CUBIC/CBICA

CBICA/CUBIC official documentation: https://sbia-wiki.uphs.upenn.edu/wiki/index.php/Main_Page
(Check this for information first! Note that you must be logged in to the UPHS VPN to access this site. Most things you need are here, though the organization is not great.)

Penn LINC documentation on CUBIC: https://pennbbl.github.io/docs/cubic

CBICA Request Tracker (must be on VPN, get help and ask questions after checking docs, click through the warning about the certificate/your connection not being private): https://cbica-portal.uphs.upenn.edu/rt/

Getting Started

Getting an account:

For a VPN Account, visit https://sbia-wiki.uphs.upenn.edu/wiki/index.php/Remote_Access#Requesting_a_VPN_Account. Likely, you do not have a UPHS account yet, and you will have to e-mail Jessica Incmikoski ([email protected]) with the UPHS Access Request form filled out: https://github.com/mackeylab/home/blob/master/UPHS%20Access%20Request.pdf. In your email, tell Jessica that you are supervised by Allyson Mackey and Dylan Tisdall. Receiving a VPN account allows you to log in to the BIG-IP VPN using your UPHS username and password, and thus access CBICA/CUBIC official documentation (see above).

To create a new CUBIC account, please contact Cassidy McDermott ([email protected]) to use the RT Tracker (https://cbica-portal.uphs.upenn.edu/rt/, must be on UPHS VPN) to submit a request for a new account, using your UPHS username as the new account. To add your account to one of our Mackey Lab shared data directories (cbpd_main_data or bpd_main_data), submit a ticket with the specified information under "Project Access", and include an email from Dylan Tisdall giving permission for read-only or read-write access to that project. Cc Dylan Tisdall and Allyson Mackey on the request. Incoming RAs who need cluster access can be handled this way.

You may also need a project directory to do your analyses in. See here for how groups and permissions on CUBIC work: https://sbia-wiki.uphs.upenn.edu/wiki/index.php/Research_Projects#Use_of_Group_Membership

What you need to download:

-Duo Authenticate (you should already have this for Penn generally): http://www.uphs.upenn.edu/network/

-The VPN client (BIG-IP Edge client): http://www.uphs.upenn.edu/network/index_vpn.html --> Penn VPN Preferred (MAC)

-x11 quartz (to open GUI applications like Freeview) : https://www.xquartz.org

-SSHFS and FUSE (for mounting locally): https://osxfuse.github.io/

-Fetch (an application I like for secure file transfer): https://www.isc.upenn.edu/how-to/fetch

Completing tutorials:

Using the CBICA cluster requires a small amount of knowledge using Linux. There are multiple tutorials on Linux.

http://linuxsurvival.com gives a good tutorial on the basics of Linux and its commands.

Commands to know: http://linuxsurvival.com/command-list/

How to get to the shell (Mac): command+space and search "terminal".

Terminal is where you will type commands to get into the Cluster.

Once you have a cluster account, and you have a VPN account, you can now log onto the cluster!

Using the Cluster

Steps to log on to cluster:

Connect to the UPHS VPN through BIG-IP FIX VPN. Click this, then hover over UPHS, then click connect. You type in your UPHS VPN account information here. Use Duo Authenticate to confirm you're you. Make sure you are connected.

Open a terminal window. Once a terminal window is open, you can log onto CUBIC with the command line ssh -Y [email protected]. Enter your password. You are now in the terminal and should see something like this!

If you want to avoid having to enter your password each time, see documentation on SSH keys here.

Hooray! From here, I'd recommend reading the PennLINC documentation on CUBIC usage available here.

Mounting the cluster locally

This allows you to use any applications (such as FSLeyes, Mango, other image viewers, Firefox, etc.) locally instead of on the very-laggy VPN connection. See instructions here.

Syncing data from CfN to CUBIC

You can use rsync to sync large amounts of data into the dropbox in your project directory. rsync will eventually time out, so you will need to either use qlogin and enter your password or set up SSH keys between CfN and CUBIC and qsub your rsync job.

I recommend using the flags below when using rsync.

rsync -prltD --chmod=Dug+rwx,Dg+s,Fug+rw,o-rwx /data/jux/mackey_group/yourdata [email protected]:/cbica/projects/projectname/folder

Using x2GoClient (NOT SURE I'D RECOMMEND, TBD)

Log onto x2goclient. To do this, find the downloaded file and open the application. https://cfn.upenn.edu/computing/wiki/doku.php?id=x2go_remote_desktop under "using the x2go client" will help with how to start a session and open a terminal within x2go.

Once a terminal window is open, you can log onto chead with the command line ssh -Y chead-local. This is much better for GUI-ed applications.

Freesurfer tutorials, tips, & helpful tools:

http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials

http://vitallongevity.utdallas.edu/cnl/wp-content/uploads/2015/10/FREESURFER_GUIDE_CNL_2015Oct.pdf