Installation via Docker

To enable deployment on the cluster and testing in a controlled setting, it is possible to launch DVID via a docker container. Images of DVID can be retrieved from the organization flyem on Docker Hub. There is also an example dataset that is wrapped into a docker volume.

To view the dataset example, one can use the built-in DVID viewer provided by dvid-console (and packaged with the DVID docker container) or NeuTu.

Note: please follow the installation instruction for docker. If run on Mac or Windows, a virtual machine is needed. This virtual machine should have enough disk space to accommodate the sample docker volumes.

Installing and Running DVID

To retrieve the DVID image:

% docker pull flyem/dvid

To run DVID:

% docker run --volumes-from <OPT:VOLUME> -p <PORT>:8000 -it flyem/dvid

where a docker volume can be specified and the port where DVID will be visible.

By default, running this container will create an empty DVID database. One can specify a docker volume that contains a DVID db at /var/dvid/db. Note: it is possible to specify a volume directly from the host machine, but it is recommended that the database be wrapped into a volume container for better portability. These volumes are light-weight and actually stored directly on host filesystem on linux or on the VM that runs the containers on Mac and Windows.

On linux, DVID can be accessed at 127.0.0.1:< PORT >. For Mac and Windows, DVID is available at the virtual machine address with the specified port. For convenience, the dvid-console is installed with dvid.

Running DVID with a Large Dataset Example

We created a docker volume for a part of the FIB-SEM medulla dataset. This includes image segmentation (not completely edited) and grayscale data. To retrieve the volume:

% docker pull flyem/dvid-fib25db

To run the volume:

% docker run --name fib25db -d flyem/dvid-fib25db

To run DVID with this example:

% docker run --volumes-from fib25db -p 8000:8000 -it flyem/dvid