Examples not working?

SBGrid Software Collection #

SBGrid is a collection of hundred of programs for structural biology. It is kept up to date by the SBGrid team without needing intervention by the Wynton admins. Each lab using SBGrid must pay a yearly fee. This covers usage by anyone in the lab, both on Wynton HPC and any other Linux or macOS computer they own. The annual price depends on how many other labs from UCSF join. Many UCSF labs are already members. See the SBGrid website for information on how to join.

Verify access to SBGrid #

The SBGrid software stack is installed on Wynton HPC, but is available only to paying members, which are listed on the SBGrid Member Labs webpage. As a Wynton HPC user part of a paying lab, you will have access to SBGrid on the Wynton HPC cluster from being part of the sbgrid Unix group. You can verify that this is get case by running:

[alice@dev2 ~]$ groups
boblab sbgrid

If sbgrid is not part of your output, then you currently do not have access to the SBGrid software on Wynton HPC. If you think this is a mistake, please contact us so we can add you.

Enable SBGrid #

SBGrid is available for interactive use on the development nodes and for use in job scripts on compute nodes. It is NOT available on the login nodes.

In order to use SBGrid software, the SBGrid environment must be enabled. To enable the SBGrid, in the shell or in a job script, do:

[alice@dev2 ~]$ source /programs/sbgrid.shrc
                  Software Support by SBGrid (www.sbgrid.org)
 Your use of the applications contained in the /programs  directory constitutes
 acceptance of  the terms of the SBGrid License Agreement included  in the file
 /programs/share/LICENSE.  The applications  distributed by SBGrid are licensed
 exclusively to member laboratories of the SBGrid Consortium.
              Run sbgrid-accept-license to remove the above message.  
 SBGrid was developed with support from its members, Harvard Medical School,    
 HHMI, and NSF. If use of SBGrid compiled software was an important element     
 in your publication, please include the following reference in your work:      
 Software used in the project was installed and configured by SBGrid.           
 cite: eLife 2013;2:e01456, Collaboration gets the most out of software.
 SBGrid installation last updated: 2022-04-12
 Please submit bug reports and help requests to:       <bugs@sbgrid.org>  or
            For additional information visit https://sbgrid.org/wiki