Squiggles research computer server: Difference between revisions

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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]].
* An RCC (Research Computer Server) account is necessary to access "Squiggles".
* If prompted, choose "others" followed by "squiggles" to indicate the server of interest.
* Register for an account at [https://docs.rcc.mcw.edu/user-guide/accounts/ MCW-Infoscope's Research Computing Center].
* The process takes 1-3 days. If having an issue contact Help-RCC <help-rcc@mcw.edu> for help
* 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 ===
=== Login to Squiggles ===
'''Choose User Ports:''' Each user has a dedicated port number for login. New users should select a sport number (##) that is not taken by other users:
'''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"
Line 18: Line 19:
|-
|-
|Jeff Stout
|Jeff Stout
|5910,5911
|5910, 5911
|-
|-
|Joe Heffernan
|Joe Heffernan
|5912
|5912
|-
|Manoj Raghavan
|5913, 5998, 5999
|-
|-
|Candida Ustine
|Candida Ustine
|5914
|5914
|-
|Manoj Raghavan
|5913
|-
|-
|Chad Carlson
|Chad Carlson
Line 74: Line 75:
|5929
|5929
|-
|-
|Vahab Youssofzadeh
|Setayesh Abiazi Shalmani
|5930
|-
|Vahab Youssof Zadeh
|5931
|5931
|-
|-
Line 80: Line 84:
|5935
|5935
|-
|-
|Cameron J Stewart  
|Rupesh Chikara
|5944
|-
|Cameron J Stewart
|5992
|5992
|}
|}


===== SSH Tunneling =====
===== SSH Tunneling =====
* ''' Power Shell Method (for 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:
<code>ssh -N -L 59##:localhost:59## squiggles.rcc.mcw.edu</code>
<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


* ''' Putty (for Windows): '''  
* '''PuTTY (Windows):'''  
[https://www.chiark.greenend.org.uk/~sgtatham/putty/ Download Putty] for SSH tunneling, and follow the below images for configuration:
[https://www.chiark.greenend.org.uk/~sgtatham/putty/ Download PuTTY] for SSH tunneling and refer to the images below for configuration:


PuTTY is an open-source software for SSH Tunneling (or SSH Port Forwarding).
PuTTY is an open-source software used for SSH Tunneling (or SSH Port Forwarding).
    
    
[[File:Putty config1.PNG]]
[[File:Putty config1.PNG]]
[[File:Putty config2 tunnel.PNG]]
[[File:Putty config2 tunnel.PNG]]


=== Create a new Session and Connecting to Squiggles ===
=== Starting a Session and Connecting to Squiggles ===
Before proceeding with either the VNC or FastX methods, ensure you've established an SSH tunnel
Ensure you've established an SSH tunnel before proceeding with either the VNC or FastX methods.


==== VNC Method ====
==== VNC Method (preferred) ====
* '''Creating & Accessing a VNC Session''':
* '''Creating & Accessing a VNC Session''':
** VNC sessions are initialized automatically during boot-up.
** VNC sessions initialize automatically upon boot-up.
** If issues arise, manually start a session with: <code>vncserver :## -geometry 1900x1200</code>, replacing <code>##</code> with your specific port number.
** If issues occur, manually initiate a session using: <code>vncserver :## -geometry 1900x1200</code>, where <code>##</code> is your specific port number.
** For access, employ the [[https://www.realvnc.com/en/connect/download/viewer/ RealVNC viewer]].
** Access the session using 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.
** Input <code>localhost:##</code> in the server address bar, where <code>##</code> corresponds to the last two digits of your port.


[[image:vncviewer.png]]
[[image:vncviewer.png]]


==== FastX Method ====
<!-- ==== FastX Method (alternative) ====
FastX is potentially a more seamless alternative to VNC, especially when handling many simultaneous users.
FastX offers a potentially smoother experience compared to VNC, especially with multiple concurrent users.
* Fetch the [https://www.starnet.com/fastx/current-client FastX client] and then:
* Download the [https://www.starnet.com/fastx/current-client FastX client] and:
** Launch FastX.
** Start FastX.
** Press '+' to set up a new connection.
** Click '+' to establish a new connection.
** Enter Connection Name, host (squiggles.rcc.mcw.edu), and your RCC username.
** Provide the Connection Name, host (squiggles.rcc.mcw.edu), and your RCC username.
** To begin a session, tap '+' and use the command <code>/etc/X11/xinit/xinitrc</code>.
** Start a session by clicking '+' and using the command <code>/etc/X11/xinit/xinitrc</code>.
 
[[File: FastX_config.png]] -->


[[File: FastX_config.png]]


=== Troubleshooting ===
=== Troubleshooting ===
* '''VNC Black Screen''': Experiencing a black screen after VNC login? Ensure you've deactivated Anaconda Python prior. Command: <code>conda deactivate</code>.
;'''Identifying Active Users'''
* '''Persistent VNC Issues''': Switch to the FastX method.
:To compile a list of users with active VNC sessions, which aids in monitoring current access to the VNC service, execute:
* '''Killing a VNC session''': In terminal, <code>vncserver -kill :xx/</code>. For manual termination:
:<code>ls -l /tmp/.X11-unix</code>
<pre>
:This information can be used to oversee session activity and ensure that resources are allocated efficiently.
rm -f /tmp/.Xxx-lock
 
rm -f /tmp/.X11-unix/Xxx
;'''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 :##</code>
:Replace <code>:##</code> with your session number.
 
;'''Manual Termination of the VNC'''
:For manual termination, proceed to remove the session files with:
:<code>rm -f /tmp/.X##-lock</code>
:<code>rm -f /tmp/.X11-unix/X##</code>
: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: when Manual Termination of the VNC does not work'''
:Use the following command, replacing <code>&lt;username&gt;</code> with the actual username:
:<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:
:<code>kill -9 &lt;PID&gt;</code>
:Where <code>&lt;PID&gt;</code> 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:
:<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>
</pre>
* '''Identifying Active Users''': Command <code>ls -l /tmp/.X11-unix</code>.

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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