temporary data to $HOME.
| style="padding:8px; background:#d1dadf; font-size:120%; font-weight:bold; text-align:left" | Cluster Funding
Instead they should use the local $TMPDIR directory for I/O-heavy use cases
and work spaces for less I/O intense multinode-jobs.

<!--
Current disk usage on home directory and quota status can be checked with the '''diskusage''' command:
$ diskusage
User Used (GB) Quota (GB) Used (%)
------------------------------------------------------------------------
<username> 4.38 100.00 4.38
-->
=== Project ===

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

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

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 <code>/pfs/10/project</code> is pure capacity, not speed.

=== Workspaces ===

Data on the fast storage pool at <code>/pfs/10/work</code> 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 <code>/pfs/10/work</code>.
Please move data to <code>/pfs/10/project</code> when you don't need it on the fast storage any more.

Each user should create workspaces at <code>/pfs/10/work</code> through the workspace tools

You can find more info on workspace tools on our general page:

:: &rarr; '''[[Workspace]]s'''

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: <code>ws_allocate -h.</code>
{| class="wikitable"
|-
!style="width:30%" | Command
!style="width:70%" | Action
|-
|<code>ws_allocate mywork 30</code>
|Allocate a work space named "mywork" for 30 days.
|-
|<code>ws_allocate myotherwork</code>
|Allocate a work space named "myotherwork" with maximum lifetime.
|-
|<code>ws_list -a</code>
|List all your work spaces.
|-
|<code>ws_find mywork</code>
|Get absolute path of work space "mywork".
|-
|<code>ws_extend mywork 30</code>
|Extend life me of work space mywork by 30 days from now.
|-
|<code>ws_release mywork</code>
|Manually erase your work space "mywork". Please remove directory content first.
|-
|-
|
* Please [[BinAC2/Acknowledgement|acknowledge]] the cluster in your publications.
|}
|}

=== 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 <code>$TMPDIR</code>, which points to <code>/scratch/<jobID></code>.

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 (<code>WORK</code> and <code>PROJECT</code>) 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 <code>WORK</code>.


=== SDS@hd ===

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

To access your Speichervorhaben, the export to BinAC 2 must first be enabled by the SDS@hd-Team. Please contact [mailto:sds-hd-support@urz.uni-heidelberg.de 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 [https://wiki.bwhpc.de/e/SDS@hd/Access/NFS#Access_your_data SDS documentation].

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

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

Latest revision as of 14:46, 29 September 2025

BinAC2 Logo RGB subtitel.svg

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

BinAC 1 -> BinAC 2 Migration


News and Events
Training & Support
User Documentation
Cluster Funding
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