Helix/Filesystems - Revision history

H Schumacher: Moved "free up space" section into its own chapter. Added "list" option to ws_share.

2026-03-30T15:29:40Z

Moved "free up space" section into its own chapter. Added "list" option to ws_share.

← Older revision		Revision as of 17:29, 30 March 2026
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	Home directories are meant for permanent storage of files that are kept being used like source codes, configuration files, executable programs.		Home directories are meant for permanent storage of files that are kept being used like source codes, configuration files, executable programs.

⚫	'''Backup'''

	The backup of the home directory can be found under <code>/home/.snapshots</code>.

	'''Disk Space'''		'''Disk Space'''
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	</pre>		</pre>

		⚫	'''Backup'''
⚫	If you need to free up space, you can...

⚫	* ...check the file sizes with <code>du -sh --apparent-size * .[^.]*</code>.
	* ~~...delete~~ ~~temporary~~ ~~files,~~ ~~for~~ ~~example~~ in ~~the~~ <code>.~~cache~~</code> ~~folder~~.		The backup of the home directory can be found under <code>/home/.snapshots</code>.
⚫	* ...use the cleaning commands by your used software (e.g. [https://wiki.bwhpc.de/e/Development/Conda#Create_Environments_and_Install_Software conda]).
⚫	* ...delete folders with temporary data created by your used software (e.g. nextflow).

	== Workspaces ==		== Workspaces ==
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	\|Sending a .ical calendar entry for reminding workspace expiring		\|Sending a .ical calendar entry for reminding workspace expiring
	\|-		\|-
	\|ws_share <share / unshare / unshare-all> <workspacename> <username> [username2]		\|ws_share <share / unshare / unshare-all / list> <workspacename> <username> [username2]
	\|ws_share allows to share an existing workspace with other users.		\|ws_share allows to share an existing workspace with other users.
	\|-		\|-
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	=== Sharing Workspaces ===		=== Sharing Workspaces ===
	To simplify sharing of workspaces you can use the command <code>ws_share</code> as described in the table above.		To simplify sharing of workspaces you can use the command <code>ws_share</code> as described in the table above.
		⚫	The command sets up the workspace to allow read-only access to the specified users.

		⚫	If you need more specific permissions, you can follow the guidelines here: →
⚫	~~This~~ ~~tool~~ ~~setup~~ ~~the needed ACLs on~~ the workspace to allow read-only access to the specified users.
			[[Workspace#Setting_Permissions_for_Sharing_Files \| Setting_Permissions_for_Sharing_Files]]

⚫	If you need more specific permissions, you can ~~also setup~~ the ~~ACLs on your own, like described~~ here:
	https://wiki.bwhpc.de/e/Workspace#Sharing_Workspace_Data_within_your_Workgroup



	== $TMPDIR ==		== $TMPDIR ==

	The variable $TMPDIR provides file space for temporary data of running jobs.		The variable <tt>$TMPDIR</tt> provides file space for temporary data of running jobs.
	Each node has its own $TMPDIR. <!-- It is possible to request a global $TMPDIR for a job. -->		Each node has its own <tt>$TMPDIR</tt>. <!-- It is possible to request a global <tt>$TMPDIR</tt> for a job. -->
	The data in $TMPDIR become unavailable as soon as the job has finished.		The data in $TMPDIR become unavailable as soon as the job has finished.

	== ~~Access to~~ SDS@hd ==		== SDS@hd Access ==

	It is possible to access your storage space on [http://sds-hd.urz.uni-heidelberg.de SDS@hd] directly on the bwForCluster Helix in /mnt/sds-hd/ on all login and compute nodes.		It is possible to access your storage space on [http://sds-hd.urz.uni-heidelberg.de SDS@hd] directly on the bwForCluster Helix in /mnt/sds-hd/ on all login and compute nodes.

			== Free up Space ==

		⚫	If you need to free up space, you can...
		⚫	* ...check the file sizes with <code>du -sh --apparent-size * .[^.]*</code>.
			* ...delete temporary files, for example in the <code>.cache</code> folder. Other folders starting with a dot might contain temporary files as well, for example <code>.local/share/Trash</code>.
		⚫	* ...use the cleaning commands by your used software (e.g. [https://wiki.bwhpc.de/e/Development/Conda#Create_Environments_and_Install_Software conda]).
		⚫	* ...delete folders with temporary data created by your used software (e.g. nextflow).

	== Troubleshooting ==		== Troubleshooting ==
	* '''Error: "Disk space exceeded"'''		* '''Error: "Disk space exceeded"'''
	*: This means that there is not enough space in your $HOME to execute the operation. ~~One~~ ~~option~~ to free up space ~~is to look into folders that start with a dot~~. ~~For example "./local/share/Trash" or ".cache".~~		*: This means that there is not enough space (e.g. in your $HOME) to execute the operation. Please [[Helix/Filesystems#Free_up_Space \| free up space]].
	*'''Error: "could not create workspace directory"'''		*'''Error: "could not create workspace directory"'''
	*:You should check the localesetting of your ssh client. Some clients (e.g. the one from MacOSX) set values that are not valid. You should overwrite LC_CTYPE and set it to a valid locale value like: <code>export LC_CTYPE=de_DE.UTF-8</code>		*:You should check the localesetting of your ssh client. Some clients (e.g. the one from MacOSX) set values that are not valid. You should overwrite LC_CTYPE and set it to a valid locale value like: <code>export LC_CTYPE=de_DE.UTF-8</code>

H Schumacher: Added bold headings for backup and disk space

2026-01-07T09:39:31Z

Added bold headings for backup and disk space

← Older revision		Revision as of 11:39, 7 January 2026
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	* workspace lifetime: files are removed at end of workspace lifetime.		* workspace lifetime: files are removed at end of workspace lifetime.
	* batch job walltime: files are removed at end of the batch job.		* batch job walltime: files are removed at end of the batch job.
	* snapshots: a copy of all files is saved at specific timepoints so that they can be restored when necessary		* snapshots: a copy of all files is saved at specific timepoints so that they can be restored when necessary. For details see the related sections.

	== $HOME ==		== $HOME ==

	Home directories are meant for permanent storage of files that are kept being used like source codes, configuration files, executable programs. ~~The backup of the home directory can be found under <code>/home/.snapshots</code>. The disk space per user is limited to 200 GB. The used disk space is displayed with the command:~~		Home directories are meant for permanent storage of files that are kept being used like source codes, configuration files, executable programs.

			'''Backup'''

			The backup of the home directory can be found under <code>/home/.snapshots</code>.

			'''Disk Space'''

			The disk space per user is limited to 200 GB. The used disk space is displayed with the command:

	<pre>		<pre>
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	== Workspaces ==		== Workspaces ==

	Workspace tools can be used to get temporary space for larger amounts of data necessary for or produced by running jobs. ~~To create a workspace you need to supply a name for the workspace and a lifetime in days. The maximum lifetime is 30 days. It is possible to extend the lifetime 10 times.~~		Workspace tools can be used to get temporary space for larger amounts of data necessary for or produced by running jobs.

			'''Usage'''

			To create a workspace you need to supply a name for the workspace and a lifetime in days. The maximum lifetime is 30 days. It is possible to extend the lifetime 10 times.

	{\| class="wikitable"		{\| class="wikitable"
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	\|-		\|-
	\|}		\|}

			'''Disk Space'''

	If you plan to produce or copy large amounts of data in workspaces, please check the availability. The used and free disk space on the workspace filesystem is displayed with the command:		If you plan to produce or copy large amounts of data in workspaces, please check the availability. The used and free disk space on the workspace filesystem is displayed with the command:

H Schumacher: Added disk space exceeded solution

2025-10-02T08:12:15Z

Added disk space exceeded solution

← Older revision		Revision as of 10:12, 2 October 2025
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	== Troubleshooting ==		== Troubleshooting ==
	*'''~~<code>~~Error: ~~could not create~~ ~~workspace~~ ~~directory!</code>~~'''		* '''Error: "Disk space exceeded"'''
			*: This means that there is not enough space in your $HOME to execute the operation. One option to free up space is to look into folders that start with a dot. For example "./local/share/Trash" or ".cache".
			*'''Error: "could not create workspace directory"'''
	*:You should check the localesetting of your ssh client. Some clients (e.g. the one from MacOSX) set values that are not valid. You should overwrite LC_CTYPE and set it to a valid locale value like: <code>export LC_CTYPE=de_DE.UTF-8</code>		*:You should check the localesetting of your ssh client. Some clients (e.g. the one from MacOSX) set values that are not valid. You should overwrite LC_CTYPE and set it to a valid locale value like: <code>export LC_CTYPE=de_DE.UTF-8</code>
	*:To make this change persistent you can add this line also to your <code>.bashrc</code> file.		*:To make this change persistent you can add this line also to your <code>.bashrc</code> file.
	*:A list of valid locales can be retrieved via <code>locale -a</code>		*:A list of valid locales can be retrieved via <code>locale -a</code>

	* '''~~Expired~~ ~~workspace~~ ~~can~~ ~~be restored~~'''		* '''Workspace lifetime is expired'''
	*:Please see chapter [[Helix/Filesystems#Restoring_expired_Workspaces\|"Restoring_expired_Workspaces"]]		*:Please see chapter [[Helix/Filesystems#Restoring_expired_Workspaces\|"Restoring_expired_Workspaces"]]

H Schumacher: Replaced path with symlink

2025-09-29T10:25:28Z

Replaced path with symlink

← Older revision		Revision as of 12:25, 29 September 2025
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	The target workspace, on the other hand, must be given with just its short name as listed by <code>ws_list</code>, without the username prefix.		The target workspace, on the other hand, must be given with just its short name as listed by <code>ws_list</code>, without the username prefix.

	NOTE: <code>ws_restore</code> can only work on the same filesystem. So you have to ensure that the new workspace allocated with <code>ws_allocate</code> is placed on the same filesystem as the expired workspace. ~~Therefor~~ you can use <code>-F <filesystem></code> flag if needed.		NOTE: <code>ws_restore</code> can only work on the same filesystem. So you have to ensure that the new workspace allocated with <code>ws_allocate</code> is placed on the same filesystem as the expired workspace. Therefore you can use <code>-F <filesystem></code> flag if needed.

	<u>Snapshots</u>: If the workspace can't be restored anymore, you can check the snapshots under <code>~~/gpfs/bwfor~~/work/.snapshots/<timepoint>/ws/</code>. Changes that happened since the last snapshot was created are lost. Caution: We try to keep the latest snapshots but we can't guarantee that snapshots will be available at all times.		<u>Snapshots</u>: If the workspace can't be restored anymore, you can check the snapshots under <code>/work/.snapshots/<timepoint>/ws/</code>. Changes that happened since the last snapshot was created are lost. Caution: We try to keep the latest snapshots but we can't guarantee that snapshots will be available at all times.

	=== Linking workspaces in Home ===		=== Linking workspaces in Home ===

H Schumacher: added info about removing unnecessary files

2025-08-01T09:28:28Z

added info about removing unnecessary files

← Older revision		Revision as of 11:28, 1 August 2025
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	homequotainfo		homequotainfo
	</pre>		</pre>

			If you need to free up space, you can...
			* ...check the file sizes with <code>du -sh --apparent-size * .[^.]*</code>.
			* ...delete temporary files, for example in the <code>.cache</code> folder.
			* ...use the cleaning commands by your used software (e.g. [https://wiki.bwhpc.de/e/Development/Conda#Create_Environments_and_Install_Software conda]).
			* ...delete folders with temporary data created by your used software (e.g. nextflow).

	== Workspaces ==		== Workspaces ==

H Schumacher: Corrected snapshot path, added warning, text/formatting adjustments

2025-05-13T13:23:53Z

Corrected snapshot path, added warning, text/formatting adjustments

← Older revision		Revision as of 15:23, 13 May 2025
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	=== Restoring expired Workspaces ===		=== Restoring expired Workspaces ===
	At expiration time your workspace will be moved to a special, hidden directory. For a short period of time you can still restore your data into a valid workspace. ~~For~~ ~~that~~, use		At expiration time or after you've released it, your workspace will be moved to a special, hidden directory. For a short period of time you can still restore your data into a valid workspace. To get a list of your expired workspaces with their <u>full names</u>, use
	<pre>		<pre>
	ws_restore -l		ws_restore -l
	</pre>		</pre>
	~~to get a list of your expired workspaces~~, ~~and then~~ restore them into an '''existing, active workspace''' <code>restored_ws</code>:		Then, restore them into an '''existing, active workspace''' <code>restored_ws</code>:
	<pre>		<pre>
	ws_restore <deleted_workspacename> restored_ws		ws_restore <deleted_workspacename> restored_ws
	</pre>		</pre>
	~~NOTE: the~~ expired workspace has to be specified using the full name ~~as listed by <code>ws_restore -l</code>~~, including username prefix and timestamp suffix (otherwise, it cannot be uniquely identified).		The expired workspace has to be specified using the '''full name''', including username prefix and timestamp suffix (otherwise, it cannot be uniquely identified).
	The target workspace, on the other hand, must be given with just its short name as listed by <code>ws_list</code>, without the username prefix.		The target workspace, on the other hand, must be given with just its short name as listed by <code>ws_list</code>, without the username prefix.

	NOTE: <code>ws_restore</code> can only work on the same filesystem! So you have to ensure that the new workspace allocated with <code>ws_allocate</code> is placed on the same filesystem as the expired workspace. Therefor you can use <code>-F <filesystem></code> flag if needed.		NOTE: <code>ws_restore</code> can only work on the same filesystem. So you have to ensure that the new workspace allocated with <code>ws_allocate</code> is placed on the same filesystem as the expired workspace. Therefor you can use <code>-F <filesystem></code> flag if needed.

	If the workspace can't be restored anymore, you can check the snapshots under <code>/gpfs/bwfor/.snapshots/</code>. Changes that happened since the last snapshot was created are lost.		<u>Snapshots</u>: If the workspace can't be restored anymore, you can check the snapshots under <code>/gpfs/bwfor/work/.snapshots/<timepoint>/ws/</code>. Changes that happened since the last snapshot was created are lost. Caution: We try to keep the latest snapshots but we can't guarantee that snapshots will be available at all times.

	=== Linking workspaces in Home ===		=== Linking workspaces in Home ===

H Schumacher: Added snapshot information

2025-03-18T16:02:19Z

Added snapshot information

← Older revision		Revision as of 18:02, 18 March 2025
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	\|-		\|-
	!scope="column" \| Backup		!scope="column" \| Backup
			\| snapshots
	\| no
			\| snapshots
	\| no
	\| no		\| no
	\|}		\|}
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	* workspace lifetime: files are removed at end of workspace lifetime.		* workspace lifetime: files are removed at end of workspace lifetime.
	* batch job walltime: files are removed at end of the batch job.		* batch job walltime: files are removed at end of the batch job.
			* snapshots: a copy of all files is saved at specific timepoints so that they can be restored when necessary

	== $HOME ==		== $HOME ==

	Home directories are meant for permanent storage of files that are kept being used like source codes, configuration files, executable programs. ~~There is currently no~~ backup ~~for~~ the home directory. The disk space per user is limited to 200 GB. The used disk space is displayed with the command:		Home directories are meant for permanent storage of files that are kept being used like source codes, configuration files, executable programs. The backup of the home directory can be found under <code>/home/.snapshots</code>. The disk space per user is limited to 200 GB. The used disk space is displayed with the command:

	<pre>		<pre>
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	NOTE: <code>ws_restore</code> can only work on the same filesystem! So you have to ensure that the new workspace allocated with <code>ws_allocate</code> is placed on the same filesystem as the expired workspace. Therefor you can use <code>-F <filesystem></code> flag if needed.		NOTE: <code>ws_restore</code> can only work on the same filesystem! So you have to ensure that the new workspace allocated with <code>ws_allocate</code> is placed on the same filesystem as the expired workspace. Therefor you can use <code>-F <filesystem></code> flag if needed.

			If the workspace can't be restored anymore, you can check the snapshots under <code>/gpfs/bwfor/.snapshots/</code>. Changes that happened since the last snapshot was created are lost.

	=== Linking workspaces in Home ===		=== Linking workspaces in Home ===
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	https://wiki.bwhpc.de/e/Workspace#Sharing_Workspace_Data_within_your_Workgroup		https://wiki.bwhpc.de/e/Workspace#Sharing_Workspace_Data_within_your_Workgroup

⚫	=== Troubleshooting ===
⚫	*'''<code>Error: could not create workspace directory!</code>'''
⚫	*:You should check the localesetting of your ssh client. Some clients (e.g. the one from MacOSX) set values that are not valid. You should overwrite LC_CTYPE and set it to a valid locale value like: <code>export LC_CTYPE=de_DE.UTF-8</code>
⚫	*:To make this change persistent you can add this line also to your <code>.bashrc</code> file.
⚫	*:A list of valid locales can be retrieved via <code>locale -a</code>

⚫	* '''Expired workspace can be restored'''
⚫	*:Please see chapter [[Helix/Filesystems#Restoring_expired_Workspaces\|"Restoring_expired_Workspaces"]]

	== $TMPDIR ==		== $TMPDIR ==
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	It is possible to access your storage space on [http://sds-hd.urz.uni-heidelberg.de SDS@hd] directly on the bwForCluster Helix in /mnt/sds-hd/ on all login and compute nodes.		It is possible to access your storage space on [http://sds-hd.urz.uni-heidelberg.de SDS@hd] directly on the bwForCluster Helix in /mnt/sds-hd/ on all login and compute nodes.

		⚫	== Troubleshooting ==
		⚫	*'''<code>Error: could not create workspace directory!</code>'''
		⚫	*:You should check the localesetting of your ssh client. Some clients (e.g. the one from MacOSX) set values that are not valid. You should overwrite LC_CTYPE and set it to a valid locale value like: <code>export LC_CTYPE=de_DE.UTF-8</code>
		⚫	*:To make this change persistent you can add this line also to your <code>.bashrc</code> file.
		⚫	*:A list of valid locales can be retrieved via <code>locale -a</code>

		⚫	* '''Expired workspace can be restored'''
		⚫	*:Please see chapter [[Helix/Filesystems#Restoring_expired_Workspaces\|"Restoring_expired_Workspaces"]]

			* '''How can I restore lost data'''
			*:Please have a look at the backup information of the respective file system.

H Schumacher: deleted section

2025-03-07T09:48:19Z

deleted section

← Older revision		Revision as of 11:48, 7 March 2025
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	*:A list of valid locales can be retrieved via <code>locale -a</code>		*:A list of valid locales can be retrieved via <code>locale -a</code>

	*'''~~<code>Error:~~ ~~only root~~ can ~~do this~~ ~~<workspacename></code>~~'''		* '''Expired workspace can be restored'''
	*:Ensure that you are using the FULL workspacename, including your account_prefix, e.g. "hd_ab123-workspacename"

	* '''Expired workspace needs to be restored'''
	*:Please see chapter [[Helix/Filesystems#Restoring_expired_Workspaces\|"Restoring_expired_Workspaces"]]		*:Please see chapter [[Helix/Filesystems#Restoring_expired_Workspaces\|"Restoring_expired_Workspaces"]]

H Schumacher: deleted snapshot section

2025-03-07T09:40:33Z

deleted snapshot section

← Older revision		Revision as of 11:40, 7 March 2025
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	* '''Expired workspace needs to be restored'''		* '''Expired workspace needs to be restored'''
	**Please see chapter [[Helix/Filesystems#Restoring_expired_Workspaces\|"Restoring_expired_Workspaces"]]		*:Please see chapter [[Helix/Filesystems#Restoring_expired_Workspaces\|"Restoring_expired_Workspaces"]]
	**If the workspace can't be restored that way, please check <code>/gpfs/bwfor/.snapshots/</code>. The file system creates snapshots at regular intervals and you can look up the latest snapshot of your workspace. Changes that happened after that are indeed lost.

	== $TMPDIR ==		== $TMPDIR ==

H Schumacher: Added to troubleshooting section

2025-03-06T23:14:59Z

Added to troubleshooting section

← Older revision		Revision as of 01:14, 7 March 2025
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	\|-		\|-
	\|ws_send_ical -m <email> foo		\|ws_send_ical -m <email> foo
	\|~~sending~~ a .ical calendar entry for reminding workspace expiring		\|Sending a .ical calendar entry for reminding workspace expiring
	\|-		\|-
	\|ws_share share/unshare/unshare-all <workspacename> <username> [username2]		\|ws_share <share / unshare / unshare-all> <workspacename> <username> [username2]
	\|ws_share allows to share an existing workspace with other users.		\|ws_share allows to share an existing workspace with other users.
	\|-		\|-
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	</pre>		</pre>

	==== Restoring expired Workspaces ====		=== Restoring expired Workspaces ===
	At expiration time your workspace will be moved to a special, hidden directory. For a short period of time you can still restore your data into a valid workspace. For that, use		At expiration time your workspace will be moved to a special, hidden directory. For a short period of time you can still restore your data into a valid workspace. For that, use
	<pre>		<pre>
Line 99:		Line 99:
	NOTE: <code>ws_restore</code> can only work on the same filesystem! So you have to ensure that the new workspace allocated with <code>ws_allocate</code> is placed on the same filesystem as the expired workspace. Therefor you can use <code>-F <filesystem></code> flag if needed.		NOTE: <code>ws_restore</code> can only work on the same filesystem! So you have to ensure that the new workspace allocated with <code>ws_allocate</code> is placed on the same filesystem as the expired workspace. Therefor you can use <code>-F <filesystem></code> flag if needed.

	==== Linking workspaces in Home ====		=== Linking workspaces in Home ===
	It might be valuable to have links to personal workspaces within a certain directory, e.g., the user home directory. The command		It might be valuable to have links to personal workspaces within a certain directory, e.g., the user home directory. The command
	<pre>		<pre>
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	** Removes links to released workspaces		** Removes links to released workspaces

	==== Sharing Workspaces ====		=== Sharing Workspaces ===
	To simplify sharing of workspaces you can use the command		To simplify sharing of workspaces you can use the command <code>ws_share</code> as described in the table above.
	<pre>
	ws_share
	</pre>

	This tool setup the needed ACLs on the workspace to allow read-only access to the specified users.		This tool setup the needed ACLs on the workspace to allow read-only access to the specified users.
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	https://wiki.bwhpc.de/e/Workspace#Sharing_Workspace_Data_within_your_Workgroup		https://wiki.bwhpc.de/e/Workspace#Sharing_Workspace_Data_within_your_Workgroup

	==== Troubleshooting ====		=== Troubleshooting ===
		⚫	*'''<code>Error: could not create workspace directory!</code>'''
	If you are getting the error:
		⚫	*:You should check the localesetting of your ssh client. Some clients (e.g. the one from MacOSX) set values that are not valid. You should overwrite LC_CTYPE and set it to a valid locale value like: <code>export LC_CTYPE=de_DE.UTF-8</code>
	<pre>
		⚫	*:To make this change persistent you can add this line also to your <code>.bashrc</code> file.
⚫	Error: could not create workspace directory!
		⚫	*:A list of valid locales can be retrieved via <code>locale -a</code>
	</pre>
⚫	~~you~~ should check the localesetting of your ssh client. Some clients (e.g. the one from MacOSX) set values that are not valid. You should overwrite LC_CTYPE and set it to a valid locale value like:
	<pre>
	export LC_CTYPE=de_DE.UTF-8
	</pre>
⚫	To make this change persistent you can add this line also to your <code>.bashrc</code> file.

		⚫	*'''<code>Error: only root can do this <workspacename></code>'''
⚫	A list of valid locales can be retrieved via
		⚫	*:Ensure that you are using the FULL workspacename, including your account_prefix, e.g. "hd_ab123-workspacename"
	<pre>
	locale -a
	</pre>

			* '''Expired workspace needs to be restored'''
	If you are getting the error:
			**Please see chapter [[Helix/Filesystems#Restoring_expired_Workspaces\|"Restoring_expired_Workspaces"]]
	<pre>
			**If the workspace can't be restored that way, please check <code>/gpfs/bwfor/.snapshots/</code>. The file system creates snapshots at regular intervals and you can look up the latest snapshot of your workspace. Changes that happened after that are indeed lost.
⚫	Error: only root can do this <workspacename>
	</pre>
⚫	~~ensure~~ that you are using the FULL workspacename, including your account_prefix, e.g. "hd_ab123-workspacename"

	== $TMPDIR ==		== $TMPDIR ==