Difference between revisions of "Squiggles research computer server"

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=== Introduction ===
 
=== Introduction ===
−
"Squiggles" is a dedicated research computer server designed for the analysis and storage of MEG, Neurophysiology, and Epilepsy data. This guide elucidates the steps to connect using either the recommended FastX connection or the traditional VNC method.
+
"Squiggles" is a dedicated research computer server tailored for the analysis and storage of MEG, Neurophysiology, and Epilepsy data. This guide outlines how to connect using either the recommended FastX connection or the traditional VNC method.
  
 
=== Access Requirements ===
 
=== Access Requirements ===
 
==== RCC Account ====
 
==== RCC Account ====
−
* To utilize "Squiggles", an RCC (Research Computer Server) account is mandatory.
 
−
* Register for an account on [[https://docs.rcc.mcw.edu/user-guide/accounts/ MCW-Infoscope's Research Computing Center]].
 
−
* If prompted, choose "others" followed by "squiggles" to indicate the server of interest.
 
−
* Adhere to the ensuing steps to kickstart a new session and gain remote access to Squiggles.
 
  
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=== Connecting to Squiggles ===
+
* An RCC (Research Computer Server) account is necessary to access "Squiggles".
−
Before proceeding with either the VNC or FastX methods, ensure you've chosen a unique port number to establish an SSH tunnel:
+
* Register for an account at [https://docs.rcc.mcw.edu/user-guide/accounts/ MCW-Infoscope's Research Computing Center].
 +
* If prompted, select "others" and then "squiggles" to specify the server you wish to access.
 +
* Account approval generally takes 1-3 days. For any issues, contact Help-RCC at <help-rcc@mcw.edu>.
  
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'''VNC User Ports:'''
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=== Login to Squiggles ===
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Each user has a dedicated port number for login (pick one that is not taken):
+
'''Choosing a User Port:''' Each user is allocated a specific port number. New users should pick a port number (##) not already in use:
  
 
{| class="wikitable"
 
{| class="wikitable"
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|5992
 
|5992
 
|}
 
|}
 +
===== SSH Tunneling =====
 +
* '''PowerShell Method (Mac/Linux/Windows):''' In a bash shell, terminal, or Windows PowerShell, execute the following to set up an SSH tunnel for the VNC Viewer:
 +
<code>ssh -L 59##:localhost:59## USER@squiggles.rcc.mcw.edu</code>
 +
where USER is your rcc user account and ## is the selected port number
  
−
==== VNC Method ====
+
* '''PuTTY (Windows):'''
 +
[https://www.chiark.greenend.org.uk/~sgtatham/putty/ Download PuTTY] for SSH tunneling and refer to the images below for configuration:
  
−
===== SSH Tunneling Method using Power Shell (for Mac/Linux/Windows) =====
+
PuTTY is an open-source software used for SSH Tunneling (or SSH Port Forwarding).
−
In a bash shell, terminal, or Windows PowerShell, execute the following to set up an SSH tunnel for the VNC Viewer:
 
−
<code>ssh -N -L 59##:localhost:59## squiggles.rcc.mcw.edu</code>
 
−
 
 
−
===== SSH Tunneling Method using Putty (for Windows) =====
 
−
PuTTY is an open-source software for SSH Tunneling (or SSH Port Forwarding)
 
−
[https://www.chiark.greenend.org.uk/~sgtatham/putty/ Download Putty] for SSH tunneling, and follow below images for configuration:
 
 
    
 
    
 
[[File:Putty config1.PNG]]
 
[[File:Putty config1.PNG]]
 
[[File:Putty config2 tunnel.PNG]]
 
[[File:Putty config2 tunnel.PNG]]
  
−
==== FastX Method ====
+
=== Starting a Session and Connecting to Squiggles ===
−
FastX is potentially a more seamless alternative to VNC, especially when handling many simultaneous users.
+
Ensure you've established an SSH tunnel before proceeding with either the VNC or FastX methods.
−
* Fetch the [https://www.starnet.com/fastx/current-client FastX client] and then:
+
 
−
  ** Launch FastX.
+
==== VNC Method (preferred) ====
−
  ** Press '+' to set up a new connection.
+
* '''Creating & Accessing a VNC Session''':
−
  ** Enter Connection Name, host (squiggles.rcc.mcw.edu), and your RCC username.
+
** VNC sessions initialize automatically upon boot-up.
−
  ** To begin a session, tap '+' and use the command <code>/etc/X11/xinit/xinitrc</code>.
+
** If issues occur, manually initiate a session using: <code>vncserver :## -geometry 1900x1200</code>, where <code>##</code> is your specific port number.
 +
** Access the session using the [[https://www.realvnc.com/en/connect/download/viewer/ RealVNC viewer]].
 +
** Input <code>localhost:##</code> in the server address bar, where <code>##</code> corresponds to the last two digits of your port.
 +
 
 +
[[image:vncviewer.png]]
 +
 
 +
==== FastX Method (alternative) ====
 +
FastX offers a potentially smoother experience compared to VNC, especially with multiple concurrent users.
 +
* Download the [https://www.starnet.com/fastx/current-client FastX client] and:
 +
** Start FastX.
 +
** Click '+' to establish a new connection.
 +
** Provide the Connection Name, host (squiggles.rcc.mcw.edu), and your RCC username.
 +
** Start a session by clicking '+' and using the command <code>/etc/X11/xinit/xinitrc</code>.
  
 
[[File: FastX_config.png]]
 
[[File: FastX_config.png]]
  
−
'''Creating & Accessing a VNC Session''':
 
−
* VNC sessions are initialized automatically during boot-up.
 
−
* If issues arise, manually start a session with: <code>vncserver :## -geometry 1900x1200</code>, replacing <code>##</code> with your specific port number.
 
−
* For access, employ the [[https://www.realvnc.com/en/connect/download/viewer/ RealVNC viewer]].
 
−
* In the server address bar, input <code>localhost:##</code>, where <code>##</code> matches the last two digits of your port.
 
  
−
[[image:vncviewer.png]]
+
=== Troubleshooting ===
 +
 
 +
;'''VNC Black Screen Issue'''
 +
:If you encounter a black screen after logging into VNC, it could be due to the Anaconda Python environment interfering with the session. To resolve this issue, deactivate Anaconda Python using the command:
 +
:<code>conda deactivate</code>
 +
 
 +
;'''Identifying Active Users'''
 +
:To compile a list of users with active VNC sessions, which aids in monitoring current access to the VNC service, execute:
 +
:<code>ls -l /tmp/.X11-unix</code>
 +
:This information can be used to oversee session activity and ensure that resources are allocated efficiently.
 +
 
 +
;'''Terminating a VNC Session'''
 +
:For situations where session termination is necessary, you can directly close a VNC session through the terminal or opt for manual termination if the direct method is insufficient. To directly terminate a session, use:
 +
:<code>vncserver -kill :xx</code>
 +
:Replace <code>:xx</code> with your session number.
 +
 
 +
:For manual termination, proceed to remove the session files with:
 +
:<code>rm -f /tmp/.Xxx-lock</code>
 +
:<code>rm -f /tmp/.X11-unix/Xxx</code>
 +
:Ensure to replace <code>Xxx</code> with the correct session identifier. This allows for the removal of stuck or unresponsive sessions that cannot be closed normally.
  
−
=== Troubleshooting ===
+
;'''Alternative Solution: Identifying Active Sessions'''
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* '''VNC Black Screen''': Experiencing a black screen after VNC login? Ensure you've deactivated Anaconda Python prior. Command: <code>conda deactivate</code>.
+
:Identifying sessions created by a specific user can be a strategic approach to session management, offering an alternative to manual session termination. This method is particularly useful for identifying and removing only unnecessary or problematic sessions. Use the following command, replacing <code>&lt;username&gt;</code> with the actual username:
−
* '''Persistent VNC Issues''': Switch to the FastX method.
+
:<code>ps -ef | grep &lt;username&gt;</code>
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* '''Killing a VNC session''': In terminal, <code>vncserver -kill :xx/</code>. For manual termination:
 
−
<pre>
 
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rm -f /tmp/.Xxx-lock
 
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rm -f /tmp/.X11-unix/Xxx
 
−
</pre>
 
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* '''Identifying Active Users''': Command <code>ls -l /tmp/.X11-unix</code>.
 

Revision as of 15:08, 13 March 2024

Introduction

"Squiggles" is a dedicated research computer server tailored for the analysis and storage of MEG, Neurophysiology, and Epilepsy data. This guide outlines how to connect using either the recommended FastX connection or the traditional VNC method.

Access Requirements

RCC Account

  • An RCC (Research Computer Server) account is necessary to access "Squiggles".
  • Register for an account at MCW-Infoscope's Research Computing Center.
  • If prompted, select "others" and then "squiggles" to specify the server you wish to access.
  • Account approval generally takes 1-3 days. For any issues, contact Help-RCC at <help-rcc@mcw.edu>.

Login to Squiggles

Choosing a User Port: Each user is allocated a specific port number. New users should pick a port number (##) not already in use:

User Port
Jeff Stout 5910,5911
Joe Heffernan 5912
Candida Ustine 5914
Manoj Raghavan 5913
Chad Carlson 5915
Chris Anderson 5916
Serena Thompson 5917
Patrick Bauer 5918
Jeff Binder 5919
Leo Fernandino 5920
Lisa Conant 5921
Aqil Izadysadr 5922
Nick Guzowski 5923
Zack Harper 5924
Bill Gross 5925
Michelle Kassel 5926
Greg McQuestion 5927
Monica Keith 5928
Priyanka Shah 5929
Vahab Youssofzadeh 5931
Songhee Kim 5935
Cameron J Stewart 5992
SSH Tunneling
  • PowerShell Method (Mac/Linux/Windows): In a bash shell, terminal, or Windows PowerShell, execute the following to set up an SSH tunnel for the VNC Viewer:

ssh -L 59##:localhost:59## USER@squiggles.rcc.mcw.edu where USER is your rcc user account and ## is the selected port number

  • PuTTY (Windows):

Download PuTTY for SSH tunneling and refer to the images below for configuration:

PuTTY is an open-source software used for SSH Tunneling (or SSH Port Forwarding).

Putty config1.PNG Putty config2 tunnel.PNG

Starting a Session and Connecting to Squiggles

Ensure you've established an SSH tunnel before proceeding with either the VNC or FastX methods.

VNC Method (preferred)

  • Creating & Accessing a VNC Session:
    • VNC sessions initialize automatically upon boot-up.
    • If issues occur, manually initiate a session using: vncserver :## -geometry 1900x1200, where ## is your specific port number.
    • Access the session using the [RealVNC viewer].
    • Input localhost:## in the server address bar, where ## corresponds to the last two digits of your port.

Vncviewer.png

FastX Method (alternative)

FastX offers a potentially smoother experience compared to VNC, especially with multiple concurrent users.

  • Download the FastX client and:
    • Start FastX.
    • Click '+' to establish a new connection.
    • Provide the Connection Name, host (squiggles.rcc.mcw.edu), and your RCC username.
    • Start a session by clicking '+' and using the command /etc/X11/xinit/xinitrc.

FastX config.png


Troubleshooting

VNC Black Screen Issue
If you encounter a black screen after logging into VNC, it could be due to the Anaconda Python environment interfering with the session. To resolve this issue, deactivate Anaconda Python using the command:
conda deactivate
Identifying Active Users
To compile a list of users with active VNC sessions, which aids in monitoring current access to the VNC service, execute:
ls -l /tmp/.X11-unix
This information can be used to oversee session activity and ensure that resources are allocated efficiently.
Terminating a VNC Session
For situations where session termination is necessary, you can directly close a VNC session through the terminal or opt for manual termination if the direct method is insufficient. To directly terminate a session, use:
vncserver -kill :xx
Replace :xx with your session number.
For manual termination, proceed to remove the session files with:
rm -f /tmp/.Xxx-lock
rm -f /tmp/.X11-unix/Xxx
Ensure to replace Xxx with the correct session identifier. This allows for the removal of stuck or unresponsive sessions that cannot be closed normally.
Alternative Solution: Identifying Active Sessions
Identifying sessions created by a specific user can be a strategic approach to session management, offering an alternative to manual session termination. This method is particularly useful for identifying and removing only unnecessary or problematic sessions. Use the following command, replacing <username> with the actual username:
ps -ef | grep <username>
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