Helix/bwVisu/Usage - Revision history

H Schumacher: Added output.log information, formatting

2026-05-06T10:34:45Z

Added output.log information, formatting

← Older revision		Revision as of 12:34, 6 May 2026
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	== Troubleshooting ==		== Troubleshooting ==
	Maintance windows and known issues are communicated via the email list or the News section at the bwVisu start page in the wiki.		Maintance windows and known issues are communicated via the email list or the ''News'' section at the bwVisu start page in the wiki.
	* Depending on the problem, it can help to look up the related bwForCluster Helix wiki pages. For example:		* Depending on the problem, it can help to look up the related bwForCluster Helix wiki pages. For example:
	*: '''Error:''' Disk space exceeded → '''[https://wiki.bwhpc.de/e/Helix/Filesystems#Troubleshooting Filesystems: Troubleshooting]'''		*: '''Error:''' Disk space exceeded → '''[https://wiki.bwhpc.de/e/Helix/Filesystems#Troubleshooting Filesystems: Troubleshooting]'''
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	* '''Issue:''' The bwVisu job fails or doesn't start.		* '''Issue:''' The bwVisu job fails or doesn't start.
	*: You can try to look for the issue yourself:		*: You can try to look for the issue yourself:
	: Reload the page without using the cache: `Strg+Shift+R` (Windows/Linux) or `Cmd+Shift+R` (Mac)		: Reload the page without using the cache: <code>Strg+Shift+R</code> (Windows/Linux) or <code>Cmd+Shift+R</code> (Mac)
	: Empty the browser cache:		: Empty the browser cache:
	:* Chrome/Edge: `Strg+Shift+Entf` → choose timeframe all → choose "Images and Files in Cache" → choose "Delete Files"		:* Chrome/Edge: <code>Strg+Shift+Entf</code> → choose timeframe all → choose ''Images and Files in Cache'' → choose ''Delete Files''
	:* Firefox: `Strg+Shift+Entf` → choose timeframe all → choose "Cache" → choose "Delete Files"		:* Firefox: <code>Strg+Shift+Entf</code> → choose timeframe all → choose ''Cache'' → choose ''Delete Files''
	:* Test alternative browser (Firefox, Chrome, Edge, ...)		: Test alternative browser (Firefox, Chrome, Edge, ...)
	:* Use a private session (without saved cookies and cache): `Strg+Shift+P` (~~Firefox~~) or `Strg+Shift+N` (~~Chrome~~).		: Use a private session (without saved cookies and cache): <code>Strg+Shift+N</code> (Chrome) or <code>Strg+Shift+P</code> (Firefox).
	*: If ~~this~~ ~~doesn~~'t ~~help~~, write to the support and provide the following information:		* '''Support:''' If you can't solve the issue, write to the support and provide the following information:
	: Date and time of the issue.		** Date and time of the issue.
			** Job-id (the number in brackets after the jobname)
	: Job-id
			** The <code>output.log</code> file that you can find when following the session id link.
	: Please report patterns that you recognize. For example:		** Please report patterns that you recognize. For example:
	:* The issue happens around a specific time of day.
	:* The issue is ~~connected~~ to ~~the~~ ~~duration~~ of ~~usage (e.g. happens always after ca. one hour)~~.		*** The issue happens around a specific time of day.
			*** The issue is connected to the duration of usage (e.g. happens always after ca. one hour).
	:* The issue appears after specific user interactions (using a specific method, opening the terminal, clicking a specific button, ...)		*** The issue appears after specific user interactions (using a specific method, opening the terminal, clicking a specific button, ...)
	*: You might be asked for further information:		: You might be asked for further information:
	: The internet browser that you user and its version. For example Firefox 128.		:* The internet browser that you user and its version. For example Firefox 128.
	: Provide more information about network traffic via a HAR-file.		:* Provide more information about network traffic via a HAR-file. First start a job and open the application. Then follow he instructions below:
	:* Instructions for Chrome/Edge:		:** Instructions for Chrome/Edge:
	:*# Open developer tools with `F12` or right click -> "Inspect"		:**# Open developer tools with <code>F12</code> or right click -> ''Inspect'' Then choose the tab ''Network''.
	:*# Choose the tab "Network"
	:*# Activate the checkbox "Preserve log"		:**# Activate the checkbox ''Preserve log''.
	:*# Reproduce the issue ~~(open~~ ~~new~~ ~~terminal)~~		:**# Reproduce the issue in the current tab.
	:*# After the problem happened again: Click the ~~Export-Symbol~~ (⬇️) in the menu of the network-tabs and choose "Export HAR..."		:**# After the problem happened again: Click the export symbol (⬇️) in the menu of the network-tabs and choose ''Export HAR...''.
	:* Instructions for Firefox:		:** Instructions for Firefox:
	:*# Open developer tools with `F12`		:**# Open developer tools with <code>F12</code> and choose the tab ''Network analysis''.
		⚫	:**# Click the settings symbol (⚙️) and activate ''Continuous Protocol''.
	:*# Choose the tab "Network analysis"
		⚫	:**# Reproduce the issue in the current tab.
⚫	:*# Click the ~~options~~ symbol (⚙️) an activate "Continuous Protocol"
		⚫	:**# After the problem happened again: Click the settings symbol again (⚙️) and choose ''Save everything as HAR''.
⚫	:*# Reproduce the issue ~~(open~~ ~~new~~ ~~terminal)~~
⚫	:*# After the problem happened again: Click the ~~option~~ symbol again (⚙️) and choose "Save everything as HAR".

H Schumacher: Added things to try and information to report.

2026-05-05T15:39:06Z

Added things to try and information to report.

@@ Line 76: / Line 76: @@
 == Troubleshooting ==
-In case of problems, it can help to look up the related bwForCluster Helix wiki pages.
+* Depending on the problem, it can help to look up the related bwForCluster Helix wiki pages. For example:
-* Error: Disk space exceeded &rarr; '''[https://wiki.bwhpc.de/e/Helix/Filesystems#Troubleshooting Filesystems: Troubleshooting]'''
+*: '''Error:''' Disk space exceeded &rarr; '''[https://wiki.bwhpc.de/e/Helix/Filesystems#Troubleshooting Filesystems: Troubleshooting]'''

H Schumacher: Added small title for sds section

2026-02-27T14:21:51Z

Added small title for sds section

← Older revision		Revision as of 16:21, 27 February 2026
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	[[File:BwVisuFiles.png\|bwVisu-files\|center\|x300px]]		[[File:BwVisuFiles.png\|bwVisu-files\|center\|x300px]]

	Data on SDS@hd (under /mnt/sds-hd) can only be accessed from within jobs. Therefore, you need to open a terminal (within a JupyterLab or Rstudio job or directly on Helix) and set a symbolic link to your SDS@hd folder in your home directory. For example like this:		'''<u>For SDS@hd users:</u>''' Data on SDS@hd (under /mnt/sds-hd) can only be accessed from within jobs. Therefore, you need to open a terminal (within a JupyterLab or Rstudio job or directly on Helix) and set a symbolic link to your SDS@hd folder in your home directory. For example like this:
	<pre>cd $HOME		<pre>cd $HOME
	mkdir sds-hd		mkdir sds-hd
	cd sds-hd		cd sds-hd
	ln -s /mnt/sds-hd/sd16a001 sd16a001</pre~~><br /~~>		ln -s /mnt/sds-hd/sd16a001 sd16a001</pre>

	=== Interactive Apps ===		=== Interactive Apps ===

H Schumacher: Added link to monitoring portal

2025-11-20T17:50:46Z

Added link to monitoring portal

← Older revision		Revision as of 19:50, 20 November 2025
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	[[File:bwVisuConcept.png\|center\|x170px]]		[[File:bwVisuConcept.png\|center\|x170px]]
	<ol>		<ol>
	<li>At the start page of the web frontend, you can start a new job by clicking on an application version in the list of pinned apps.</li>		<li> At the start page of the web frontend, you can start a new job by clicking on an application version in the list of pinned apps.</li>
	<li>You will now see the application description and options to adjust the job resources.</li>		<li>You will now see the application description and options to adjust the job resources.</li>
	<ul>		<ul>
			<li> To find the best resource settings for your jobs, please have a look at the [https://helix-monitoring.bwservices.uni-heidelberg.de/ bwForCluster Helix monitoring portal] . There, you can see how much of the requested resources where actually used by your jobs.
	<li>At the bottom of the page, beneath the <code>Launch</code> button, you can find a link for accessing the logs/session data of all your jobs.</li>		<li> At the bottom of the page, beneath the <code>Launch</code> button, you can find a link for accessing the logs/session data of all your jobs.</li>
	<li>The interface can differ per app because each app can have individual configuration options. </li>		<li>The interface can differ per app because each app can have individual configuration options. </li>
	[[File:bwVisuRStudio.png\|bwVisu-rstudio\|center\|x200px]]</li>		[[File:bwVisuRStudio.png\|bwVisu-rstudio\|center\|x200px]]</li>

H Schumacher: Added shell info

2025-11-04T11:58:32Z

Added shell info

← Older revision		Revision as of 13:58, 4 November 2025
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	In the navigation bar, the user has the following options:		In the navigation bar, the user has the following options:

	<code>Files</code> — <code>Interactive Apps</code> — <code>My Interactive Sessions</code>		<code>Files</code> — <code>Interactive Apps</code> — <code>My Interactive Sessions</code> — <code>Shell</code>

	=== Files ===		=== Files ===
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	At bwVisu, it is possible to start several interactive apps simultaneously. Here, one can view an overview of currently running interactive apps and completed sessions. It is also possible to view the log for each session. As soon as one starts an interactive app, one is automatically redirected here. Even if you log out of bwVisu and log back in, you can still see the information and logs from the finished interactive apps here until you delete it.		At bwVisu, it is possible to start several interactive apps simultaneously. Here, one can view an overview of currently running interactive apps and completed sessions. It is also possible to view the log for each session. As soon as one starts an interactive app, one is automatically redirected here. Even if you log out of bwVisu and log back in, you can still see the information and logs from the finished interactive apps here until you delete it.

			=== Shell ===
			For bwForCluster Helix users only: After entering your OTP and password a shell on the login node of bwForCluster Helix opens. This way, you can for example create workspaces when you need more space. Please look up the details under [[Helix/Filesystems#Workspaces \| Helix Workspaces]]. They can't be seen in the File Viewer but are available within the bwVisu jobs.

	== Start a Job ==		== Start a Job ==

H Schumacher: Added troubleshooting section

2025-10-06T14:25:34Z

Added troubleshooting section

← Older revision		Revision as of 16:25, 6 October 2025
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	The job will terminate when the job runtime requested in the job submission form has expired To terminate an application yourself, you can click the delete button or end the application in the interactive session. If the app is terminated in the interactive session, the window no longer shows <code>Running</code> but <code>Completed</code>. With the <code>Delete</code> button, you end the session and also remove the list entry from <code>My Interactive Sessions</code>.		The job will terminate when the job runtime requested in the job submission form has expired To terminate an application yourself, you can click the delete button or end the application in the interactive session. If the app is terminated in the interactive session, the window no longer shows <code>Running</code> but <code>Completed</code>. With the <code>Delete</code> button, you end the session and also remove the list entry from <code>My Interactive Sessions</code>.

			== Troubleshooting ==
			In case of problems, it can help to look up the related bwForCluster Helix wiki pages.
			For example:
			* Error: Disk space exceeded → '''[https://wiki.bwhpc.de/e/Helix/Filesystems#Troubleshooting Filesystems: Troubleshooting]'''

H Schumacher: Added info about SDS@hd access

2025-06-24T11:13:24Z

Added info about SDS@hd access

← Older revision		Revision as of 13:13, 24 June 2025
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	=== Files ===		=== Files ===

	Here, you can access your home directory on Helix ~~and data on SDS@hd (under /mnt/sds-hd)~~. In a graphical user interface, files can be downloaded and uploaded, and new files and folders can be created. You will encounter an error message if you try to see data that you have no access to.~~<br />~~		Here, you can access your home directory on Helix. In a graphical user interface, files can be downloaded and uploaded, and new files and folders can be created. You will encounter an error message if you try to see data that you have no access to.

	In the Home Directory the results and logs from the apps are stored. You get the following interface:		In the Home Directory the results and logs from the apps are stored. You get the following interface:

	[[File:BwVisuFiles.png\|bwVisu-files\|center\|x300px]]		[[File:BwVisuFiles.png\|bwVisu-files\|center\|x300px]]

			Data on SDS@hd (under /mnt/sds-hd) can only be accessed from within jobs. Therefore, you need to open a terminal (within a JupyterLab or Rstudio job or directly on Helix) and set a symbolic link to your SDS@hd folder in your home directory. For example like this:
			<pre>cd $HOME
			mkdir sds-hd
			cd sds-hd
			ln -s /mnt/sds-hd/sd16a001 sd16a001</pre><br />

	=== Interactive Apps ===		=== Interactive Apps ===

H Schumacher: Added explanation on how to change the window size

2025-05-22T22:17:28Z

Added explanation on how to change the window size

← Older revision		Revision as of 00:17, 23 May 2025
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	* '''noVNC menu''' within the running application		* '''noVNC menu''' within the running application
	** When you open the application you can see an additional menu on the left with options. For the ones using the application in view-only mode it is helpful to select the option to show a dot instead of not showing the mouse cursor at all. Therefore go to "Options" and then "Expand".		** When you open the application you can see an additional menu on the left with options. For the ones using the application in view-only mode it is helpful to select the option to show a dot instead of not showing the mouse cursor at all. Therefore go to "Options" and then "Expand".
	** For copying data, you need to use the clipboard. When copying something locally, you need to put it into the clipboard before you can use it within the application. The same goes the other way around.		** For copying data, you need to use the clipboard. When copying something locally, you need to put it into the clipboard before you can use it within the application. The same goes the other way around.
			* '''Adjust window size''' and position of the app by executing a right click at the edge of the app window frame, so that a menu shows up.

	== Terminate a Job ==		== Terminate a Job ==

H Schumacher: clipboard

2025-02-18T12:31:56Z

clipboard

← Older revision		Revision as of 14:31, 18 February 2025
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	** Compression slider: Before opening the application, you can choose the compression level to use. 0 means no compression while 9 offers the best compression but uses more CPU resources on the cluster which can be slower.		** Compression slider: Before opening the application, you can choose the compression level to use. 0 means no compression while 9 offers the best compression but uses more CPU resources on the cluster which can be slower.
	** Image Quality slider: Before opening the application, you can choose the image quality level. With this you can control the desired JPEG quality.		** Image Quality slider: Before opening the application, you can choose the image quality level. With this you can control the desired JPEG quality.
	** View Only (Share-able Link) button: By clicking this button the application opens in view only mode. You can share this link with collaborators or students while you launch ~~Fiji~~ normally for yourself. This way, others can follow what you are doing. For every job you need to generate a new link.		** View Only (Share-able Link) button: By clicking this button the application opens in view only mode. You can share this link with collaborators or students while you launch your noVNC application normally for yourself. This way, others can follow what you are doing. For every job you need to generate a new link.
	* '''noVNC menu''' within the running application		* '''noVNC menu''' within the running application
	** When you open the application you can see an additional menu on the left with options. For the ones using the application in view-only mode it is helpful to select the option to show a dot instead of not showing the mouse cursor at all. Therefore go to "Options" and then "Expand".		** When you open the application you can see an additional menu on the left with options. For the ones using the application in view-only mode it is helpful to select the option to show a dot instead of not showing the mouse cursor at all. Therefore go to "Options" and then "Expand".
			** For copying data, you need to use the clipboard. When copying something locally, you need to put it into the clipboard before you can use it within the application. The same goes the other way around.

	== Terminate a Job ==		== Terminate a Job ==

H Schumacher: noVNC section

2025-01-28T12:40:44Z

noVNC section

@@ Line 43: / Line 43: @@
 <li> Connect to the job with your browser by clicking <code>connect to &lt;application&gt;</code>. </li>
 </ol>
 == Terminate a Job ==