Squiggles research computer server: Difference between revisions

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|Jeff Stout
|Jeff Stout
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|5910, 5911
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|Joe Heffernan
|Joe Heffernan
|5912
|5912
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|Manoj Raghavan
|5913, 5998, 5999
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|Candida Ustine
|Candida Ustine
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|Manoj Raghavan
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|Chad Carlson
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|Vahab Youssofzadeh
|Setayesh Abiazi Shalmani
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|Vahab Youssof Zadeh
|5931
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|Cameron J Stewart  
|Rupesh Chikara
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===== SSH Tunneling =====
===== 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:
* '''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:
Line 121: Line 128:


=== Troubleshooting ===
=== 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>
:Alternativey, modify your `.vnc/xstartup` script e.g., using,
:<code>nano ~/.vnc/xstartupc</code>
:to adjust the `PATH` and deactivate Conda before starting the desktop environment. Here's an example modification to include in your `.vnc/xstartup` script:
<pre style="margin-left: 20px;">
#!/bin/sh
# Log environment variables to help with debugging
printenv > ~/vnc_environment.log
unset SESSION_MANAGER
unset DBUS_SESSION_BUS_ADDRESS
# exec /etc/X11/xinit/xinitrc
# Adjust PATH and deactivate Conda
export PATH=/usr/local/bin:/usr/bin:/bin:$PATH
conda deactivate
gnome-session
</pre>
;'''Identifying Active Users'''
;'''Identifying Active Users'''
:To compile a list of users with active VNC sessions, which aids in monitoring current access to the VNC service, execute:
:To compile a list of users with active VNC sessions, which aids in monitoring current access to the VNC service, execute:
Line 154: Line 135:
;'''Terminating a VNC Session'''
;'''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:
: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>
:<code>vncserver -kill :##</code>
:Replace <code>:xx</code> with your session number.
:Replace <code>:##</code> with your session number.


;'''Manual Termination of the VNC'''
:For manual termination, proceed to remove the session files with:
:For manual termination, proceed to remove the session files with:
:<code>rm -f /tmp/.Xxx-lock</code>
:<code>rm -f /tmp/.X##-lock</code>
:<code>rm -f /tmp/.X11-unix/Xxx</code>
:<code>rm -f /tmp/.X11-unix/X##</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.
:Ensure to replace <code>X##</code> with the correct session identifier. This allows for removing stuck or unresponsive sessions that cannot be closed normally.


;'''Alternative Solution: Identifying Active Sessions and Terminating a VNC Session'''
;'''Alternative Solution: when Manual Termination of the VNC does not work'''
: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:
:Use the following command, replacing <code>&lt;username&gt;</code> with the actual username:
:<code>ps -ef | grep &lt;username&gt;</code>
:<code>ps -ef | grep &lt;username&gt;</code>
:This will list all processes related to the specified user. You can then terminate unwanted sessions by killing the process IDs:
:This will list all processes related to the specified user. You can then terminate unwanted sessions by killing the process IDs:
:<code>kill -9 &lt;PID&gt;</code>
:<code>kill -9 &lt;PID&gt;</code>
:Where <code>&lt;PID&gt;</code> is the process ID obtained from the output of the previous command.
:Where <code>&lt;PID&gt;</code> is the process ID obtained from the previous command's output.


:To check the environment variables active during a VNC session, which can help in troubleshooting further issues, view the VNC environment log:
:Optional: To check the environment variables active during a VNC session, which can help in troubleshooting further issues, view the VNC environment log:
:<code>cat ~/vnc_environment.log</code>
:<code>cat ~/vnc.log</code>
 
;'''VNC connection‑closed / black‑screen issue'''
:Anaconda’s base environment can interfere with VNC and close the session. 
:Deactivate it after login:
:<code>conda deactivate</code>
 
;'''Disable Conda auto‑activation (so you don’t have to run <code>conda deactivate</code> each time)'''
:If you seldom need Conda inside VNC, turn off automatic activation:
:* Run <code>conda config --set auto_activate_base false</code> (this updates <code>~/.condarc</code>), **or** 
:* Edit <code>~/.bashrc</code> and comment out / delete the line that calls <code>conda activate base</code>.
:After logging out and back in, Conda will stay inactive by default; activate it later with <code>conda activate &lt;env&gt;</code> only when needed.
</pre>

Latest revision as of 15:23, 21 April 2025

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
Manoj Raghavan 5913, 5998, 5999
Candida Ustine 5914
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
Setayesh Abiazi Shalmani 5930
Vahab Youssof Zadeh 5931
Songhee Kim 5935
Rupesh Chikara 5944
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


Troubleshooting

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 :##
Replace :## with your session number.
Manual Termination of the VNC
For manual termination, proceed to remove the session files with:
rm -f /tmp/.X##-lock
rm -f /tmp/.X11-unix/X##
Ensure to replace X## with the correct session identifier. This allows for removing stuck or unresponsive sessions that cannot be closed normally.
Alternative Solution: when Manual Termination of the VNC does not work
Use the following command, replacing <username> with the actual username:
ps -ef | grep <username>
This will list all processes related to the specified user. You can then terminate unwanted sessions by killing the process IDs:
kill -9 <PID>
Where <PID> is the process ID obtained from the previous command's output.
Optional: To check the environment variables active during a VNC session, which can help in troubleshooting further issues, view the VNC environment log:
cat ~/vnc.log
VNC connection‑closed / black‑screen issue
Anaconda’s base environment can interfere with VNC and close the session.
Deactivate it after login:
conda deactivate
Disable Conda auto‑activation (so you don’t have to run conda deactivate each time)
If you seldom need Conda inside VNC, turn off automatic activation:
  •  Run conda config --set auto_activate_base false (this updates ~/.condarc), **or**
  •  Edit ~/.bashrc and comment out / delete the line that calls conda activate base.
After logging out and back in, Conda will stay inactive by default; activate it later with conda activate <env> only when needed.
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