Squiggles research computer server

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
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).

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.

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 :xx

Replace :xx with your session number.

Manual Termination of the VNC

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 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 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

You can run the command twice. Also, you can run this command to check if conda has been deactivated properly:

which python

Alternatively, modify your `~/.bashrc` script, for example, using:

nano ~/.bashrc

and comment out the line starting with export PATH=/.../miniconda ...

Disconnect and reconnect to squiggles through ssh, run `conda deactivate`, and then start a new VNC session.

You can also adjust the startup file. Here's an example modification to include in your `.vnc/xstartup` script:

#!/bin/sh
 
unset SESSION_MANAGER
unset DBUS_SESSION_BUS_ADDRESS
# exec /etc/X11/xinit/xinitrc
 
gnome-session