SBGrid User Guide


The Biological Sciences Division provides access to SBGrid which is a suite of over 400 scientific software applications used by the global structural biology community. Access to SBGrid is available with a graphical user interface for Mac or command line versions for Mac and Linux. All software is installed and run locally on the workstation/laptop. A full list of available software can be found on this SBGrid search page.

Contents

Connecting from on and off-Campus

If you are within the UChicago campus network, you can connect directly. If off-campus, you will need to first connect through the UChicago Virtual Private Network (cVPN).

Connecting from Linux

Mounting the NFS share is done through the use of the fstab file and requires access to sudo. Be aware that editing this file incorrectly can cause your entire system to be inaccessible.

  1. Make a backup copy of the fstab file 
    $ sudo cp /etc/fstab /etc/fstab-BACKUP
  2. Open the file to edit:
    $ sudo vim /etc/fstab
  3. Add the following line to the bottom of the file:
    sbgrid.bsd.uchicago.edu:/opt/sbgrid   /opt/sbgrid   nfs  defaults,_netdev,noauto               0 0
    1. _netdev option tells the system to wait until the network is up before trying to mount the share
    2. noauto option will not mount the NFS share until it is accessed the first time
  4. To save the change and leave the editor, press the ESC key, followed by a colon : then the letters wq and hit the Enter key.
  5. Reload the systemctl daemon 
    $ sudo systemctl daemon-reload
  6. To mount the share now without rebooting: 
    $ sudo mount /opt/sbgrid
  7. Create a symlink (required for some SBGrid software) 
    $ sudo ln -s /opt/sbgrid /programs

Connecting from macOS

Fully configuring SBGrid on macOS requires rebooting the workstation/laptop. The process for mounting the NFS share in a way that can be used by SBGrid on macOS is best described by SBGrid's own documentation:

Using SBGrid with MacOS

Note: On newer versions of macOS (Sequoia 15+), you must specify the NFS version when mounting:

sudo mount -t nfs -o vers=4 sbgrid.bsd.uchicago.edu:/opt/sbgrid /programs

Alternatively, you may be able to use SSHFS:

Setting up sshfs on OS X (Mac) systems

Using SBGrid

Download links for the CLI binary, as well as full documentation on using SBGrid on your workstation/laptop can be found here:

https://sbgrid.org/wiki/sbgrid-cli

Other Requirements

Linux workstations may require additional software to be installed before using SBGrid software, and macOS requires additional software to use the GUI. Information on additional requirements can be found on SBGrid's Workstation Setup page.