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Relion RELION is installed on our HPC clusters. We make use of of singularity containers to make the program portable across different HPC architectures and also to facilitate compilation and redistribution.

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We ask that you keep your relion RELION data in the following directories:

• Proposal based: if you are working on data from an official Proposal with a designated proposal code (eg CS10, C002, etc), then you should ask for a 'group' directory under
   /sdf/group/cryoem/g/<PROPOSAL>.
• Team project: if you intend to share your data with other collaborators (either internal or external), please also ask for a directory under the 'group' space.

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• Using 'X Server' on your local (laptop/desktop) machine.
  • You can install XQuartz on mac. You should already be running one on Linux. 
• Using FastX in a browser
  • https://fastx3.slac.stanford.edu:3300
  • Click "I Accept"
  • Log in with your SLAC unix credentials
  • Launch a new session (centos7- or iris- gnome seem to work well), selecting @slac_public_login
  • At the terminal, treat it as your 'local' computer, i.e. ssh -Y ... into the sdf server as indicated below

To bring up the relion GUI:

• • + button) and go to the Command tab in the session configuration pop-up

  • Enter the following in the form fields:
    Command:

    Code Block
    language bash
    xterm -ls -e "ssh sdf-login"

    Window Mode (either works):

    Single – Single window mode in which the session is contained to one window (Set a window size. Default 1024 x 768. Changing this doesn't seem to improve resolution)
    Multiple – Multiple window mode in which the session can have multiple independent windows
    
    Run As User:
    Leave blank/default (will log-in as the user you used to log in to FastX)
    
    Name (Optional):
    Name of the session
    
    

  • Click "Launch" to start the FastX session. A new tab/window will pop up (depending on your browser settings) with an open xterm window prompting you to log in


    to the SDF bastion hosts.
  • Log in with your SDF credentials (this should be your SLAC Windows/Active Directory login).

To bring up the RELION GUI:

# Following the instructions above will land you in your 'SDF Home' directory. DO 

# log onto the 'login' node of the cluster: use your username in place of <username>
# the -Y enables X forwarding to allow the GUI to display locally on your laptop.
ssh -Y <username>@sdf-login01.slac.stanford.edu
 
# by default you will be logged into your 'AFS Home'. Please do NOT use this space for your 
# CryoEM work; there is 
# insufficient disk space (quota: 25GB) and it is also not very performant. You should 
# use the project directory defined in the "Data Location" section above, e.g.:
cd /sdf/group/cryoem/g/<PROPOSAL>
 
# if you're starting a new relionRELION 'project':
mkdir my_new_project
cd my_new_project

# to see what modules are installed:
module avail

# load the modules you plan to use within relionRELION e.g. (module versions in this example are the most current as of 
# 2022-09-28):
module load motioncor2/1.34.24
module load ctffind/4.1.13
 
# start the relion GUI
module load relion/3.1.2
relionver4.0 


# answerstart Yesthe at promptrelion GUI
relion

Using the Batch Queues

The default settings provided by the relion RELION container should work.

Checking on Batch Jobs

As you click submit job to the queue on the relion RELION gui, in the terminal window that you launched relion RELION from, it should output the jobid.

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Using Scratch

Under the Compute tab in relionRELION, there are options to prestage pre-stage the data into either RAM or (say) local disk to speed up your job by increasing the performance of access to the data.

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