Squiggles research computer server: Difference between revisions

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=== Introduction ===
=== Introduction ===
"Squiggles" is a dedicated research computer server for the analysis and storage of MEG, Neurophysiology, and Epilepsy data. Users can connect to it using either the FastX connection (recommended) or the older VNC method. This guide provides detailed steps for both methods.
"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 ====
Before accessing "Squiggles", users need an RCC (Research Computer Server) account.
 
* Submit requests at [https://infoscope.mcw.edu/RCC/Research-Computing-Center.html MCW-Infoscope's Research Computing Center]
* An RCC (Research Computer Server) account is necessary to access "Squiggles".
* If prompted, select "others" and "squiggles" to specify the server.
* Register for an account at [https://docs.rcc.mcw.edu/user-guide/accounts/ MCW-Infoscope's Research Computing Center].
* Follow the subsequent instructions to initiate a new session and remotely access Squiggles.
* 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:


=== How to Access Squiggles ===
==== VNC Method ====
Configuration:
* For Windows: Download [https://www.chiark.greenend.org.uk/~sgtatham/putty/ Putty].
* For Mac/Linux: Use a bash shell or terminal.
=====VNC User Ports:=====
Users must log in using their designated port numbers. Below is the list of users and their respective ports:
{| class="wikitable"
{| class="wikitable"
|-
|-
Line 22: 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 78: Line 75:
|5929
|5929
|-
|-
|Vahab Youssofzadeh
|Setayesh Abiazi Shalmani
|5930
|-
|Vahab Youssof Zadeh
|5931
|5931
|-
|-
Line 84: Line 84:
|5935
|5935
|-
|-
|Cameron J Stewart  
|Rupesh Chikara
|5944
|-
|Cameron J Stewart
|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


===Creating a VNC session===
* '''PuTTY (Windows):'''
VNC sessions are created at bootup using the above port numbers.
[https://www.chiark.greenend.org.uk/~sgtatham/putty/ Download PuTTY] for SSH tunneling and refer to the images below for configuration:
If a session fails, use the command: <code>vncserver :## -geometry 1900x1200</code> where ## corresponds to your port number.


===Connecting to Squiggles===
PuTTY is an open-source software used for SSH Tunneling (or SSH Port Forwarding).
====For Mac or Linux====
 
From a bash shell / terminal type the following. This will open a tunnel over ssh to log into VNC Viewer (see below).
[[File:Putty config1.PNG]]
<code>/ssh -N -L 59**:localhost:59** squiggles.rcc.mcw.edu</code>
[[File:Putty config2 tunnel.PNG]]
 
====For Windows====
An SSH tunnel must be performed using Putty or with windows 10 you can use the ssh command above.
 
Download Putty:
https://www.chiark.greenend.org.uk/~sgtatham/putty/


[[File:Putty config1.PNG]]
=== Starting a Session and Connecting to Squiggles ===
Ensure you've established an SSH tunnel before proceeding with either the VNC or FastX methods.


[[File:Putty config2 tunnel.PNG]]
==== VNC Method (preferred) ====
* '''Creating & Accessing a VNC Session''':
** VNC sessions initialize automatically upon boot-up.
** 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.


===Logging into VNC session===
[[image:vncviewer.png]]


Once connected to squiggles over ssh
<!-- ==== 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>.


====Creating a VNC session====
[[File: FastX_config.png]] -->
VNC sessions will be created at bootup using the port numbers above
If the VNC session fails or is not working:
<code>vncserver :## -geometry 1900x1200</code> (This will open a vnc session on port 59## with a resolution of 1900x1200)  The ## must match your port number for this to work.


====Connecting to a VNC session====
Use realvnc viewer to log into your VNC session. 
=====VNC viewer download=====
Realvnc has been tested to work - https://www.realvnc.com/en/connect/download/viewer/
=====Log in using RealVNC=====
Open vncviewer
In the top bar that accepts a VNC Server address <br />
type localhost:##  (where ## are the last two digits of your port number 59##)
[[image:vncviewer.png]]
Log into the VNC session using your VNC password <br />
Once the VNC window is open, log into the server using your RCC password
=====Killing a VNC session=====
From the terminal try, <br />
<pre>
vncserver -kill :xx/
</pre>
For a manual kill (if asked) try, <br />
<pre>
rm -f /tmp/.Xxx-lock
rm -f /tmp/.X11-unix/Xxx
</pre>


=====List of users=====
=== Troubleshooting ===
From the terminal try, <br />
;'''Identifying Active Users'''
<code>ls -l /tmp/.X11-unix</code>
: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.


=====Common issues & Solutions=====
;'''Terminating a VNC Session'''
FastX is an alternative to VNC viewer
: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.


* Before a VNC session is created, anaconda python must be deactivated. Enter <code>conda deactivate</code> into the terminal. If the user does not deactivate anaconda python, VNC will start, but a black screen is shown after logging in.
;'''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.


==== FastX Connection (alternative connection) ====
;'''Alternative Solution: when Manual Termination of the VNC does not work'''
FastX is an alternative to VNC connect. It provides a more straightforward connection than VNC. Previously, we had an issue with a large number of users logging in at once using the VNC. FastX resolves this issue.
: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.


The FastX server is installed on squiggles. You will need to download the client - https://www.starnet.com/fastx/current-client
: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>


[[File: FastX_config.png]]
;'''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>


Steps to setup the connection: <br />   
;'''Disable Conda auto‑activation (so you don’t have to run <code>conda deactivate</code> each time)'''
1. Open fastX <br />
:If you seldom need Conda inside VNC, turn off automatic activation:
2. Click the plus to start a new connection <br />
:* Run <code>conda config --set auto_activate_base false</code> (this updates <code>~/.condarc</code>), **or**  
3. Enter the Connection Name, host (squiggles.rcc.mcw.edu), and user (rcc username) <br />
:* Edit <code>~/.bashrc</code> and comment out / delete the line that calls <code>conda activate base</code>.
4. Click the plus to enter a session.  Use /etc/X11/xinit/xinitrc for the command <br />
: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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