Workspaces/Advanced Features: Difference between revisions

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== Detailed Topics ==
== Multiple Filesystem Locations ==


=== Commands ===
{| class="wikitable"
|-
!style="width:40%" | Works on cluster
!style="width:10%" | bwUC 3.0
!style="width:10%" | BinAC2
!style="width:10%" | Helix
!style="width:10%" | JUSTUS 2
!style="width:10%" | NEMO2
|-
|<tt>-F</tt> option (multiple filesystems)
|style="background-color:#90EE90; text-align:center;" | ✓
|style="background-color:#FFB6C1; text-align:center;" | ✗
|style="background-color:#FFB6C1; text-align:center;" | ✗
|style="background-color:#FFB6C1; text-align:center;" | ✗
|style="background-color:#FFB6C1; text-align:center;" | ✗
|}


* '''[[Workspaces/Advanced_Features/ws_allocate|ws_allocate]]''' - Create and extend workspaces (detailed options)
Some clusters offer multiple filesystem locations for workspaces with different characteristics:
* '''[[Workspaces/Advanced_Features/ws_list|ws_list]]''' - List workspaces (sorting, filtering)
* '''[[Workspaces/Advanced_Features/ws_find|ws_find]]''' - Find workspace paths for scripts
* '''[[Workspaces/Advanced_Features/ws_extend|ws_extend]]''' - Extend workspace lifetime
* '''[[Workspaces/Advanced_Features/ws_release|ws_release]]''' - Release (delete) workspaces with immediate deletion options
* '''[[Workspaces/Advanced_Features/ws_restore|ws_restore]]''' - Restore expired or released workspaces
* '''[[Workspaces/Advanced_Features/ws_register|ws_register]]''' - Create symbolic links to workspaces


=== Configuration & Features ===
'''bwUniCluster 3.0:'''
* Default workspace filesystem (Lustre)
* Flash-based workspace filesystem (<tt>ffuc</tt>) - for KIT/HoreKa users only
** Lower latency and better performance for small files
** SSDs instead of hard disks
** Shared between bwUniCluster 3.0 and HoreKa


* '''[[Workspaces/Advanced_Features/Filesystems|Multiple Filesystem Locations]]''' - Choosing the right filesystem for your workload
'''Example creating workspace on flash filesystem:'''
* '''[[Workspaces/Advanced_Features/Reminders|Reminders & Configuration]]''' - Email reminders and ~/.ws_user.conf setup
* '''[[Workspaces/Advanced_Features/Sharing|Sharing Workspaces]]''' - Group workspaces, ws_share, ACLs, Unix permissions
* '''[[Workspaces/Advanced_Features/Quotas|Quotas & Limits]]''' - Cluster-specific limits and checking quotas


=== Best Practices ===
$ ws_allocate -F ffuc myworkspace 60


* '''[[Workspaces/Advanced_Features/Best_Practices|Best Practices]]''' - Recommendations for different use cases
Use <tt>ws_list -l</tt> or <tt>ws_find -l</tt> to see available filesystem locations on your cluster.


== Quick Navigation ==
== ws_allocate - Create and Extend Workspaces ==


=== By Task ===
{| class="wikitable"
|-
!style="width:40%" | Works on cluster
!style="width:10%" | bwUC 3.0
!style="width:10%" | BinAC2
!style="width:10%" | Helix
!style="width:10%" | JUSTUS 2
!style="width:10%" | NEMO2
|-
|<tt>ws_allocate -x -u</tt> (extend other user's workspace)
| style="text-align:center;" |
| style="text-align:center;" |
| style="text-align:center;" |
| style="text-align:center;" |
|style="background-color:#90EE90; text-align:center;" | ✓
|}


'''Creating and Managing:'''
=== Basic Usage ===
* Create workspace → [[Workspaces#Create_Workspace|Basic]] | [[Workspaces/Advanced_Features/ws_allocate|Advanced]]
* List workspaces → [[Workspaces#List_Your_Workspaces|Basic]] | [[Workspaces/Advanced_Features/ws_list|Advanced]]
* Extend lifetime → [[Workspaces#Extend_Workspace_Lifetime|Basic]] | [[Workspaces/Advanced_Features/ws_extend|Advanced]]
* Release workspace → [[Workspaces#Release_.28Delete.29_Workspace|Basic]] | [[Workspaces/Advanced_Features/ws_release|Advanced]]
* Restore workspace → [[Workspaces#Restore_Workspace|Basic]] | [[Workspaces/Advanced_Features/ws_restore|Advanced]]


'''Collaboration:'''
Execution of:
* Work with groups → [[Workspaces#Work_with_Groups_.28Share_Workspaces.29|Basic]] | [[Workspaces/Advanced_Features/Sharing#Group_Workspaces|Advanced]]
* Share with users → [[Workspaces/Advanced_Features/Sharing#Sharing_with_ws_share|ws_share]] | [[Workspaces/Advanced_Features/Sharing#ACLs:_Access_Control_Lists|ACLs]] | [[Workspaces/Advanced_Features/Sharing#Regular_Unix_Permissions|Unix Permissions]]


'''Configuration:'''
$ ws_allocate myWs 30
* Email reminders → [[Workspaces/Advanced_Features/Reminders|Reminders]]
* Default settings → [[Workspaces/Advanced_Features/Reminders#Configuration_File:_.7E.2F.ws_user.conf|~/.ws_user.conf]]
* Workspace links → [[Workspaces/Advanced_Features/ws_register|ws_register]]


'''Resources:'''
e.g. returns:
* Filesystem selection → [[Workspaces/Advanced_Features/Filesystems|Filesystems]]
* Check quotas → [[Workspaces/Advanced_Features/Quotas#Checking_Workspace_Quotas|Quota Commands]]
Workspace created. Duration is 720 hours.
* Cluster limits → [[Workspaces/Advanced_Features/Quotas|Quotas & Limits]]
Further extensions available: 3
/work/workspace/scratch/username-myWs-0


=== By Experience Level ===
The command returns the path to the new directory, which can be captured in a variable:


'''Beginners:'''
$ SCRDIR=$(ws_allocate myWs 10)
* Start with the main [[Workspaces]] guide
* Review [[Workspaces/Advanced_Features/Best_Practices|Best Practices]]


'''Intermediate Users:'''
'''Important:''' Creating a workspace a second time with the same command is a no-operation - it always returns the same path. This makes it safe and encouraged to use such a line in batch jobs which are part of a series of jobs working on the same data, no matter if the job was running before or not.
* [[Workspaces/Advanced_Features/Filesystems|Choose optimal filesystem]]
* [[Workspaces#Work_with_Groups_.28Share_Workspaces.29|Set up group workspaces]]
* [[Workspaces/Advanced_Features/ws_allocate#Using_Workspaces_in_Batch_Jobs|Use in batch jobs]]
* [[Workspaces/Advanced_Features/ws_restore#Helix-specific_-_Workspace_Snapshots|Snapshot recovery (Helix)]]


'''Advanced Users:'''
=== All Options and When to Use Them ===
* [[Workspaces/Advanced_Features/Sharing|Advanced sharing methods]] (ACLs)

* [[Workspaces/Advanced_Features/ws_release#Immediate_Deletion_.28Free_Quota_Instantly.29|Immediate deletion for quota management]]
{| class="wikitable"
* Set up [[Workspaces/Advanced_Features/Reminders#Configuration_File:_.7E.2F.ws_user.conf|~/.ws_user.conf]]
|-
!style="width:20%" | Option
!style="width:40%" | Description
!style="width:40%" | When to Use
|-
|<tt>-F <filesystem></tt>
|Specify the filesystem where the workspace should be created
|'''Optional''' - Most clusters have only one default filesystem. Use only when you need specific storage characteristics (speed, capacity) or to balance load across multiple filesystems. List available locations with <tt>ws_list -l</tt> or <tt>ws_find -l</tt>
|-
|<tt>-g</tt>
|Create a group-readable workspace
|'''Recommended''' when working in a team and others need to read your data. The workspace will be visible to group members with <tt>ws_list -g</tt>
|-
|<tt>-G <groupname></tt>
|Create a group-writable workspace with sticky bit
|'''Recommended''' for collaborative work where team members need to write data. Ensures all created files belong to the group. Can be set as default in <tt>~/.ws_user.conf</tt>
|-
|<tt>-m <mailaddress></tt>
|Set email address for reminders
|'''Optional''' - Email addresses come from your identity provider. Only use this option to override with a different address. Can be set as default in <tt>~/.ws_user.conf</tt>
|-
|<tt>-r <days></tt>
|Set reminder to be sent n days before expiration
|'''Optional''' - Email reminders are sent automatically. Use this only to customize when the reminder starts (e.g., 3, 5, or 7 days before). Can be set as default in <tt>~/.ws_user.conf</tt>
|-
|<tt>-x</tt>
|Extend an existing workspace
|Use when you need more time. Each extension consumes one of the available extensions
|-
|<tt>-u <username></tt>
|Used with <tt>-x</tt> to extend another user's workspace
|Use when a group member is absent and their shared workspace needs extension. Requires group write access <tt>-G</tt>
|-
|<tt>-c <comment></tt>
|Add a comment to the workspace
|Use to document the purpose of the workspace for yourself and collaborators
|-
|<tt>-d <duration></tt>
|Duration in days (alternative to positional argument)
|Use if you prefer explicit option syntax: <tt>ws_allocate -n myWs -d 30</tt>
|-
|<tt>-n <name></tt>
|Workspace name (alternative to positional argument)
|Use if you prefer explicit option syntax: <tt>ws_allocate -n myWs -d 30</tt>
|}

=== Duration Settings ===

If you do not specify a lifetime, a default lifetime will be used (see the [[Workspaces/Advanced_Features#Cluster-Specific_Workspace_Limits|Cluster-Specific Workspace Limits]])). The maximum lifetime may be limited by the operations team. If you specify a longer lifetime, it will be capped to the maximum, and you will see a message that it was changed.

For more information read the program's help: <tt>$ ws_allocate -h</tt> or <tt>man ws_allocate</tt>

== ws_list - List Workspaces ==

Beyond the basic options shown in the main [[Workspaces]] guide, <tt>ws_list</tt> supports additional sorting and filtering:

'''Sorting options:'''
* <tt>-N</tt> - Sort by name (alphabetical)
* <tt>-C</tt> - Sort by creation date
* <tt>-R</tt> - Sort by remaining time (see what expires soon)
* <tt>-r</tt> - Reverse sort order

'''Display format options:'''
* <tt>-s</tt> - Short format (only names, good for scripts)
* <tt>-t</tt> - Terse format
* <tt>-v</tt> - Verbose format with all metadata

'''Filtering options:'''
* <tt>-F <location></tt> - List workspaces on specific filesystem only
* <tt>-g</tt> - List group workspaces (if you're in the same group)
* <tt>-l</tt> - List available filesystem locations

'''Example listing group workspaces:'''

$ ws_list -g

This shows all workspaces that were created with <tt>-g</tt> or <tt>-G</tt> flags by members of your group.

'''Note:''' To list expired workspaces that can be restored, use <tt>ws_restore -l</tt>. See [[#ws_restore_-_Restore_Expired_Workspace|ws_restore]] for details.

For more information: <tt>$ ws_list -h</tt> or <tt>man ws_list</tt>

== ws_find - Find Workspace Path ==

<tt>ws_find</tt> returns the full path to a workspace, useful for scripts and automation.

'''Basic usage:'''

$ ws_find myWs

'''Options:'''
* <tt>-F <filesystem></tt> - Search workspace on specific filesystem
* <tt>-l</tt> - List valid filesystem names

'''Example in scripts:'''

$ WORKSPACE=$(ws_find myProject)
$ cd "$WORKSPACE"

For more information: <tt>$ ws_find -h</tt> or <tt>man ws_find</tt>

== ws_extend - Extend Workspace Lifetime ==

Beyond the basic extension shown in the main [[Workspaces]] guide:

* <tt>-F filesystem</tt> - Extend workspace on specific filesystem
* <tt>ws_allocate -x</tt> - Alternative command for extension
* You can shorten workspace lifetime even if no extensions are available

'''Group workspace extensions:'''

Group members can extend group-writable workspaces (requires group write access <tt>ws_allocate -G</tt>):

$ ws_allocate -x -u <username> <workspace_id> <days>

Replace <tt><username></tt> with the workspace owner's username. This is useful when the workspace owner is unavailable and the workspace needs to be extended.

For more information: <tt>$ ws_extend -h</tt> or <tt>man ws_extend</tt>

== Getting Reminders ==

{| class="wikitable"
|-
!style="width:40%" | Works on cluster
!style="width:10%" | bwUC 3.0
!style="width:10%" | BinAC2
!style="width:10%" | Helix
!style="width:10%" | JUSTUS 2
!style="width:10%" | NEMO2
|-
|Email reminders
|style="background-color:#90EE90; text-align:center;" | ✓
|style="background-color:#90EE90; text-align:center;" | ✓
|style="background-color:#90EE90; text-align:center;" | ✓
|style="background-color:#90EE90; text-align:center;" | ✓
|style="background-color:#90EE90; text-align:center;" | ✓
|-
|<tt>ws_send_ical</tt> (calendar reminders)
|style="background-color:#90EE90; text-align:center;" | ✓
|style="background-color:#FFB6C1; text-align:center;" | ✗
|style="background-color:#90EE90; text-align:center;" | ✓
|style="background-color:#FFB6C1; text-align:center;" | ✗
|style="background-color:#FFB6C1; text-align:center;" | ✗
|}

'''Email reminders:''' Sent automatically using email addresses from your identity provider. You can customize the reminder timing with <tt>-r <days></tt>:

$ ws_allocate -r 7 myWs 30 # Reminder 7 days before expiry
$ ws_allocate -r 3 -m custom@example.com myWs 30 # Custom timing and different email address

'''Update reminder only''' (without extending workspace):

$ ws_allocate -r <days> -x <workspace> 0 # Update reminder time
$ ws_allocate -r <days> -u <username> -x <workspace> 0 # Update reminder time and take over
# another user's workspace reminders

This is useful when you want to change the reminder timing without extending the workspace lifetime, or when taking over responsibility for reminders on a colleague's workspace.

'''Calendar reminder''' (bwUniCluster 3.0, Helix):

$ ws_send_ical <workspace> <email>

=== ~/.ws_user.conf Configuration File ===

{| class="wikitable"
|-
!style="width:40%" | Works on cluster
!style="width:10%" | bwUC 3.0
!style="width:10%" | BinAC2
!style="width:10%" | Helix
!style="width:10%" | JUSTUS 2
!style="width:10%" | NEMO2
|-
|<tt>~/.ws_user.conf</tt> configuration file
|style="background-color:#90EE90; text-align:center;" | ✓
|style="text-align:center;" |
|style="text-align:center;" |
|style="text-align:center;" |
|style="background-color:#90EE90; text-align:center;" | ✓
|}

You can set defaults in <tt>~/.ws_user.conf</tt> (YAML format) to avoid typing the same options repeatedly:

<pre>
duration: 30 # Default workspace lifetime (first line must not start with #!)
reminder: 5 # Days before expiration to send reminder
groupname: projectgroup # Default group for -G option (e.g., bw11a000)
# mail: custom@example.com # Optional - only to override email from identity provider
</pre>

'''Important:''' Some versions mistakenly interpret a leading <tt>#</tt> comment as email. '''First line must be a setting''', not a comment. Inline comments are fine.

'''Benefits:'''
* Simplifies commands: <tt>ws_allocate myWs</tt> instead of <tt>ws_allocate -r 5 -G groupname myWs 30</tt>
* Ensures consistent settings across all operations
* Automatic group collaboration when <tt>groupname</tt> is set

== Cooperative Usage (Group Workspaces and Sharing) ==

When working in teams, workspaces can be shared in multiple ways.

<div style="border: 3px solid red; padding: 15px; background-color: #ffe6e6; margin: 10px 0;">
'''WARNING: NEVER use chmod 777 or a+rwx on workspaces!'''

Do '''NOT''' make your workspace readable or writable by everyone (<tt>chmod 777</tt>, <tt>chmod a+rwx</tt>, or <tt>chmod o+rwx</tt>). This is a severe security risk:
* Anyone on the system can read, modify, or delete your data
* Malicious users can inject code into your workspace
* Your data and results become unreliable
* You violate security policies and may lose access privileges

'''Always use proper sharing methods:''' Use <tt>-g</tt>/<tt>-G</tt> flags, <tt>ws_share</tt>, or group-based permissions instead.
</div>

'''Important:''' Not all sharing methods are available on all clusters. The availability depends on:
* Filesystem type and ACL support
* Cluster-specific workspace tool configuration
* Unix group setup and permissions

If one sharing method doesn't work on your cluster, try an alternative approach. The <tt>-g</tt> and <tt>-G</tt> flags are most widely supported.

=== Group Workspaces ===

{| class="wikitable"
|-
!style="width:40%" | Works on cluster
!style="width:10%" | bwUC 3.0
!style="width:10%" | BinAC2
!style="width:10%" | Helix
!style="width:10%" | JUSTUS 2
!style="width:10%" | NEMO2
|-
|<tt>-g</tt> option (group-readable)
|style="text-align:center;" |
|style="text-align:center;" |
|style="text-align:center;" |
|style="text-align:center;" |
|style="background-color:#90EE90; text-align:center;" | ✓
|-
|<tt>-G</tt> option (group-writable)
|style="text-align:center;" |
|style="text-align:center;" |
|style="text-align:center;" |
|style="text-align:center;" |
|style="background-color:#90EE90; text-align:center;" | ✓
|}

When a workspace is created with <tt>-g</tt> it becomes a group workspace that is visible to others with <tt>ws_list -g</tt> (if in same group), and is group readable:

$ ws_allocate -g myWs 30

When created with <tt>-G <groupname></tt> the workspace becomes writable as well, and gets group sticky bit:

$ ws_allocate -G projectgroup myWs 30

The group can be specified in the <tt>~/.ws_user.conf</tt> file as well.

'''Important:''' Group members can extend group-writable workspaces (created with <tt>-G</tt>) even if the original creator is absent:

$ ws_allocate -x -u <username> <workspace_id> <days>

This requires group write access to the workspace. This is useful when the workspace owner is unavailable and the workspace needs to be extended.

'''Recommendations:'''
* Use <tt>-g</tt> when team members only need to read your results
* Use <tt>-G</tt> for collaborative work where everyone writes data
* Set <tt>groupname</tt> in <tt>~/.ws_user.conf</tt> if you always work with the same group

=== Sharing with ws_share ===

{| class="wikitable"
|-
!style="width:40%" | Works on cluster
!style="width:10%" | bwUC 3.0
!style="width:10%" | BinAC2
!style="width:10%" | Helix
!style="width:10%" | JUSTUS 2
!style="width:10%" | NEMO2
|-
|<tt>ws_share</tt> command (ACL-based)
| style="text-align:center;" |
| style="text-align:center;" |
| style="text-align:center;" |
| style="text-align:center;" |
|style="background-color:#90EE90; text-align:center;" | ✓
|}

With <tt>ws_share</tt> you can share workspaces with users outside your group, using ACLs (if supported by underlying filesystem).

'''Note:''' This feature requires ACL support on the filesystem. If <tt>ws_share</tt> doesn't work on your cluster, use manual ACL commands (<tt>setfacl</tt>) or fall back to Unix group permissions.

'''Share workspace with users:'''

$ ws_share share myWs username1 username2 # Grant read access to one or more users
$ ws_share share -F filesystem myWs user1 # Share on specific filesystem

'''Unshare workspace from users:'''

$ ws_share unshare myWs username1 # Remove access from specific user(s)
$ ws_share unshare-all myWs # Remove access from all users

'''List users with access:'''

$ ws_share list myWs # Show all users with read access

These operations are applied to all files and directories in the workspace.

'''Options:'''
* <tt>-F <filesystem></tt>, <tt>--filesystem</tt>: Specify the workspace filesystem
* <tt>-h</tt>, <tt>--help</tt>: Show help message

'''Recommendation:''' Use <tt>ws_share</tt> for selective sharing with individual users, especially when they are not in your Unix group.

=== ACLs: Access Control Lists ===

{| class="wikitable"
|-
!style="width:40%" | Works on cluster
!style="width:10%" | bwUC 3.0
!style="width:10%" | BinAC2
!style="width:10%" | Helix
!style="width:10%" | JUSTUS 2
!style="width:10%" | NEMO2
|-
|<tt>setfacl</tt>/<tt>getfacl</tt> (ACLs)
| style="text-align:center;" |
| style="text-align:center;" |
| style="text-align:center;" |
| style="text-align:center;" |
|style="background-color:#90EE90; text-align:center;" | ✓
|}

ACLs (Access Control Lists) provide fine-grained permission control beyond standard Unix permissions. They allow sharing with specific users and groups, and support default ACLs that new files automatically inherit.

'''Note:''' ACL support varies by filesystem. Not all clusters support ACLs on workspace filesystems. If ACL commands fail, use regular Unix permissions instead.

'''Key advantages:'''
* Share with specific users (not just groups)
* Default ACLs - new files automatically inherit permissions
* More flexible than Unix permissions

'''Note:''' ACLs take precedence over standard Unix permissions. View ACLs with <tt>ls -l</tt> (shown as "+" after permissions).

==== Quick Examples ====

Set workspace path in variable:

$ DIR=$(ws_find my_workspace)

'''View current ACLs:'''

$ getfacl "$DIR"

'''Important note on syntax:''' In all commands below, <tt>user:</tt> and <tt>group:</tt> are <tt>setfacl</tt> keywords. Replace <tt>username</tt> with the actual user login name (e.g., <tt>alice</tt>, <tt>jdoe</tt>) and <tt>groupname</tt> with the actual Unix group name (e.g., <tt>bw11a000</tt>).

'''Grant read-only access to a user:'''

$ setfacl -Rm user:username:rX,default:user:username:rX "$DIR"
# Example with actual username:
$ setfacl -Rm user:alice:rX,default:user:alice:rX "$DIR"

'''Grant read-write access to a user:'''

$ setfacl -Rm user:username:rwX,default:user:username:rwX "$DIR"
# Example with actual username:
$ setfacl -Rm user:jdoe:rwX,default:user:jdoe:rwX "$DIR"

'''Grant read-only access to a group:'''

$ setfacl -Rm group:groupname:rX,default:group:groupname:rX "$DIR"
# Example with actual groupname:
$ setfacl -Rm group:bw11a000:rX,default:group:bw11a000:rX "$DIR"

'''Remove all ACLs:'''

$ setfacl -Rb "$DIR"

==== Key Options ====

* <tt>-R</tt>: Apply to all files and subdirectories
* <tt>-m</tt>: Modify (add or change ACL entries)
* <tt>-b</tt>: Remove all ACL entries
* <tt>user:username:rwX</tt>: Set permissions for specific user (replace <tt>username</tt> with actual login)
* <tt>group:groupname:rwX</tt>: Set permissions for specific group (replace <tt>groupname</tt> with actual group)
* <tt>default:</tt> prefix: New files inherit these ACLs automatically
* <tt>r</tt>: Read permission
* <tt>w</tt>: Write permission
* <tt>X</tt>: Execute only on directories and already-executable files (capital X)

'''Important:''' Always use the <tt>default:</tt> prefix to ensure new files get the correct permissions automatically.

==== Recommendation ====

'''Always prefer <tt>ws_allocate -G</tt> or <tt>ws_share</tt> first.''' Use manual ACLs only for complex scenarios like:
* Sharing with specific users outside your group
* Different permissions for different users
* Fine-grained control not possible with <tt>-G</tt> or <tt>ws_share</tt>

=== Regular Unix Permissions ===

{| class="wikitable"
|-
!style="width:40%" | Works on cluster
!style="width:10%" | bwUC 3.0
!style="width:10%" | BinAC2
!style="width:10%" | Helix
!style="width:10%" | JUSTUS 2
!style="width:10%" | NEMO2
|-
|<tt>chmod</tt>/<tt>chgrp</tt> (Unix permissions)
|style="background-color:#90EE90; text-align:center;" | ✓
|style="background-color:#90EE90; text-align:center;" | ✓
|style="background-color:#90EE90; text-align:center;" | ✓
|style="background-color:#90EE90; text-align:center;" | ✓
|style="background-color:#90EE90; text-align:center;" | ✓
|}

Use standard Unix permissions with <tt>chmod</tt> and <tt>chgrp</tt> when you and your collaborators share a common Unix group.

'''CRITICAL WARNING:'''
* '''NEVER use chmod 777 or a+rwx''' - makes your data accessible to everyone on the system
* '''NEVER use chmod o+rwx or chmod o+w''' - allows anyone to modify or delete your files
* Only set group permissions (<tt>g+r</tt>, <tt>g+w</tt>) for your specific research group

==== Quick Examples ====

Set workspace path in variable:

$ DIR=$(ws_find my_workspace)

'''Read-only access for group:'''

$ chgrp -R mygroup "$DIR"
$ chmod -R g+rX "$DIR"

'''Read-write access for group:'''

$ chgrp -R mygroup "$DIR"
$ chmod -R g+rswX "$DIR"

==== Key Options ====

* <tt>-R</tt>: Apply to all files and subdirectories
* <tt>g+r</tt>: Group read permission
* <tt>g+w</tt>: Group write permission
* <tt>g+x</tt>: Group execute permission
* <tt>X</tt>: Execute only on directories and already-executable files (capital X)
* <tt>s</tt>: Setgid bit (set-group-ID) - new files inherit the directory's group ownership

'''Important:''' The setgid bit (<tt>g+s</tt>) ensures new files belong to the correct group, but their permissions depend on your <tt>umask</tt>. With the default umask (<tt>0022</tt>), new files will NOT be group-writable automatically. You must either:
* Set <tt>umask 0002</tt> in your shell so new files are group-writable by default, OR
* Manually run <tt>chmod g+w</tt> on new files, OR
* Use ACLs with <tt>default:</tt> entries (which override umask and handle permissions automatically)

==== Recommendation ====

'''Always prefer <tt>ws_allocate -G groupname</tt> over manual Unix permissions.''' It handles everything automatically and correctly, including the sticky bit and proper permissions on all new files.

Use manual <tt>chmod</tt>/<tt>chgrp</tt> only when <tt>-G</tt> is not available on your cluster or for fixing permissions on existing data.

== ws_release - Release (Delete) Workspace ==

Release a workspace when you no longer need it:

'''Basic usage:'''

$ ws_release myWs

'''Syntax:''' <tt>ws_release [options] workspace_name</tt>

'''What happens when you release:'''
* The workspace ID can be reused immediately
* The directory becomes inaccessible to the user
* The data is '''not deleted immediately''' - it is moved to a deleted area
* '''Released workspaces:''' Can be recovered using <tt>ws_restore</tt> for a short grace period (typically 1 hour after release)
* '''Expired workspaces:''' Can be recovered for a longer period (system-dependent, typically 7-30 days after expiration, configured via <tt>keeptime</tt> in <tt>/etc/ws.conf</tt>)
* Final deletion happens automatically during cleanup runs (usually nighttime)
* '''Important:''' Released workspace data may still count toward your quota until final deletion occurs

=== Options ===

{| class="wikitable"
|-
!style="width:30%" | Option
!style="width:70%" | Description
|-
|<tt>-n <name></tt>
|Workspace name (alternative to positional argument)
|-
|<tt>-F <filesystem></tt>
|Specify filesystem where the workspace is located
|-
|<tt>--delete-data</tt>
|Delete all data immediately. '''WARNING: Workspace can NOT BE RECOVERED'''
|}

=== Immediate Deletion (Free Quota Instantly) ===

{| class="wikitable"
|-
!style="width:40%" | Works on cluster
!style="width:10%" | bwUC 3.0
!style="width:10%" | BinAC2
!style="width:10%" | Helix
!style="width:10%" | JUSTUS 2
!style="width:10%" | NEMO2
|-
|<tt>ws_release --delete-data</tt> (immediate deletion)
|style="background-color:#90EE90; text-align:center;" | ✓
| style="text-align:center;" |
| style="text-align:center;" |
| style="text-align:center;" |
|style="background-color:#90EE90; text-align:center;" | ✓
|}

If you need to free quota immediately instead of waiting for the grace period, you have two options:

'''Option 1: Use --delete-data flag''' (recommended if available on your cluster):

$ ws_release --delete-data myWs

'''Availability:''' Check if this flag is available on your cluster with <tt>ws_release -h</tt>.

'''Option 2: Manual deletion before release''' (works on all clusters):

See the section on [[#Using_rm_for_Manual_Deletion|using rm for manual deletion]] below for the safe method.

'''CRITICAL WARNING:''' Both methods permanently delete data that '''cannot be recovered''', even by system administrators.

'''When to use immediate deletion:'''
* ✓ You're certain you don't need the data anymore
* ✓ You've already backed up important results to permanent storage
* ✓ You're hitting quota limits and need space immediately
* ✗ Don't use if there's any chance you might need the data
* ✗ Don't use if you haven't verified your backup worked

'''Best practice:''' Use regular <tt>ws_release myWs</tt> (without immediate deletion) as your default. Only use immediate deletion when you're absolutely certain and need immediate quota relief.

=== Using rm for Manual Deletion ===

If <tt>ws_release --delete-data</tt> is not available on your cluster, you can manually delete data before releasing:

$ rm -rf -- "$(ws_find myWs)"
$ ws_release myWs

'''Why this is safe:'''
* <tt>--</tt> prevents path from being interpreted as option (even if it starts with <tt>-</tt>)
* Quotes around <tt>$(ws_find myWs)</tt> handle paths with spaces safely
* If <tt>ws_find</tt> fails or returns empty, <tt>rm</tt> fails with "missing operand" (no deletion occurs)
* Direct and simple - no complex patterns or subshells needed

== ws_restore - Restore Expired Workspace ==

{| class="wikitable"
|-
!style="width:40%" | Works on cluster
!style="width:10%" | bwUC 3.0
!style="width:10%" | BinAC2
!style="width:10%" | Helix
!style="width:10%" | JUSTUS 2
!style="width:10%" | NEMO2
|-
|<tt>ws_restore</tt>
|style="background-color:#90EE90; text-align:center;" | ✓
|style="background-color:#90EE90; text-align:center;" | ✓
|style="background-color:#90EE90; text-align:center;" | ✓
|style="background-color:#90EE90; text-align:center;" | ✓
|style="background-color:#90EE90; text-align:center;" | ✓
|}

For a certain (system-specific) grace time following workspace expiration, a workspace can be restored.

'''Syntax:''' <tt>ws_restore [options] workspace_name target_name | -l</tt>

=== Restore Procedure ===

'''(1) Display restorable workspaces:'''

$ ws_restore -l

This will list all workspaces that can still be recovered. You can use <tt>-b</tt> or <tt>--brief</tt> to hide the unavailability date in the list.

'''(2) Create a new workspace as the target for the restore:'''

$ ws_allocate restored 60

'''(3) Restore the expired workspace:'''

$ ws_restore <full_name_of_expired_workspace> restored

'''Important:'''
* The expired workspace must be specified using the '''full name''' as printed by <tt>ws_restore -l</tt> (not as printed by <tt>ws_list</tt>!), including username prefix and timestamp suffix (otherwise it cannot be uniquely identified)
* The target workspace must be given with just its '''short name''' as listed by <tt>ws_list</tt>, without the username prefix
* '''<tt>ws_restore</tt> can only work on the same filesystem.''' Ensure the new workspace is on the same filesystem as the expired workspace. Use <tt>-F <filesystem></tt> flag if needed

Example:

$ ws_restore username-myWs-0 restored

=== Options ===

{| class="wikitable"
|-
!style="width:30%" | Option
!style="width:70%" | Description
|-
|<tt>-l</tt>, <tt>--list</tt>
|List restorable workspaces. '''Use this first''' to see what can be recovered
|-
|<tt>-b</tt>, <tt>--brief</tt>
|Do not show unavailability date in list (used with <tt>-l</tt>)
|-
|<tt>-n <name></tt>
|Workspace name (alternative to positional argument)
|-
|<tt>-t <target></tt>
|Existing target workspace name (alternative to positional argument)
|-
|<tt>-F <filesystem></tt>
|Specify filesystem where the workspace is located
|-
|<tt>-u <username></tt>
|Username (for restoring other users' workspaces if permitted)
|}

=== If Workspace Cannot Be Restored ===

If the workspace is not visible/restorable, it has been '''permanently deleted''' and cannot be restored, not even by system administrators.

'''Helix-specific - Workspace Snapshots:'''

On Helix, if the workspace can't be restored anymore using <tt>ws_restore</tt>, you can check the snapshots under:

/work/.snapshots/<timepoint>/ws/

'''Important notes about snapshots:'''
* Snapshots are point-in-time copies of the workspace filesystem
* Changes that happened since the last snapshot was created are lost
* Browse available snapshot timepoints in <tt>/work/.snapshots/</tt>
* '''Caution:''' The Helix team tries to keep the latest snapshots, but they cannot guarantee that snapshots will be available at all times
* Snapshots are a last resort when <tt>ws_restore</tt> no longer works

'''How to use snapshots:'''

$ ls /work/.snapshots/ # List available snapshot timepoints
$ cd /work/.snapshots/2025-11-15_00.00.00/ws/
$ ls # Find your old workspace directory
$ cp -r username-myWs-0 /path/to/active/workspace/ # Copy data to active workspace

Contact Helix support if you need assistance with snapshot recovery.

'''Please remember:''' Workspaces are intended solely for temporary work data, and there is '''no backup''' of data in the workspaces.

'''Recommendation:''' Email reminders are sent automatically. You can optionally customize reminder timing with <tt>-r</tt> option to be notified earlier, giving you time to extend the workspace or backup important data to appropriate permanent storage.

=== Cluster-Specific Information ===

Grace periods for expired/released workspaces vary by cluster and are configured via the <tt>keeptime</tt> parameter in <tt>/etc/ws.conf</tt>:

{| class="wikitable"
|-
!style="width:30%" | Cluster
!style="width:35%" | Expired Workspace Retention (<tt>keeptime</tt>)
!style="width:35%" | Released Workspace Grace Period
|-
|bwUniCluster 3.0
|30 days
|~1 hour
|-
|Helix
|System-specific (check with support)
|~1 hour
|-
|JUSTUS 2
|System-specific (check with support)
|~1 hour
|-
|BinAC2
|System-specific (check with support)
|~1 hour
|-
|NEMO2
|30 days
|~1 hour
|}

'''Note:'''
* '''Expired workspaces''' (reached end of lifetime) are kept for <tt>keeptime</tt> days configured in <tt>/etc/ws.conf</tt>
* '''Released workspaces''' (via <tt>ws_release</tt>) are deleted faster - typically within 1 hour
* '''Actual deletion''' happens during automated cleanup runs, typically during nighttime
* This allows users to recover accidentally released workspaces quickly, while giving more time for expired workspaces

== Cluster-Specific Workspace Limits ==

Different clusters have different workspace policies configured in <tt>/etc/ws.conf</tt>. Below is an overview of typical settings:

{| class="wikitable"
|-
!style="width:15%" | Cluster
!style="width:15%" | Default Lifetime
!style="width:15%" | Max Lifetime
!style="width:15%" | Max Extensions
!style="width:20%" | User Quota
!style="width:20%" | Inode Quota
|-
|bwUniCluster 3.0
|1 day
|60 days
|3 times
|40 TiB
|20 million
|-
|JUSTUS 2
|7 days
|90 days
|Unlimited
|20 TiB
|5 million
|-
|Helix
|N/A
|30 days
|10 times
|10 TiB
|None
|-
|BinAC2
|N/A
|30 days
|5 times
|None
|None
|-
|NEMO2
|30 days
|100 days
|100 times
|5 TiB per workspace
|None
|}

'''Configuration parameters in <tt>/etc/ws.conf</tt>:'''
* <tt>duration</tt> - Maximum lifetime in days
* <tt>maxextensions</tt> - Number of times a workspace can be extended
* <tt>keeptime</tt> - Days to keep expired workspaces before final deletion (typically 7-30 days)
* Released workspaces have a shorter grace period (~1 hour) regardless of <tt>keeptime</tt>

'''Note:''' Check your specific cluster documentation for current quotas and settings, as they may change. Use <tt>ws_list -l</tt> to see available filesystems and their properties on your cluster.

== Checking Workspace Quotas ==

The command to check workspace quota usage varies by cluster and filesystem:

'''Lustre-based clusters (bwUniCluster 3.0, JUSTUS 2):'''

$ lfs quota -uh $(whoami) /lustre/work # or appropriate workspace path
$ lfs quota -uh $(whoami) /pfs/work9 # bwUniCluster 3.0

'''NEMO2 (Weka filesystem):'''

$ nemoquota # Shows HOME and workspace quotas
$ df --si $(ws_find workspace_name) # Check specific workspace

'''Helix (IBM Spectrum Scale):'''

$ workquotainfo # Shows workspace quota info

'''BinAC2:'''
* No quota limits enforced on workspaces
* Check available space with <tt>df</tt> command

'''General tip:''' Always check disk usage before large data operations to ensure sufficient space is available.

== ws_register - Register Workspace Links ==

The <tt>ws_register</tt> command creates or updates symbolic links to your workspaces in a directory of your choice. This provides a convenient way to access all your workspaces from a single location.

'''Syntax:''' <tt>ws_register [-h] [--version] [-F FILESYSTEM] directory</tt>

'''Usage:'''

$ ws_register ~/workspaces

This will create symbolic links to all your workspaces in the <tt>~/workspaces</tt> directory. The command creates subdirectories for each filesystem (e.g., <tt>scratch/</tt>) and places workspace links inside them.

Example:

$ mkdir -p ~/my_workspaces
$ ws_register ~/my_workspaces
$ ls -l ~/my_workspaces/scratch/
lrwxrwxrwx 1 user group 45 Nov 17 10:30 user-myWs -> /work/workspace/scratch/user-myWs-0
lrwxrwxrwx 1 user group 48 Nov 17 10:30 user-project1 -> /work/workspace/scratch/user-project1-0

'''Note:''' Links use the full workspace names (including username prefix), organized by filesystem subdirectory.

=== Options ===

{| class="wikitable"
|-
!style="width:30%" | Option
!style="width:70%" | Description
|-
|<tt>directory</tt>
|Directory in which links shall be created/updated (required positional argument)
|-
|<tt>-F <filesystem></tt>, <tt>--filesystem <filesystem></tt>
|Filesystem to search workspaces in. Only create links for workspaces on this filesystem
|-
|<tt>-h</tt>, <tt>--help</tt>
|Show help message
|-
|<tt>--version</tt>
|Show program's version number and exit
|}

'''When to use:'''
* '''Recommended''' if you work with multiple workspaces and want quick access
* Use in your <tt>~/.bashrc</tt> or login scripts to automatically update links at login
* Useful for organizing workspaces by project or purpose

'''Example in login script:'''

<pre>
# In ~/.bashrc or ~/.profile
# Only run in interactive shells to avoid issues with scp, rsync, etc.
if [ -t 0 ] && [ -z "$SSH_ORIGINAL_COMMAND" ] && command -v ws_register >/dev/null 2>&1; then
mkdir -p ~/workspaces >/dev/null 2>&1
ws_register ~/workspaces >/dev/null 2>&1
fi
</pre>

== Using Workspaces in Batch Jobs ==

'''Recommended approach:''' Create your workspace manually before submitting jobs, then reference it in your job scripts using <tt>ws_find</tt>.

'''(1) Create workspace once (on login node):'''

$ ws_allocate myProject 60

'''(2) Use in job scripts with ws_find:'''

<pre>
#!/bin/bash
#SBATCH --job-name=my_job
#SBATCH --time=24:00:00

# Find existing workspace
WORKSPACE=$(ws_find myProject)

# Change to workspace
cd $WORKSPACE

# Your computation here
./my_program --input input.dat --output results.dat
</pre>

'''Warning:''' Avoid using <tt>ws_allocate</tt> directly in job scripts that run frequently. While <tt>ws_allocate</tt> is safe to call multiple times on the same workspace name (it returns the existing workspace), you should not create too many workspaces unnecessarily. Create workspaces manually when needed, then use <tt>ws_find</tt> in your job scripts to locate them.

== Best Practices and Recommendations ==

=== For All Users ===

# '''Set up ~/.ws_user.conf''' - Configure default reminder timing, duration, and groupname to avoid typing them repeatedly (see [[Workspaces/Advanced_Features#.7E.2F.ws_user.conf_Configuration_File|configuration guide]])
# '''Email reminders are automatic''' - Notifications are sent automatically using your identity provider email; only use <tt>-r</tt> to customize reminder timing if needed
# '''Custom email only if needed''' - Only use <tt>-m</tt> option to override the email address from your identity provider
# '''Use ws_register''' - Create symbolic links to your workspaces in a convenient directory (see [[Workspaces/Advanced_Features#ws_register_-_Register_Workspace_Links|ws_register guide]])
# '''Create workspaces manually''' - Create workspaces on the login node before submitting jobs, then use <tt>ws_find</tt> in your job scripts (see [[#Using_Workspaces_in_Batch_Jobs|Using Workspaces in Batch Jobs]])
# '''Track your workspaces''' - Regularly run <tt>ws_list -R</tt> to see which workspaces will expire soon
# '''Backup important data''' - Workspaces are temporary and not backed up - copy results to appropriate permanent storage (check your cluster/site policies for backup locations)
# '''Clean up regularly''' - Release workspaces you no longer need to keep filesystems organized

=== For Short-term Jobs (hours to days) ===

# Use default or shorter durations
# Consider using a single workspace for a series of related jobs
# Use <tt>ws_find</tt> in job scripts to locate the workspace (see [[#Using_Workspaces_in_Batch_Jobs|Using Workspaces in Batch Jobs]])
# Copy results to permanent storage when jobs complete
# Release workspace when no longer needed (see [[#Release_.28Delete.29_Workspace|Release Workspace]])

=== For Long-term Campaigns (weeks to months) ===

# Request maximum allowed duration (see [[Workspaces/Advanced_Features#Cluster-Specific_Workspace_Limits|Cluster-Specific Workspace Limits]])
# Email reminders are sent automatically; optionally customize reminder timing with <tt>-r</tt> option
# Use <tt>ws_list -R</tt> regularly to monitor remaining time (see [[#List_Your_Workspaces|List Your Workspaces]])
# Plan data archival to appropriate permanent storage before expiration (check cluster/site policies)

=== For Collaborative Work ===

# Use <tt>ws_allocate -G groupname</tt> for shared write access (see [[#Create_Group_Workspace|Create Group Workspace]])
# Set <tt>groupname</tt> in <tt>~/.ws_user.conf</tt> if you always work with the same group (see [[Workspaces/Advanced_Features#.7E.2F.ws_user.conf_Configuration_File|configuration guide]])
# Use <tt>ws_allocate -g</tt> for read-only sharing within group
# Use <tt>ws_list -g</tt> to see all group workspaces (see [[#List_Group_Workspaces|List Group Workspaces]])
# Team members can extend group workspaces (see [[#Extend_Group_Workspace|Extend Group Workspace]])
# Take over reminder responsibility when colleague is unavailable (see [[#Manage_Reminders_for_Group_Workspace|Manage Reminders]])
# Document the workspace location for your team members
# For advanced sharing scenarios (ACL-based, ws_share), see the [[Workspaces/Advanced_Features#Cooperative_Usage_.28Group_Workspaces_and_Sharing.29|Advanced Features guide]]

=== For Managing Multiple Filesystems ===

# '''Note:''' Most clusters have only one default filesystem - the <tt>-F</tt> option is rarely needed
# Use <tt>ws_list -l</tt> first to check if multiple filesystems are available on your cluster
# Use <tt>-F</tt> option only if you need specific filesystem for performance or capacity needs (see [[Workspaces/Advanced_Features#Multiple_Filesystem_Locations|filesystem options]])
# '''bwUniCluster 3.0 filesystems:'''
#* '''Default Lustre filesystem:''' Standard workspace location, best for large files and sequential I/O
#* '''Flash filesystem (ffuc):''' SSD-based storage for KIT/HoreKa users, shared between bwUniCluster 3.0 and HoreKa
#* Use flash filesystem for workloads with many small files, random I/O, AI/ML training, or compilation
#* Balance load: use <tt>-F ffuc</tt> when appropriate to reduce load on default filesystem
# '''General guidelines:'''
#* Flash-based filesystems (SSD/NVMe): Use for many small files, low-latency requirements, random I/O
#* Standard Lustre/parallel filesystems: Best for large files and sequential I/O patterns

=== For Different Data Types ===

# '''Large sequential I/O:''' Use standard workspace filesystem (Lustre best for very large files, Weka excellent for both large and small)
# '''Many small files or random access:''' Use flash-based workspace filesystem like Weka (NEMO2) or bwUniCluster ffuc, or stage to <tt>$TMPDIR</tt>
# '''Data read multiple times on single node:''' Copy to <tt>$TMPDIR</tt> at job start for best performance
# '''Temporary data for single node:''' Always use <tt>$TMPDIR</tt>, not workspaces
# '''Multi-node temporary data:''' Use workspaces (not suitable for <tt>$TMPDIR</tt>)
# '''AI/ML training data:''' Use Weka (NEMO2) or flash filesystems for best performance, or stage to <tt>$TMPDIR</tt> for repeated access
# '''Compilation/build directories:''' Use flash-based filesystems (Weka, ffuc) or <tt>$TMPDIR</tt> for better performance

=== For Quota Management ===

* Use <tt>ws_release --delete-data</tt> for immediate deletion (see [[#Release_.28Delete.29_Workspace|Release Workspace]])
* For clusters without <tt>--delete-data</tt> option, use [[Workspaces/Advanced_Features#Using_rm_for_Manual_Deletion|manual deletion method]]
* Remember: released workspaces may still count toward quota during grace period (~1 hour)

Latest revision as of 17:43, 2 December 2025

This document covers advanced features and detailed configuration options for the HPC workspace tools. For basic daily usage, see the main Workspaces guide.

Almost Complete Command Reference

Task Command
Create workspace for 30 days ws_allocate myWs 30
Create with custom email ws_allocate -m custom@example.com -r 3 myWs 30
Create group-writable workspace ws_allocate -G groupname myWs 30
Create on specific filesystem ws_allocate -F filesystem myWs 30
List all your workspaces ws_list
List by remaining time ws_list -R
List available filesystems ws_list -l or ws_find -l
Find workspace path ws_find myWs
Extend workspace by 40 days ws_extend myWs 40 or ws_allocate -x myWs 40
Share with another user ws_share share myWs username
List shared users ws_share list myWs
Send calendar reminder ws_send_ical myWs user@example.com
Release workspace ws_release myWs
List restorable workspaces ws_restore -l
Register workspace links ws_register ~/workspaces

Detailed Topics

Commands

  • ws_allocate - Create and extend workspaces (detailed options)
  • ws_list - List workspaces (sorting, filtering)
  • ws_find - Find workspace paths for scripts
  • ws_extend - Extend workspace lifetime
  • ws_release - Release (delete) workspaces with immediate deletion options
  • ws_restore - Restore expired or released workspaces
  • ws_register - Create symbolic links to workspaces

Configuration & Features

Best Practices

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