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 the SBGrid’s Report Software Bug form. The Wynton sysadmins do not fix problems in SBGrid software.
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.
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.
2021-05-28: All our development nodes, including the GPU one, have CPUs that are compatible with the SBGrid software tools.
⚠️ 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 one or more of the compute nodes which your job ran on does not support. Many of the default versions of programs included with SBGrid work best on “modern” compute nodes with newer CPU architectures/features. For SBGrid this means Intel “Haswell+” CPUs/Motherboards. (Though read the documentation for the SBGrid software you are trying to use, if you encounter an error that references “Illegal Instructions”. You may be able to specify a version of the software compiled for “pre-Haswell” CPUs.) Alternatively, if you want to use the newer version of the 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*|qb3-as*|qb3-at*", a group of more modern nodes. (The pipe sign, |, is used to indicate the OR operator in resource requests, telling your job to run on any node whose hostname value matches the patterns given.)
⚠️If you are using SBGrid programs with GPU support, please note that SBGrid programs are compiled for specific versions of cuda. Also note the newest Nvidia A40 GPUs on the qb3-atgpu* nodes require the use of programs compiled against cuda-11.0.2 or greater. As of 09/16/2022, most default versions of GPU compatible versions of SBGrid programs are not compiled against cuda-11.0.2 or greater. You may need to specify a beta version of the SBGrid programs or avoid the qb3-atgpu* nodes. See the SBGrid documentation for your specific program.
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
<http://sbgrid.org/bugs>
For additional information visit https://sbgrid.org/wiki
********************************************************************************