Using the SBGrid Environment
Support for Site Administrators
Support for Developers
Hardware Support Notes
COOT is present in several titles and many versions in SBGrid. Selecting the application and version of the
coot executable can be accomplished on-the-fly in a single step in the SBGrid capsule environment. Here are some examples of managing COOT in SBGrid capsules, but this should work for any application with duplicate executables and multiple versions.
To confirm that capsules are enabled, run
If capsules are enabled, the output should be :
$ sbcap status Active
If capsules are InActive, they can be enable with the
sbcap on command followed by
source /programs/sbgrid.shrc or
.cshrc for tcsh users.
sbwhich command will show which
coot executable is in use :
$ sbwhich coot /programs/x86_64-linux/ccp4/7.1/ccp4-7.1/bin/coot
or alternatively the
--sbwhich flag can be used
$ coot --sbwhich /programs/x86_64-linux/ccp4/7.1/ccp4-7.1/bin/coot
By default we use the CCP4 release of COOT in SBGrid. This version is stable, supported and the same for MacOS and Linux. But it is easy to change.
SBGrid capsules provide an additional set of flags for all executables, prefixed with
--sbapp:. For more info see the documentation for capsules here. To list all the installed tiles that provide
$ coot --sbapp:l ccp4 ccpem coot
coot is present in the titles ccp4, ccpem, and coot.
To see all the titles with details use
$ coot --sbapp:L Titles containing coot Title 1 of 3: Version information for: /programs/x86_64-linux/ccp4 Default version: 7.1 In-use version: 7.1 Installed versions: 7.1 7.1.006 7.0 7.0.078 6.3.0 Other available versions: 7.1.006 7.0 7.0.078 6.3.0 Overrides use this shell variable: CCP4_X Title 2 of 3: Version information for: /programs/x86_64-linux/ccpem Default version: 1.4.1 In-use version: 1.4.1 Installed versions: 1.4.1 1.4.0 1.3.0 20200722 Other available versions: 1.4.0 1.3.0 20200722 Overrides use this shell variable: CCPEM_X Title 3 of 3: Version information for: /programs/x86_64-linux/coot Default version: 0.9.1 In-use version: 0.9.1 Installed versions: 0.9.1 0.8.9.2-pre-revision-7884 0.8.9 0.8.8 Other available versions: 0.8.9.2-pre-revision-7884 0.8.9 0.8.8 Overrides use this shell variable: COOT_X │···········
sbapp:d will print the title and version along with the available versions for the title.
$ coot --sbapp:d Capsule:coot using ccp4 version 7.1 Version information for: /programs/x86_64-linux/ccp4 Default version: 7.1 In-use version: 7.1 Installed versions: 7.1 7.1.006 7.0 7.0.078 6.3.0 Other available versions: 7.1.006 7.0 7.0.078 6.3.0 Overrides use this shell variable: CCP4_X │···········
We are running
coot from ccp4 version 7.1 and there are several other versions available.
SBGrid uses CCP4's
coot by default, but that can be changed with a configuration file in the ~/.sbgrid_capsules directory. A default title can be specified for any duplicate executable by creating a file with the name of the executable that contains a single line with the name of the application. For coot this would be:
mkdir -p ~/.sbgrid_capsule echo coot > ~/.sbgrid_capsule/coot
If we do this, we can see:
$ coot --sbwhich /programs/x86_64-linux/coot/0.9.1/bin/coot
coot comes from the applciation title coot. The default version there is 0.9.1.
Let's switch to CCPEM as the provider of the
To do that we just edit the configuration file:
$ echo ccpem > ~/.sbgrid_capsule/coot $ coot --sbwhich /programs/x86_64-linux/ccpem/1.4.1/bin/coot $ coot --version 0.9-pre (revision-count 0) [with guile 1.8.8 embedded] [with python 2.7.15 embedded] Builder_info: CCP-EM, Oxfordshire, UK Binary type: Linux-x86_64-scientific-linux-6.10-python-gtk2
The version of a title is set by the
<TITLE_X> variable where
<TITLE> is the title of an application in uppercase. You can see this variable in the
sbgrid-info -l output.
$ sbgrid-info -l ccpem Version information for: /programs/x86_64-linux/ccpem Default version: 1.4.1 In-use version: 1.4.1 Installed versions: 1.4.1 1.4.0 1.3.0 20200722 Other available versions: 1.4.0 1.3.0 20200722 Overrides use this shell variable: CCPEM_X
To use coot from CCPEM version 1.3.0, we set the CCPEM_X variable to 1.3.0
$ export CCPEM_X=1.3.0 $ sbwhich coot /programs/x86_64-linux/ccpem/1.3.0/bin/coot
coot has a --version flag that can be used to confirm the version
Set the title for the
coot executable to "coot" to use Paul Emsley's builds for linux :
echo coot > ~/.sbgrid_capsule/coot $ coot --version 0.9.1 (revision-count 10157) [with guile 1.8.8 embedded] [with python 2.7.15 embedded] Builder_info: built by: Paul Emsley build-host: charybdis on: Wed 21 Oct 0247.16 BST 2020 Binary type: Linux-x86_64-scientific-linux-7.6-python-gtk2
This is the latest version. To switch to an older version, just set the COOT_X variable to that version:
$ export COOT_X=0.8.8 $ coot --version 0.8.8 (revision-count 6690) [with guile 1.8.8 embedded]
To return to using
coot from CCP4, the SBGrid default, remove the config file:
$rm ~/.sbgrid_capsule/coot $ coot --sbwhich /programs/x86_64-linux/ccp4/7.1/ccp4-7.1/bin/coot $ coot --version 0.9 (revision-count 9932) [with guile 1.8.8 embedded] [with python 2.7.16 embedded] Builder_info: CCP4, Oxfordshire Binary type: Linux-x86_64-scientific-linux-6.10-python-gtk2
The version of
coot changes to the version provided by the CCP4 version specified by CCP4_X.
For questions or to report bugs, please email firstname.lastname@example.org