DEPRECATED: Installing HNN on Windows 10 Pro (Docker Desktop)

Prerequisite: Virtualization support

There are two related requirements needed for Docker to be able to run HNN in a virtual machine on your Windows system

  1. Hardware virtualization features (manual setting)

    If not already enabled, it may be necessary to manually set these through your PC manufacturer’s BIOS settings. Only old systems do not support this feature. However, if Docker cannot turn this feature on from its installer, you may need to reboot your computer and change your PC manufacturer’s BIOS settings. You can check whether it is enabled from the Task Manger. The picture below shows that hardware virtualization is disabled and will need to be manually enabled in the BIOS.

    See for more details.

    If you run into problems enabling hardware virtualization support, we recommend that you follow the native install instructions instead. Also running our VirtualBox VM with HNN pre-installed is possible without hardware virtualization support.

  2. Hyper-V support (will be enabled during Docker Desktop install below)

    While it is necessary to turn on Hyper-V for using HNN with Docker, you should be aware that it will not allow you to also run virtual machines through applications such as VirtualBox. We recommend that you let Docker automatically attempt to turn this feature on during installation. Alternatively, the procedure below allows you to verify that it is turned on and enable it if necessary.

    1. Start typing “Turn Windows features on or off” in the search bar next to start menu and click on it to launch the control panel dialog window shown below.
    2. Make sure that “Hyper-V” and “Hyper-V Platform” is turned on as shown in the image below

    3. If you enabled Hyper-V, please reboot your computer before continuing below to install docker.

Prerequisite: VcXsrv

  1. Download the installer from []
  2. Run the installer, choosing any installation folder.
  3. Start the XLaunch desktop app from the VcXsrv folder in the start menu.
  4. Choose “Multiple windows” and change “Display number” at ‘0’. Click ‘Next’.
  5. Select “Start no client” and click ‘Next’.
  6. Under “Extra settings” make sure that “Disable access control” is checked.
  7. Click “Save configuration” to create a shortcut with the settings we just chose. Click “Finish” and an “X” icon will appear in the lower-right dock signaling that VcXsrv has started.
  8. A message from Windows firewall to allow connections may pop up. If it does, choose options allowing connections to the VcXsrv when connected to both public and private networks.

Prerequisite: Docker Desktop

  1. In order to download Docker Desktop, you’ll need to sign up for a Docker Hub account. It only requires an email address to confirm the account. Sign up here: Docker Hub Sign-up
  2. Download the installer (requires logging in to your Docker Hub account): Docker Desktop
  3. Run the installer. DO NOT check “Use Windows containers instead of Linux containers”.
  4. Start the Docker Desktop app from the start menu or desktop (requires logging in to your Docker Hub account). This takes about 30 seconds and the Docker icon will appear in the lower-right dock
  5. When Docker Desktop is initializing, it may prompt you to turn on Hyper-V.
    • If you get a message similar to the screen below, click ‘Ok’ and restart your computer.

  6. Docker Desktop will start after the install has completed and the Docker icon will show up in the lower-right dock with a message “Docker Desktop is running”
    • If you get the error message shown below, there was a problem turning on hardware support for virtualization, which is required for Docker on Windows. This may be fixable by changing settings in your PC manufacturer’s BIOS. See the note on “Hardware virtualization features” under the “Prerequisite: Virtualization support” heading at the top of this page.

  7. Increase the number of cores that Docker can use (we recommend all cores) by right-clicking on the Docker Desktop icon in the lower-right dock and then clicking “Settings”. Choose the “Advanced” tab, and adjust the CPU slider all the way to the right.

  8. Reboot your computer after installing Docker

Start HNN

  1. Verify that VcXsrv (XLaunch application) and Docker are running. VcXsrv will not start automatically after a reboot. The Docker Desktop icon should be present in the lower-right dock. To confirm that Docker is running properly, typing the following in a new cmd.exe window.

     C:\Users\myuser> docker info
  2. Clone or download the HNN repo. Chose one of the following methods:

    • Option 1: Cloning (requires Git for Windows)

      1. First install Git for Windows
      2. Type the following in a cmd.exe window. If you already have a previous version of the repository, bring it up to date with the command git pull origin master instead of the git clone command below.

        C:\Users\myuser> git clone
        C:\Users\myuser> cd hnn\installer\windows
    • Option 2: Downloading a HNN release

      1. Download the source code (zip) for our latest HNN release from our GitHub releases page
      2. Open the .zip file and click “Extract all”. Choose any destination folder on your machine.
      3. Open a cmd.exe window and change to the directory part of the extracted HNN release shown below:

        C:\Users\myuser> cd REPLACE-WITH-FOLDER-EXTRACTED-TO\hnn\installer\windows
  3. Start the Docker container. Note: the jonescompneurolab/hnn Docker image will be downloaded from Docker Hub (about 2 GB). The docker-compose command can be used to manage Docker containers described in the specification file docker-compose.yml.

     C:\Users\myuser\hnn\installer\windows> docker-compose run hnn
     Pulling hnn (jonescompneurolab/hnn:)...
     latest: Pulling from jonescompneurolab/hnn
     34dce65423d3: Already exists
     796769e96d24: Already exists
     2a0eada9611d: Already exists
     d6830a7cd972: Already exists
     ddf2bf28e180: Already exists
     77bf1279b29f: Pull complete
     6c8ddf82616f: Pull complete
     a991616934ba: Pull complete
     2cece6240c19: Pull complete
     df826e7d26b9: Pull complete
     824d51cbc89d: Pull complete
     0d16f27c744b: Pull complete
     Digest: sha256:0c27e2027828d2510a8867773562bbc966c509f45c9921cc2d1973c575d327b3
     Status: Downloaded newer image for jonescompneurolab/hnn:latest
  4. If a prompt appears from the lower-right and ask you to share the drive, click ‘Share’.
    • If starting the GUI doesn’t work the first time, the first thing to check is VcXsrv settings have “Disable access control” (see above). Then restart VcXsrv and try starting the HNN container again.
  5. A window will pop up stating “Docker needs to access your computer’s filesystem”. This is necessary to share data and parameter files that HNN creates with your Windows OS. Enter your Windows login password.

  6. The HNN GUI should show up. Make sure that you can run simulations by clicking the ‘Run Simulation’ button. This will run a simulation with the default configuration. After it completes, graphs should be displayed in the main window.
  7. You can now proceed to running the tutorials at . Some things to note:
    • A directory called “hnn_out” exists both inside the container (at /home/hnn_user/hnn_out) and outside (in the directory set by step 2) that can be used to share files between the container and your host OS.
    • The HNN repository with sample data and parameter files exists at /home/hnn_user/hnn_source_code
    • If you run into problems starting the Docker container or the GUI is not displaying, please see the Docker troubleshooting section

Updgrading to a new version of HNN

  1. Verify that VcXsrv and Docker are running. VcXsrv will not start automatically after a reboot by default.
  2. Open a Command Prompt (cmd.exe)

     C:\Users\myuser> cd hnn\installer\windows
     C:\Users\myuser\hnn\installer\windows> docker-compose up --no-start
     Recreating mac_hnn_1 ... done
     C:\Users\myuse\rhnn\installer\windows> docker-compose run hnn

Editing files within HNN container

You may want run commands or edit files within the container. To access a command shell in the container, start the container using docker-compose run hnn in one Command Prompt window and open another Command Prompt window to use docker exec as shown below:

C:\Users\myuser> docker exec -ti windows_hnn_1 bash

If you’d like to be able to copy files from the host OS without using the shared directory, you do so directly with docker cp.

Uninstalling HNN

If you want to remove the container and 1.5 GB HNN image, run the following commands from a cmd.exe window. You can then remove Docker Desktop using “Add/Remove Programs”

C:\Users\myuser> docker rm -f windows_hnn_1
C:\Users\myuser> docker rmi jonescompneurolab/hnn


If you run into other issues with the installation, please open an issue on our GitHub. Our team monitors these issues and will be able to suggest possible fixes.

For other HNN software issues, please visit the HNN bulletin board