Instructions and scripts to run relion & cryosparc on LS6

• a valid account with available allocation on LS6
• a valid cryosparc license id get a cryosparc license
• knowledge of transfering files to and from LS6
• background on working with relion & cryosparc

• start a vis session here
  • select:
    • System Lonestar6
    • Application DCV remote desktop
    • Project - this is the allocation which will be charged for the usage
    • Queue - gpu-a100
    • Nodes - the number of nodes - currently only 1 node is supported
    • Job Name - optional, but useful if you are running multiple jobs
    • Time limit - Important - limits the maximum time of the session
    • Reservation - Ignore unless you have made special arrangements
    • VNC Desktop Resolution - should be disabled
  • e.g. (with Project not yet selected)
  • Click submit
  • If all is well, you should be presented with a new TAP Job Status screen
  • e.g.
  • Click Connect
    • At times, LS6 might be quite busy and it may take awhile for Connect to appear. Appropriate messages are displayed when this happens.
  • A new screen will appear where you will need to enter your credentials (not shown)
  • Finally you will be presented (typically in a new tab) a window with the GUI desktop running on the allocated compute node
  • e.g.
  • Properly End your session when you are done or you allocation will continue to be charged until the Time Limit you initially set expires
    • N.B. the window END SESSION HERE allows you to end the job within the GUI window
    • You can also switch to the Analysis Portal Tab and click End Job
• Easy way after first job
  • At the bottom right of the TACC vis window are listed past jobs. You can click details to see details. Click resubmit to start a job again with previous settings

• commands below are in the terminal window of the GUI

• Install the helper tools in your home directory
• cd ~ && git clone https://github.com/ehb54/cryoem_uth cryoem

• make a new or change to previously existing Relion project directory
  • relion_project_1 below is arbitrary, name it as you wish
  • make new
    • mkdir $WORK/relion_project_1
  • change to existing
    • cd $WORK/relion_project_1
• run relion
  • ~/cryoem/relion
    • the first time usage:
      • it will take a few minutes while it downloads and installs - depends on the load on LS6 file systems and network
    • accepts standard relion command line arguments

• ~/cryoem/cryosparc
  • first time usage:
    • make sure you have your cryosparc license available
    • you will need to enter various install information such as email, username, a new password, etc.
      • the username, password are unrelated to any existing username and passwords. Set as you wish. They are used to log into cryosparc
    • downloads & installs
    • it can take about 30 minutes or more to install depending on the load on LS6 file systems and network
  • when provided no command arguments or start or restart:
    • starts the server
    • starts the web browser
  • accepts standard cryosparcm command line arguments
    • start|stop|restart|status

• issues
  • please report issues encountered here

• configuration
  • update the contents of this file if needed