Examples not working?

SBGrid Software Collection

Access to SBGrid software on Wynton HPC is limited to paying members of the SBGrid Consortium.

For bug reports related to SBGrid software, please use SBGrid's Report Software Bug form. The Wynton sysadmins do not fix SBGrid problems.

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 Mac computer they own. The annual price depends on how many other labs from UCSF join. There are approximately 12 UCSF labs currently enrolled. See https://sbgrid.org/join/ 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 of the SBGrid Consortium. Wynton HPC users who are SBGrid members are part of the sbgrid Unix group on the Wynton HPC cluster. You can verify this by running:

[alice@dev2 ~]$ groups
boblab sbgrid

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

Enable SBGrid

⚠️ Among the development nodes, SBGrid works best on dev2 and dev3. On dev1 and gpudev1, the CPUs are older and some of the SBGrid software tools assumes newer CPUs resulting in run-time errors, e.g. 'Illegal instruction'.

⚠️ If you are running SBGrid software and receive an error message regarding "Illegal Instructions", this means that the version of the software you are trying to run requires a CPU feature that some of the compute nodes do not support. Many of the default versions of programs included with SBGrid work best on "modern" compute nodes with modern CPUs. For SBGrid this means Intel "Haswell+" CPUs/Motherboards. (Though read the documentation for the software you are trying to use, if you encounter an error that references "Illegal Instructions". You may be able to use a version of the software compiled for "pre-Haswell" CPUs.) Alternatively, if you want to use the newer software, you will need to make sure your SBGrid job ends up a on a node with a modern CPU. To do this, specify SGE option "-l hostname=qb3-id*", a group of more modern 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: 2021-07-30
 Please submit bug reports and help requests to:       <bugs@sbgrid.org>  or
                                                       <http://sbgrid.org/bugs>
            For additional information visit https://sbgrid.org/wiki
********************************************************************************