Squiggles research computer server: Difference between revisions

From MEG Wiki
Jump to navigation Jump to search
No edit summary
 
(136 intermediate revisions by the same user not shown)
Line 1: Line 1:
=== 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]
* If prompted, select "others" and "squiggles" to specify the server.
* Follow the subsequent instructions to initiate a new session and remotely access Squiggles.


=== How to Access Squiggles ===
* An RCC (Research Computer Server) account is necessary to access "Squiggles".
==== VNC Method ====
* Register for an account at [https://docs.rcc.mcw.edu/user-guide/accounts/ MCW-Infoscope's Research Computing Center].
Configuration:
* If prompted, select "others" and then "squiggles" to specify the server you wish to access.
* For Mac/Linux: Use a bash shell or terminal.
* Account approval generally takes 1-3 days. For any issues, contact Help-RCC at <help-rcc@mcw.edu>.
From a bash shell/terminal, type the following to open a tunnel over SSH and log into VNC Viewer:


/ssh -N -L 59**:localhost:59** squiggles.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:


* For Windows:
Download [https://www.chiark.greenend.org.uk/~sgtatham/putty/ Putty].
Images for configuration:
[[File:Putty config1.PNG]]
[[File:Putty config2 tunnel.PNG]]
=====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 34: 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 90: Line 75:
|5929
|5929
|-
|-
|Vahab Youssofzadeh
|Setayesh Abiazi Shalmani
|5930
|-
|Vahab Youssof Zadeh
|5931
|5931
|-
|-
Line 96: Line 84:
|5935
|5935
|-
|-
|Cameron J Stewart  
|Rupesh Chikara
|5944
|-
|Cameron J Stewart
|5992
|5992
|}
|}


===Creating a VNC session===
===== SSH Tunneling =====
* VNC sessions are created at bootup using the above port numbers.
* '''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:
* If a session fails, use the command: <code>vncserver :## -geometry 1900x1200</code> where <code>##</code> corresponds to your port number.
<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


===Connecting to a VNC session===
* '''PuTTY (Windows):'''
* Use [https://www.realvnc.com/en/connect/download/viewer/ Realvnc] viewer to access your VNC session.
[https://www.chiark.greenend.org.uk/~sgtatham/putty/ Download PuTTY] for SSH tunneling and refer to the images below for configuration:
* In the server address bar, type localhost:## where ## are the last two digits of your port number.
* Log in using your VNC and RCC passwords as required.


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


* FastX offers a more user-friendly connection than VNC and addresses issues related to a large number of simultaneous VNC users.
=== Starting a Session and Connecting to Squiggles ===
* Download the [https://www.starnet.com/fastx/current-client FastX client] and follow these steps:
Ensure you've established an SSH tunnel before proceeding with either the VNC or FastX methods.
** Open FastX.
** Click the '+' to initiate a new connection.
** Provide the Connection Name, host (squiggles.rcc.mcw.edu), and user (your RCC username).
** To enter a session, click the '+' and use /etc/X11/xinit/xinitrc as the command.


====Common issues & Solutions====
==== VNC Method (preferred) ====
* '''VNC Black Screen:''' If VNC shows a black screen after login, ensure Anaconda Python is deactivated before creating the VNC session. Use the <code>conda deactivate</code> command in the terminal.
* '''Creating & Accessing a VNC Session''':
* '''FastX as an Alternative:''' If you experience persistent issues with VNC, consider using the FastX method described above.
** 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.


====For Mac or Linux====
[[image:vncviewer.png]]
From a bash shell / terminal type the following. This will open a tunnel over ssh to log into VNC Viewer (see below).
<code>/ssh -N -L 59**:localhost:59** squiggles.rcc.mcw.edu</code>


====For Windows====
<!-- ==== FastX Method (alternative) ====
An SSH tunnel must be performed using Putty or with windows 10 you can use the ssh command above.
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>.


Download Putty:
[[File: FastX_config.png]] -->
https://www.chiark.greenend.org.uk/~sgtatham/putty/


[[File:Putty config1.PNG]]


[[File:Putty config2 tunnel.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:
:<code>ls -l /tmp/.X11-unix</code>
:This information can be used to oversee session activity and ensure that resources are allocated efficiently.


===Logging into 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:
:<code>vncserver -kill :##</code>
:Replace <code>:##</code> with your session number.


Once connected to squiggles over ssh
;'''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.


====Creating a VNC session====
;'''Alternative Solution: when Manual Termination of the VNC does not work'''
VNC sessions will be created at bootup using the port numbers above
:Use the following command, replacing <code>&lt;username&gt;</code> with the actual username:
If the VNC session fails or is not working:
:<code>ps -ef | grep &lt;username&gt;</code>
<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.
: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.


====Connecting to a VNC session====
:Optional: To check the environment variables active during a VNC session, which can help in troubleshooting further issues, view the VNC environment log:
Use realvnc viewer to log into your VNC session. 
:<code>cat ~/vnc.log</code>
=====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=====
;'''VNC connection‑closed / black‑screen issue'''
From the terminal try, <br />
:Anaconda’s base environment can interfere with VNC and close the session. 
<code>ls -l /tmp/.X11-unix</code>
:Deactivate it after login:
:<code>conda deactivate</code>


=====Common issues & Solutions=====
;'''Disable Conda auto‑activation (so you don’t have to run <code>conda deactivate</code> each time)'''
FastX is an alternative to VNC viewer
: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** 
* 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.
:* 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.
==== FastX Connection (alternative connection) ====
   
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.
</pre>
 
The FastX server is installed on squiggles. You will need to download the client - https://www.starnet.com/fastx/current-client
 
[[File: FastX_config.png]]
 
Steps to setup the connection: <br /> 
1. Open fastX <br />
2. Click the plus to start a new connection <br />
3. Enter the Connection Name, host (squiggles.rcc.mcw.edu), and user (rcc username) <br />
4. Click the plus to enter a session.  Use /etc/X11/xinit/xinitrc for the command <br />

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.
Retrieved from "https://www.neuro.mcw.edu/meg/index.php?title=Squiggles_research_computer_server&oldid=547"