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Migrate to CPU Cluster Barnard (Outdated)

Note

We highly recommand to first read the entire page carefully, and then execute the steps.

The migration can only be successful as a joint effort of HPC team and users. We value your feedback. Please provide it directly via our ticket system. For better processing, please add "Barnard:" as a prefix to the subject of the support ticket.

Login to Barnard

You use login[1-4].barnard.hpc.tu-dresden.de to access the system from campus (or VPN). In order to verify the SSH fingerprints of the login nodes, please refer to the page Fingerprints.

All users have new empty HOME file systems, this means you have first to ...

... install your public SSH key on Barnard
  • Please create a new SSH keypair with ed25519 encryption, secured with a passphrase. Please refer to this page for instructions.
  • After login, add the public key to your .ssh/authorized_keys file on Barnard.

Data Management and Data Transfer

Filesystems on Barnard

Our new HPC system Barnard also comes with two new Lustre filesystems, namely /data/horse and /data/walrus. Both have a capacity of 20 PB, but differ in performance and intended usage, see below. In order to support the data life cycle management, the well-known workspace concept is applied.

  • The /project filesystem is the same on Taurus and Barnard (mounted read-only on the compute nodes).
  • The new work filesystem is /data/horse.
  • The slower /data/walrus can be considered as a substitute for the old /warm_archive- mounted read-only on the compute nodes. It can be used to store e.g. results.

Workspaces on Barnard

The filesystems /data/horse and /data/walrus can only be accessed via workspaces. Please refer to the workspace page, if you are not familiar with the workspace concept and the corresponding commands. You can find the settings for workspaces on these two filesystems in the section Settings for Workspaces.

Data Migration to New Filesystems

Since all old filesystems of Taurus will be shutdown by the end of 2023, your data needs to be migrated to the new filesystems on Barnard. This migration comprises

  • your personal /home directory,
  • your workspaces on /ssd, /beegfs and /scratch.

It's your turn

You are responsible for the migration of your data. With the shutdown of the old filesystems, all data will be deleted.

Make a plan

We highly recommand to take some minutes for planing the transfer process. Do not act with precipitation.

Please do not copy your entire data from the old to the new filesystems, but consider this opportunity for cleaning up your data. E.g., it might make sense to delete outdated scripts, old log files, etc., and move other files, e.g., results, to the /data/walrus filesystem.

Generic login

In the following we will use the generic login marie and workspace numbercrunch (cf. content rules on generic names). Please make sure to replace it with your personal login.

We have four new Datamover nodes that have mounted all filesystems of the old Taurus and new Barnard system. Do not use the Datamover from Taurus, i.e., all data transfer need to be invoked from Barnard! Thus, the very first step is to login to Barnard.

The command dtinfo will provide you the mount points of the old filesystems

marie@barnard$ dtinfo
[...]
directory on datamover      mounting clusters   directory on cluster

/data/old/home              Taurus              /home
/data/old/lustre/scratch2   Taurus              /scratch
/data/old/lustre/ssd        Taurus              /lustre/ssd
[...]

In the following, we will provide instructions with comprehensive examples for the data transfer of your data to the new /home filesystem, as well as the working filesystems /data/horse and /data/walrus.

Migration of Your Home Directory

Your personal (old) home directory at Taurus will not be automatically transferred to the new Barnard system. Please do not copy your entire home, but clean up your data. E.g., it might make sense to delete outdated scripts, old log files, etc., and move other files to an archive filesystem. Thus, please transfer only selected directories and files that you need on the new system.

The steps are as follows:

  1. Login to Barnard, i.e.,

    ssh login[1-4].barnard.tu-dresden.de

  2. The command dtinfo will provide you the mountpoint

    marie@barnard$ dtinfo
[...]
directory on datamover      mounting clusters   directory on cluster

/data/old/home              Taurus              /home
[...]

  3. Use the dtls command to list your files on the old home directory

    marie@barnard$ dtls /data/old/home/marie
[...]

  4. Use the dtcp command to invoke a transfer job, e.g.,

    marie@barnard$ dtcp --recursive /data/old/home/marie/<useful data> /home/marie/

Note, please adopt the source and target paths to your needs. All available options can be queried via dtinfo --help.

Warning

Please be aware that there is no synchronisation process between your home directories at Taurus and Barnard. Thus, after the very first transfer, they will become divergent.

Please follow these instructions for transferring you data from ssd, beegfs and scratch to the new filesystems. The instructions and examples are divided by the target not the source filesystem.

This migration task requires a preliminary step: You need to allocate workspaces on the target filesystems.

Preliminary Step: Allocate a workspace

Both /data/horse/ and /data/walrus can only be used with workspaces. Before you invoke any data transer from the old working filesystems to the new ones, you need to allocate a workspace first.

The command ws_list -l lists the available and the default filesystem for workspaces.

marie@barnard$ ws_list -l
available filesystems:
horse (default)
walrus

As you can see, /data/horse is the default workspace filesystem at Barnard. I.e., if you want to allocate, extend or release a workspace on /data/walrus, you need to pass the option --filesystem=walrus explicitly to the corresponding workspace commands. Please refer to our workspace documentation, if you need refresh your knowledge.

The most simple command to allocate a workspace is as follows

marie@barnard$ ws_allocate numbercrunch 90

Please refer to the table holding the settings (cf. subsection workspaces on Barnard) for the max. duration and ws_allocate --help for all available options.

Migration to work filesystem /data/horse

We are synchronizing the old /scratch to /data/horse/lustre/scratch2/ (last: October 18). If you transfer data from the old /scratch to /data/horse, it is sufficient to use dtmv instead of dtcp since this data has already been copied to a special directory on the new horse filesystem. Thus, you just need to move it to the right place (the Lustre metadata system will update the correspoding entries).

The workspaces within the subdirectories ws/0 and ws/1, respectively. A corresponding data transfer using dtmv looks like

marie@barnard$ dtmv /data/horse/lustre/scratch2/ws/0/marie-numbercrunch/<useful data> /data/horse/ws/marie-numbercrunch/

Please do NOT copy those data yourself. Instead check if it is already sychronized to /data/horse/lustre/scratch2/ws/0/marie-numbercrunch.

In case you need to update this (Gigabytes, not Terabytes!) please run dtrsync like in

marie@barnard$ dtrsync -a /data/old/lustre/scratch2/ws/0/marie-numbercrunch/<useful data>  /data/horse/ws/marie-numbercrunch/

The old ssd filesystem is mounted at /data/old/lustre/ssd on the datamover nodes and the workspaces are within the subdirectory ws/. A corresponding data transfer using dtcp looks like

marie@barnard$ dtcp --recursive /data/old/lustre/ssd/ws/marie-numbercrunch/<useful data> /data/horse/ws/marie-numbercrunch/

The old beegfs filesystem is mounted at /data/old/beegfs on the datamover nodes and the workspaces are within the subdirectories ws/0 and ws/1, respectively. A corresponding data transfer using dtcp looks like

marie@barnard$ dtcp --recursive /data/old/beegfs/ws/0/marie-numbercrunch/<useful data> /data/horse/ws/marie-numbercrunch/
Migration to /data/walrus

We are synchronizing the old /scratch to /data/horse/lustre/scratch2/ (last: October 18). The old scratch filesystem has been already synchronized to /data/horse/lustre/scratch2 nodes and the workspaces are within the subdirectories ws/0 and ws/1, respectively. A corresponding data transfer using dtcp looks like

marie@barnard$ dtcp --recursive /data/horse/lustre/scratch2/ws/0/marie-numbercrunch/<useful data> /data/walrus/ws/marie-numbercrunch/

Please do NOT copy those data yourself. Instead check if it is already sychronized to /data/horse/lustre/scratch2/ws/0/marie-numbercrunch.

In case you need to update this (Gigabytes, not Terabytes!) please run dtrsync like in

marie@barnard$ dtrsync -a /data/old/lustre/scratch2/ws/0/marie-numbercrunch/<useful data>  /data/walrus/ws/marie-numbercrunch/

The old ssd filesystem is mounted at /data/old/lustre/ssd on the datamover nodes and the workspaces are within the subdirectory ws/. A corresponding data transfer using dtcp looks like

marie@barnard$ dtcp --recursive /data/old/lustre/ssd/<useful data> /data/walrus/ws/marie-numbercrunch/

The old beegfs filesystem is mounted at /data/old/beegfs on the datamover nodes and the workspaces are within the subdirectories ws/0 and ws/1, respectively. A corresponding data transfer using dtcp looks like

marie@barnard$ dtcp --recursive /data/old/beegfs/ws/0/marie-numbercrunch/<useful data> /data/walrus/ws/marie-numbercrunch/
Migration from /warm_archive

We are synchronizing the old /warm_archive to /data/walrus/warm_archive/. Therefor, it can be sufficient to use dtmv instead of dtcp (No data will be copied, but the Lustre system will update the correspoding metadata entries). A corresponding data transfer using dtmv looks like

marie@barnard$ dtmv /data/walrus/warm_archive/ws/marie-numbercrunch/<useful data> /data/walrus/ws/marie-numbercrunch/

Please do NOT copy those data yourself. Instead check if it is already sychronized to /data/walrus/warm_archive/ws.

In case you need to update this (Gigabytes, not Terabytes!) please run dtrsync like in

marie@barnard$ dtrsync -a /data/old/warm_archive/ws/marie-numbercrunch/<useful data>  /data/walrus/ws/marie-numbercrunch/

When the last compute system will have been migrated the old file systems will be set write-protected and we start a final synchronization (scratch+walrus). The target directories for synchronization /data/horse/lustre/scratch2/ws and /data/walrus/warm_archive/ws/ will not be deleted automatically in the meantime.

Software

Barnard is running on Linux RHEL 8.7. All application software was re-built consequently using Git and CI/CD pipelines for handling the multitude of versions.

We start with release/23.10 which is based on software requests from user feedback of our HPC users. Most major software versions exist on all hardware platforms.

Please use module spider to identify the software modules you need to load.

Slurm

  • We are running the most recent Slurm version.
  • You must not use the old partition names.
  • Not all things are tested.

Note that most nodes on Barnard don't have a local disk and space in /tmp is very limited. If you need a local disk request this with the Slurm feature --constraint=local_disk to sbatch, salloc, and srun.