Installation on Physical Clusters¶
There are two software requirements for the LigandScout Remote server application (iserver). These have to be installed on the host machine, that is part of the HPC cluster to be used for computations:
- HPC cluster or computer running Linux
- Java Version 1.8+
- SGE, PBS, or TORQUE Cluster Management Software (Scheduler). E.g.
Installing the Server Application (iserver)¶
If you do not have access to a physical HPC cluster, you can skip this section and use LigandScout Remote in the AWS cloud.
Start by downloading iserver from the official Inte:Ligand download servers:
Then, unpack the archive using the following command:
tar -xvzf iserver_*_.tar.gz
After unpacking, you will find a folder named
ligandscout_server. Within that folder is a text file named
As discussed below, it is required to edit this file with some basic information about your environment in order to start using iserver.
Required Filesystem Paths¶
application.properties file starts with a mandatory configuration section. Each of these options requires the setting of a filesystem path.
Every filesystem path has to be accessible for all compute nodes as well as for the master node where the iserver application is running.
iscreen.path.executable= libsize.path.executable= idbgen.path.executable=
# directories considered by the monitoring process, # which looks for newly added compound databases (.ldb format required) ldb.directories= ldb.directories.monitoring.recursive=true
.ldbscreening databases. Multiple locations can be given via comma-separation, e.g:
ldb.directories.monitoring.recursiveis set to true (default), subdirectories of the given locations will also be searched for viable
More advanced configuration is possible using the later sections of the
application.properties file. Those are described in the server configuration section of this documentation.
Working with SGE¶
SGE is currently the default resource manager (scheduler). Therefore, it is usually not required to adjust the configuration of
iserver if SGE is used as scheduler.
However, if you experience issues about missing drmaa libraries, it is required to change the iserver startup script. This documentation will shortly contain more detailed information about this issue. In the meanwhile, please contact email@example.com, if you experience this problem.
Working with PBS or TORQUE¶
If the cluster resource manager (scheduler) in use is PBS or TORQUE, you need to set the
scheduler configuration option in the
application.properties file to
torque, because the default setting is
Running the server¶
The iserver application is a conventional Java program. For convenience, a startup script is included that starts the
.jar with reasonable default settings.
The program can therefore be run by simply executing this script:
It is recommended to create a dedicated system user for running iserver. All jobs submitted with iserver will belong to this new user. This approach helps administrators to manage and monitor scheduler resources.
screen to Prevent Shutdown on Logout¶
In order to keep the server running after you quit your SSH/terminal session, we recommend using
screen and the program will enter a session that lives on after you have logged
out. From this session you can then execute the
iserver startup script. To leave the screen session, use
Usage instructions for
Starting the server on system startup¶
In most cases, it is desired to have iserver automatically start on system startup. The possible ways to do this depend on your operating system. Please consult with your system administrator and ask for the preferred way of adding a startup application.
One simple option is to use the Cron system. Start by typing
Please note that
Cron is a simple and efficient method to achieve this, but it is most likely not the best method. For newer versions of Ubuntu, Debian, and CentOS we recommend to use the
systemd init service. Furthermore, it is recommended to create a separate user for running the iserver application.
Please read the changelog for the version you want to update to. It is located at Version Dependencies. The changelog might give additional instructions or hints about new configuration settings you might want to use.
Automatic Update using
Starting with isever 1.1.9, a script is included to help with the update process. The script allows to update from a downloaded installation archive or directly from the wwww.inteligand.com web servers:
$ ./update.sh -h Usage: update.sh [-v version] [-f local archive] A script to update iserver to a specified version. If no internet connection is available, a local archive can be used for updating. Either '-v' or '-f' have to be set. If both options are supplied, '-v' is ignored. It is recommended to stop the server process before starting the update procedure. This script has to be located in the iserver installation directory. Options: -h show this usage information -v version that should be downloaded and installed from www.inteligand.com, e.g. '1.1.8' -f local iserver installation archive file (*.tar.gz)
Before invoking the script, stop the iserver process. The script automatically downloads and extracts newer versions of
ilib-server-<version>.jar and of the startup script
iserver. If you made changes to the startup script, you will need to re-apply these changes after updating.
To manually update an existing iserver installation, download the latest release from the link above and unpack the archive to a temporary directory:
mkdir temporary mv iserver_*_.tar.gz temporary cd temporary tar -xvzf iserver_*_.tar.gz
Before continuing, stop the iserver process. Then, copy the files
ilib-server-<version>.jar that have just been extracted from the
tar.gz archive into the directory of your existing iserver installation. If there are existing files with the same names, replace them. You can then rename your installation directory to reflect the new server version, even though this is not required.
To summarize, updating only requires replacing the startup script
iserver and the Java executable
ilib-server-<version>.jar with the target version's files.