Application Software Management
The Virtual Cluster instances are based on a standard Linux distribution
(Rocky 8) with additional packages installed
from different third-party repositories. All packages used on any instance
of a Virtual Cluster are cached in a local directory /var/repo.
This allows to provide a well defined and tested environment in first place.
General Software Installation and Update#
Warning
Updating software packages naturally brings the system into an untested state as Schrödinger can’t test all possible combinations of different package versions released after a Virtual Cluster has been deployed as the software release cycle and the quality assurance process for each package is not under control of Schrödinger. Thus, we recommend to follow the procedure described in this section and test the system after an update has been performed.
Additional software from the standard third-party repositories can be
installed using the package manager of the operating system (dnf):
sudo dnf install <PACKAGE>
downloads and installs the package with the given name from one of the enabled repositories. The installed software packages can be updated using one of the following commands. The command:
sudo dnf update
performs a full update of all packages for which a newer version is available in the repositories, while:
dnf update <PACKAGE>
updates only a particular software package.
System Update#
When performing a full update of the system, it is strongly recommended
to perform the update only while the cluster is idle, i.e. when no
dynamic instances are running (see Instance Mangement)
and no jobs are currently processed.
It is recommended to keep software versions consistent on all instances,
which can be achieved by running the update command (dnf update) on all
instances at the same time.
Note
Don’t forget, that the instance templates need to be updated in order to apply the update to the dynamically created instances. To achieve this, template instances need to be updated, and then the instance templates need to be recreated from these template instances (see Instance Mangement).
System Downgrade#
When an update casues issues, it is possible to revert the update using
the dnf history command. All installed packages are available as rpm
versions either in the dnf cache or in /var/repo/dnf, so that it
is always possible to revert to the previously installed version of a
package. The command:
dnf history
shows all executed transactions and the command:
dnf history undo <ID>
undos the operation with the specified ID.
Schrödinger Suite Installation and Update#
Schrödinger Suite installations on the Virtual Cluster can be managed using the program:
/opt/schrodinger/suite/update-manager
This program also manages the integration of the Schrödinger Suite in the Virtual Cluster environment after the installation process has completed.
Warning
A manual installation and configuration of the Schrödinger Suite is strongly discouraged as a smooth operation of the Virtual Cluster cannot be guaranteed.
Check for New Versions#
For an overview of all installed versions of the Schrödinger Suite as well as versions available for download, the following command can be used:
/opt/schrodinger/suite/update-manager list
The program highlights if a newer version than installed on the Virtual Cluster is available for download from the Schrödinger server.
Installing a Release of Schrödinger Suite#
To install a version of Schrödinger Suite on the Virtual Cluster the following command can be used:
sudo /opt/schrodinger/suite/update-manager install -v <version>
Note
Downloading the Schrödinger Suite requires valid credentials for the Schrödinger website.
Upgrading Job Server#
The Job Server version installed on the Virtual Cluster needs to be at least as new as the version of the Schrödinger Suite used to submit jobs, i.e., installation of a new Schrödinger Suite version on the Virtual Cluster requires an update of Job Server as well. In order to update Job Server for a certain version of the Schrödinger Suite the following command can be used:
sudo /opt/schrodinger/suite/update-manager jobserver-upgrade -v <version>
The upgrade of Job Server does not affect any jobs running on the cluster.
Uninstalling a Release of Schrödinger Suite#
To uninstall a release of Schrödinger Suite on the Virtual Cluster the following command can be used:
sudo /opt/schrodinger/suite/update-manager uninstall -v <version>
Note
The default version cannot be uninstalled. Please set another version as the default before uninstalling the current default version (see Changing the Default Version).
Changing the Default Version#
Among the installed Schrödinger Suite versions, one is defined as default.
The installation directory of this default version is added to the PATH
for each user, the shortcuts on the graphical desktops point to this
version, and the SCHRODINGER environment variable points
to the default version. The command:
/opt/schrodinger/suite/update-manager list
displays the default version. The default version can be changed using the command:
sudo /opt/schrodinger/suite/update-manager default -v <version>