ChemLocator is shipped as a set of Docker images, in order to minimise installation complexity, and to guarantee consistency.
{info} What is Docker?
While Docker has become quite mainstream recently, it is still relatively normal not to have any experience with it, hence a short introduction:
Docker is a tool which allows applications to be packaged complete with all their dependencies into images. These images are little bit like lightweight snapshots of an OS, the application, and any extra libraries it might need. An image is used to create a container, which is quite similar to a VM, with several important distinctions (such as containers not reserving large amounts of unused memory for themselves, unlike VMs).
It is recommended that a relatively recent version of the Docker Engine is used
to run ChemLocator containers. At the time of writing, ChemLocator images are
built using version 19.03.8.
You can test the version of Docker installed by running:
docker --versionA typical ChemLocator installation requires multiple Docker images to work
together. While this can be set up with manual Docker commands, we provide an
example docker-compose.yml file which describes and connects the required images
in a correct manner. Some installations of Docker do not ship with the
docker-compose tool by default, and it needs to be installed separately. You
should ensure that is installed. For Ubuntu, the installation is as follows:
sudo apt install docker-composeIn some cases, it is possible for the docker login command to no longer function
correctly after the installation of docker-compose. If you recieve the following
error message after a login attempt:
Error saving credentials: error storing credentials - err: exit status 1, out: 'Cannot autolaunch D-Bus without X11 $DISPLAY'
Then it is possible that the Docker installation needs to be fixed. In our experience the following command tends to fix the above issue:
sudo apt install gnupg2 passAlternatively, searching for the error on the internet provides more in depth discussions and solutions.
While Docker itself can be installed on Windows, Mac OS, and Linux, it is really a Linux native technology. The versions of Docker for Windows and Mac OS work by making use of a single Linux Virtual Machine instance to provide the native functionality needed, which is less than ideal. This is perfectly fine for demo environments, but for production environments, a host machine running Linux is recommended.
Docker is well supported on just about all Linux distributions, and you are free to choose your organisation's favourite distro. If you do not have a preferred choice, the ChemLocator team recommends either CentOS, or Ubuntu.
Official guides can be found on docs.docker.com:
By default, a Linux-based Docker installation will not place any limits on CPU and memory usage. There is no further action needed.
If you re running a ChemLocator environment using either the Docker Desktop for
Windows or Mac OS, there are limits imposed by default, which cause a number of
problems. (To repeat the above advice: it is not recommended to run
ChemLocator on a Windows or Mac OS host in production environments.) Navigate
to the Resources section of the settings, and increase the CPU, memory, and
disk space allocations as appropriate.
On systemd-based distributions such as Ubuntu, the docker service can be set
to start automatically if the server is rebooted. This is done as follows:
sudo systemctl enable dockerThe first time after an installation, it may be necessary to start docker:
sudo systemctl start docker