BioHPC User Portal
Biomedical High-Performance Computing

SBGrid on BioHPC

SBGrid is a collection of commonly used stuctural biology software, curated by the SBGrid consortium.
 

License / Access

SBGRID is available to SBGRID member labs under the license below:

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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.
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Information about joining SBGRID can be obtained from the SBGRID consortium via: https://sbgrid.org/join/

Supported Applications

SBGrid offers a collection of over 400 structural biology applications available on Linux and macOS systems. This collection includes both open-source and commercial software, such as:

  • PyMOL: Available with incentive builds for advanced molecular visualization.
  • Schrodinger Small-Molecule Drug Discovery Suite: Provided for labs in North America to support drug discovery research.

For a complete list of supported applications, visit: SBGrid Supported Software.

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SBGrid software is installed only on the compute nodes.

Login nodes (nucleus004 and nucleus005) do not have SBGrid available.
Users must start an interactive job or reserve a Web Visualization before loading SBGrid.

Command:
source /programs/sbgrid.shrc

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BioHPC nucleus and thin clients

BioHPC offers access to SBGrid on its thin clients and cluster systems.

Initializing the SBGrid shell environment

To use SBGrid software on BioHPC's Nucleus or thin clients, you need to configure your shell to initialize the SBGrid environment. Any BioHPC users that wishes to use the software at Nucleus or thin clieints needs to configure their shell to initialize the SBGrid shell environment.

For bash and other sh-compliant shells:

. /programs/sbgrid.shrc  

For csh and tcsh, add the following line to your ~/.cshrc:

source /programs/sbgrid.cshrc

Overriding Software Versions

Most of the software titles installed in the SBGrid software collection have several versions available. We try to provide at least three versions of each software package, although very old or very new applications may have fewer versions.

Display Available Versions

To list the available versions of a software title, you can use the sbgrid utility. Running sbgrid -l will list the versions for your current platform. From a Linux machine, a search for CCP4 versions looks like this:

$  sbgrid-info -l pymol
  Version information for: /programs/x86_64-linux/ccp4

Default version:                    6.4.0
In-use version:                     6.4.0
Other available versions:           6.3.0 6.2.0
Overrides use this shell variable:  CCP4_X

Running sbgrid -L will print the available versions for the three current platforms (OS X PowerPC and Intel, Linux).

$  sbgrid-info -L gnuplot
  Version information for: /programs/x86_64-linux/gnuplot

Default version:                    4.6.4
In-use version:                     4.6.4
Other available versions:           4.6.0 4.4.3 4.2.6
Overrides use this shell variable:  GNUPLOT_X

  Version information for: /programs/i386-linux/gnuplot

Default version:                    4.6.0
Other available versions:           4.4.3 4.2.6
Overrides use this shell variable:  GNUPLOT_L

  Version information for: /programs/i386-mac/gnuplot

Default version:                    4.6.4
Other available versions:           4.4.3 4.2.6 4.6.0
Overrides use this shell variable:  GNUPLOT_M
Overriding Default Versions

To override the default version of a software title, you need to create an override file. The shell configuration scripts will read this file and override the default version.

The override file is named .sbgrid.conf and should be placed in your $HOME directory. The syntax for overrides is a simple key=value pair. E.g. it should look like this:

APPLICATION_X=1.2
APPLICATION_X is the name of the application followed by an underscore and the shorthand initial for the architecture. The last field on the line is the software version number you want to use. The initials for each software branch are:

Software Directory    Shorthand Initial
i386-linux    _L
x86_64-linux    _X
i386-mac    _M
To quickly open the overrides file in your default $EDITOR, you can run sbgrid-overrides -e.

When you open a new shell, you will see a message about the overridden version. Note that a site administrator can create sitewide or machine-specific overrides as well.

The example output below shows CCP4 on linux being changed from the default version:

 Configuration options in effect for this shell:
  Variable             Setting         Configuration
   PYMOL_X      3.1.6.1         personal

Disabling a Software Package

To disable a specific software package, set its version to “disable” in your ~/.sbgrid.conf file.