Neurodesktop

• 1: Neurodesk App
• 2: Linux
• 3: MacOS
• 4: Windows
• 5: Play
• 6: Nectar Virtual Desktop Service
• 7: Cloud
• 8: Data Storage

1 - Neurodesk App

Minimum System Requirements

1. At least 5GB free space for neurodesktop base image
2. Docker requirements.

Installing Docker

The Neurodesk App requires Docker to be installed on your computer. If you already have Docker installed, you can skip this step.

• Docker Desktop for Windows
• Docker Desktop for Mac
• Docker Engine for Linux

After installation, open a terminal (Linux/macOS) or command prompt (Windows) and run the following command to verify that Docker is working correctly:

docker --version
docker run hello-world

Downloading Neurodesk App

• Debian, Ubuntu Linux Installer
• Red Hat, Fedora, SUSE Linux Installer
• Arch-based package via AUR
• macOS Intel Installer, macOS Apple silicon Installer
• Windows Installer

Installing Neurodesk App

If you have an existing Neurodesk App installation, please first uninstall it by following the uninstall instructions here. Then, install the app for your system:

• Debian, Ubuntu Linux Installer: sudo apt install -f ./NeurodeskApp-Setup-Debian.deb
• Red Hat, Fedora, SUSE Linux Installer: sudo rpm -i NeurodeskApp-Setup-Fedora.rpm
• Arch-based package via AUR: yay neurodesk (or follow instructions here)
• macOS Installer: Double click the downloaded dmg file, then drag the NeurodeskApp.app to the Applications folder; for starting the app: Right click on the NeurodeskApp.app and select “Open”. For Apple Silicon systems (M1/M2): Make sure to enable Rosetta support in the docker settings for best performance!
• Windows Installer: Double click the downloaded exe file; Accept to install from an unknown publisher with Yes; then accept the license agreement and click finish at the end.

Launching Neurodesk App

The Neurodesk App can be launched directly from your operating system’s application menu, or by running the neurodeskapp command in the command line.

Note that the Neurodesk App will set the File Browser’s root directory based on the launch method used. The default working directory is the user’s home directory - this can be customized from the Settings dialog.

Sessions and Projects

Sessions represent local project launches and connections to existing Neurodesk servers. Each Neurodesk UI window in the app is associated with a separate session and sessions can be restored with the same configuration later on.

Session start options

You can start a new session by using the links at the Start section of the Welcome Page.

• Open Local Neurodesk.. creates a new session in the default working directory.
• Connect to remote Neurodesk server.. creates a session by connecting to a remote Neurodesk server.

Previously opened sessions are stored as part of application data and they are listed on the Welcome Page. Clicking an item in the Recent sessions list restores the selected session.

Connecting to local Neurodesk

Neurodesk App creates new Neurodesk sessions by launching a locally running Neurodesk server and connecting to it. To open a local instance, click the Open Local Neurodesk.. button in the Start section of the Welcome Page.

This will show a Jupyterlab interface. There are two options to interact with Neurodesk through this interface:

• By clicking the NeurodeskApp icon on the right. This will launch a new window to start a Neurodesk interface.
• By module loading containers on the left bar. You can interact with loaded modules through the command line interface.

Connecting to a remote Neurodesk Server

It can also connect to an existing Neurodesk server instance that is running remotely. In order to connect to a server, click the Connect to remote Neurodesk server.. button in the Start section of the Welcome Page.

This will launch a dialog that automatically lists the remote Neurodesk server instances.

Select a server from the list or enter the URL of the Neurodesk application server. If the server requires a token for authentication, make sure to include it as a query parameter of the URL as well (/lab?token=<token-value>). After entering a URL hit Enter key to connect.

If the Persist session data option is checked, then the session information is stored and Neurodesk App will re-use this data on the next launch. If this option is not checked, the session data is automatically deleted at the next launch and servers requiring authentication will prompt for re-login.

You can delete the stored session data manually at any time by using the Clear History option in the Privacy tab of Settings dialog.

Configuration and data files

Neurodesk App stores data in ~/neurodesktop-storage for Linux and Mac, or C:/neurodesktop-storage for Windows, as default.

Add a Custom Data Directory

Neurodesk App stores its data in the following locations:

• By default, /home/jovyan/neurodesktop-storage in the app (which is bound with local directory ~/neurodesktop-storage in Unix or C:/neurodesktop-storage in Windows)

• By choice, in the settings window below, select Additional Directory on the left side bar, click Change button to select the local directory, then click Apply & restart. The next time you start the app, the data from the local directory can be found in /home/jovyan/data.

Uninstalling Neurodesk App

Debian, Ubuntu Linux

sudo apt-get purge neurodeskapp # remove application
sudo rm /usr/bin/neurodeskapp # remove command symlink
rm -rf ~/.config/neurodeskapp # to remove application cache

Red Hat, Fedora, SUSE Linux

sudo rpm -e neurodeskapp # remove application
sudo rm /usr/bin/neurodeskapp # remove command symlink
rm -rf ~/.config/neurodeskapp # to remove application cache

Arch-based Linux distributions

sudo pacman -Rs neurodeskapp-bin

macOS

Find the application installation NeurodeskApp.app in Finder (in /Applications or ~/Applications) and move to Trash by using CMD + Delete. Clean other application generated files using:

rm -rf ~/Library/neurodeskapp # to remove application cache
rm -rf ~/Library/Application\ Support/neurodeskapp # to remove user data

Windows

On Windows, go to Windows Apps & Features dialog using Start Menu -> Settings -> Apps and uninstall Neurodesk App as shown below.

In order to remove application cache, delete C:\Users\<username>\AppData\Roaming\neurodeskapp directory.

2 - Linux

Minimum System Requirements

1. At least 3GB free space for neurodesktop base image
2. Docker requirements. Details found under https://docs.docker.com/get-docker/

Quickstart

0. Install Docker or Podman

Install Docker from here: https://docs.docker.com/get-docker/. Additional information is available below. Alternatively, Neurodesk also works with Podman (https://podman.io/).

To set up Neurodesk on Ubuntu, ensure both Podman client and server are installed. Follow the Podman installation instructions provided at https://podman.io/docs/installation for server setup.

sudo apt update && sudo apt upgrade -y
sudo apt install curl
echo "deb https://download.opensuse.org/repositories/devel:/kubic:/libcontainers:/stable/xUbuntu_20.04/ /" | sudo tee /etc/apt/sources.list.d/devel:kubic:libcontainers:stable.list
curl -L "https://download.opensuse.org/repositories/devel:/kubic:/libcontainers:/stable/xUbuntu_20.04/Release.key" | sudo apt-key add -
sudo apt update
sudo apt-get -y install podman

For the client setup, execute the following commands.

systemctl --user --now enable podman.socket
sudo loginctl enable-linger $USER
ssh-keygen -t ed25519 -f ~/.ssh/id_ed25519
cat  ~/.ssh/id_ed25519.pub | cat >> ~/.ssh/authorized_keys
podman system connection add development --identity ~/.ssh/id_ed25519 ssh://$USER@$HOSTNAME/run/user/$UID/podman/podman.sock

1. Optional: only for ARM64 hardware

Neurodesk supports ARM64 hardware through binfmt

To enable Neurodesk on ARM64 hardware run this setup step:

sudo docker run --privileged --rm tonistiigi/binfmt --install all

2. Run Neurodesktop

Before the first run, create a local folder where the downloaded applications will be stored, e.g. mkdir ~/neurodesktop-storage

Then use one of the following options to run Neurodesktop:

Option 1 (Recommended for local installations): Neurodesk-App

Instructions on installing and using the app: https://www.neurodesk.org/docs/getting-started/neurodesktop/neurodeskapp/

Option 2 (Advanced and for remote installations): Using Terminal

0. If the Linux machine is remote (e.g. in the cloud), connect to the machine with a port forwarding first:

ssh -L 8888:127.0.0.1:8888 USER@IP

1. then start neurodesktop:

1.a) with a persistent home directory:

docker volume create neurodesk-home &&
sudo docker run \
  --shm-size=1gb -it --privileged --user=root --name neurodesktop \
  -v ~/neurodesktop-storage:/neurodesktop-storage \
  --mount source=neurodesk-home,target=/home/jovyan \
  -e NB_UID="$(id -u)" -e NB_GID="$(id -g)" \
  -p 8888:8888 \
  -e NEURODESKTOP_VERSION=2024-03-27 vnmd/neurodesktop:2024-03-27

1.b) without a persistent home directory:

sudo docker run \
  --shm-size=1gb -it --privileged --user=root --name neurodesktop \
  -v ~/neurodesktop-storage:/neurodesktop-storage \
  -e NB_UID="$(id -u)" -e NB_GID="$(id -g)" \
  -p 8888:8888 \
  -e NEURODESKTOP_VERSION=2024-03-27 vnmd/neurodesktop:2024-03-27

chmod a+rwx ~/neurodesktop-storage

2. Once neurodesktop is downloaded, leave the terminal open and check which server neurodesktop is running on (Avoid pressing CTRL+C).

3. To access neurodesktop, open your web browser and type in one of the provided URLs in your terminal (e.g. http://127.0.0.1:8888/lab?token=your_unique_token).

"http://127.0.0.1:8888 wants to
See text and images copied to the clipboard".

4. Press on “Desktop Auto-Resolution” under “ALL CONNECTIONS”

5. If it is the first time you have used Neurodesktop, wait until the desktop appears (it may take a few seconds). Otherwise, it should appear instantaneously.

6. Neurodesk is now ready to use! See the tutorials page for advice on how to use Neurodesk.

7. For an optimal experience, switch your browser to full-screen mode by following the instructions for your browser here: https://www.thewindowsclub.com/open-chrome-edge-or-firefox-browser-in-full-screen-mode

Deleting neurodesktop:

When done processing your data it is important to stop and remove the container - otherwise the next start or container update will give an error ("… The container name “/neurodesktop” is already in use…")

1. Click on the terminal from which you ran neurodesktop

2. Press Ctrl-C

3. Run:

docker stop neurodesktop

4. Run:

docker rm neurodesktop

Installing Docker

For general installation instructions, refer to https://docs.docker.com/get-docker/

RHEL/CentOS (yum-based)

Refer to https://docs.docker.com/engine/install/centos/

One example to install docker in a yum-based distribution could look like this:

sudo dnf install -y yum-utils 
sudo yum-config-manager --add-repo https://download.docker.com/linux/centos/docker-ce.repo
sudo dnf install docker-ce docker-ce-cli containerd.io
# or if dnf not found: sudo yum install docker-ce docker-ce-cli containerd.io
sudo systemctl enable docker
sudo systemctl start docker
sudo docker version
sudo docker info
sudo groupadd docker
sudo usermod -aG docker $USER
sudo chown root:docker /var/run/docker.sock
newgrp docker

Ubuntu/Debian (apt-based)

Refer to https://docs.docker.com/engine/install/ubuntu/

One example to install docker in a apt-based distribution could look like this:

sudo apt-get update
sudo apt-get install ca-certificates curl gnupg
sudo install -m 0755 -d /etc/apt/keyrings
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /etc/apt/keyrings/docker.gpg
sudo chmod a+r /etc/apt/keyrings/docker.gpg
echo \
  "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu \
  $(. /etc/os-release && echo "$VERSION_CODENAME") stable" | \
  sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
sudo apt-get update

GPU support

RHEL/CentOS (yum-based)

sudo yum install nvidia-container-toolkit -y

Ubuntu/Debian (apt-based)

sudo apt install nvidia-container-toolkit -y

Running neurodesktop container with GPU

sudo docker run \
  --shm-size=1gb -it --privileged --user=root --name neurodesktop \
  -v ~/neurodesktop-storage:/neurodesktop-storage \
  -e NB_UID="$(id -u)" -e NB_GID="$(id -g)" \
  --gpus all \
  -p 8888:8888 -e NEURODESKTOP_VERSION=2024-03-27 \
  vnmd/neurodesktop:2024-03-27

Running tensorflow (w/ GPU)

Using tensorflow (python)

mamba install tensorflow-gpu
python

import tensorflow as tf
print("Num GPUs Available: ", len(tf.config.list_physical_devices('GPU')))

Using tensorflow (singularity container in neurodesktop)

singularity pull docker://tensorflow/tensorflow:latest-gpu
singularity run --nv tensorflow_latest-gpu.sif
python

import tensorflow as tf
print("Num GPUs Available: ", len(tf.config.list_physical_devices('GPU')))

Using an RDP Client

Startup Neurodesktop using the following command:

sudo docker run \
  --shm-size=1gb -it --privileged --user=root --name neurodesktop \
  -v ~/neurodesktop-storage:/neurodesktop-storage \
  -e NB_UID="$(id -u)" -e NB_GID="$(id -g)" \
  -p 8888:8888 -p 3390:3389 \
  -e NEURODESKTOP_VERSION=2024-03-27 vnmd/neurodesktop:2024-03-27

Open your RDP client and connect to Computer localhost:3390

Use the following details to login if prompted

username

user

password

password

Using VNC

To enable VNC and disable RDP, startup Neurodesktop using the following command:

sudo docker run \
  --shm-size=1gb -it --privileged --user=root --name neurodesktop \
  -v ~/neurodesktop-storage:/neurodesktop-storage \
  -e NB_UID="$(id -u)" -e NB_GID="$(id -g)" \
  -p 8888:8888 \
  -e NEURODESKTOP_VERSION=2024-03-27 vnmd/neurodesktop:2024-03-27 --vnc

To enable both VNC and RDP, startup Neurodesktop using the following command:

sudo docker run \
  --shm-size=1gb -it --privileged --user=root --name neurodesktop \
  -v ~/neurodesktop-storage:/neurodesktop-storage \
  -e NB_UID="$(id -u)" -e NB_GID="$(id -g)" \
  -p 8888:8888 \
  -e NEURODESKTOP_VERSION=2024-03-27 vnmd/neurodesktop:2024-03-27 --vnc --rdp

Using a VNC Client

Startup Neurodesktop using the following command:

sudo docker run \
  --shm-size=1gb -it --privileged --user=root --name neurodesktop \
  -v ~/neurodesktop-storage:/neurodesktop-storage \
  -e NB_UID="$(id -u)" -e NB_GID="$(id -g)" \
  -p 8888:8888 -p 5901:5901 \
  -e NEURODESKTOP_VERSION=2024-03-27 vnmd/neurodesktop:2024-03-27 --vnc

Install the Tiger VNC client

sudo apt install tigervnc-client

Run the VNC Client and connect to localhost::5901

Enter password and click Ok.

3 - MacOS

Quickstart

1. Install Docker or Podman

Install Docker from here: https://docs.docker.com/get-docker/

Alternatively, Neurodesk also works with Podman, follow the Podman installation instructions provided at https://podman.io/docs/installation.

2. Run Neurodesktop

Use one of the following options to run Neurodesktop:

Option 1 (Recommended): Neurodesk-App

Instructions on installing and using the app: https://www.neurodesk.org/docs/getting-started/neurodesktop/neurodeskapp/

Option 2 (Advanced): Using Terminal

Create a local folder where the downloaded applications will be stored, e.g. ~/neurodesktop-storage

1. Open a terminal, and type the following command to automatically download the neurodesktop container and run it

1.a) with a persistent home directory:

docker volume create neurodesk-home &&
docker run \
--shm-size=1gb -it --privileged --user=root --name neurodesktop \
-v ~/neurodesktop-storage:/neurodesktop-storage \
--mount source=neurodesk-home,target=/home/jovyan \
-e NB_UID="$(id -u)" -e NB_GID="$(id -g)" \
-p 8888:8888 -e NEURODESKTOP_VERSION=2024-03-27 vnmd/neurodesktop:2024-03-27

1.b) without a persistent home directory:

docker run \
--shm-size=1gb -it --privileged --user=root --name neurodesktop \
-v ~/neurodesktop-storage:/neurodesktop-storage \
-e NB_UID="$(id -u)" -e NB_GID="$(id -g)" \
-p 8888:8888 -e NEURODESKTOP_VERSION=2024-03-27 vnmd/neurodesktop:2024-03-27

If you get errors in neurodesktop then check if the ~/neurodesktop-storage directory is writable for all users. If it is not, run chmod a+rwx ~/neurodesktop-storage

2. Once neurodesktop is downloaded, leave the terminal open and check which server neurodesktop running on (Avoid pressing CTRL+C).

3. To access neurodesktop, open your web browser and navigate to one of the URLs shown in your terminal (e.g. http://127.0.0.1:8888/lab?token=your_unique_token).

3. If prompted, press on “Desktop Auto-Resolution” under “ALL CONNECTIONS”

4. If it is the first time you use Neurodesktop, wait until the desktop appears (it may take a few seconds). Otherwise, it should appear instantaneously.

5. Neurodesk is ready to use! See the tutorials page for advice on how to use Neurodesk.

Deleting neurodesktop:

When done processing your data it is important to stop and remove the container - otherwise the next start or container update will give an error ("… The container name “/neurodesktop” is already in use…")

1. Click on the terminal from which you ran neurodesktop

2. Press control-C

3. Type:

docker stop neurodesktop

4. Type:

docker rm neurodesktop

Using an RDP Client

Startup Neurodesktop using the following command:

docker run \
--shm-size=1gb -it --privileged --user=root --name neurodesktop \
-v ~/neurodesktop-storage:/neurodesktop-storage \
-p 3390:3389 -p 8888:8888 \
-e NEURODESKTOP_VERSION=2024-03-27 vnmd/neurodesktop:2024-03-27

Open your RDP client and connect to Computer localhost:3390

Use the following details to login if prompted

username

user

password

password

Using VNC

To enable VNC and disable RDP, startup Neurodesktop using the following command:

docker run \
--shm-size=1gb -it --privileged --user=root --name neurodesktop \
-v ~/neurodesktop-storage:/neurodesktop-storage \
-e VNC_ENABLE=true -p 8888:8888 \
-e NEURODESKTOP_VERSION=2024-03-27 vnmd/neurodesktop:2024-03-27

Using a VNC Client

Startup Neurodesktop using the following command:

docker run \
--shm-size=1gb -it --privileged --user=root --name neurodesktop \
-v ~/neurodesktop-storage:/neurodesktop-storage \
-e VNC_ENABLE=true -p 5901:5901 -p 8888:8888 \
-e NEURODESKTOP_VERSION=2024-03-27 vnmd/neurodesktop:2024-03-27

Open a VNC Client and connect to port 5901

4 - Windows

Minimum System Requirements

1. At least 3GB free space for neurodesktop base image
2. Docker requirements. Details found under https://docs.docker.com/get-docker/
3. If installing docker using WSL, minimum 20GB space recommended for WSL with Ubuntu

Quickstart

1. Install Docker or Podman

Install Docker from here: https://docs.docker.com/get-docker/

Alternatively, Neurodesk also works with Podman, follow the Podman installation instructions provided at https://podman.io/docs/installation.

2. Run Neurodesktop

Use one of the following options to run Neurodesktop:

Option 1 (Recommended): Neurodesk-App

Instructions for installing and using the app: https://www.neurodesk.org/docs/getting-started/neurodesktop/neurodeskapp/

Option 2 (Advanced): Using Terminal

1. Open a terminal (e.g. Powershell), and type the following command to automatically download the neurodesktop container and run it

1.a) with a persistent home directory:

docker volume create neurodesk-home

docker run --shm-size=1gb -it --privileged --user=root --name neurodesktop -v C:/neurodesktop-storage:/neurodesktop-storage --mount source=neurodesk-home,target=/home/jovyan -p 8888:8888 -e NEURODESKTOP_VERSION=2024-03-27 vnmd/neurodesktop:2024-03-27

1.b) without a persistent home directory:

docker run --shm-size=1gb -it --privileged --user=root --name neurodesktop -v C:/neurodesktop-storage:/neurodesktop-storage -p 8888:8888 -e NEURODESKTOP_VERSION=2024-03-27 vnmd/neurodesktop:2024-03-27

2. Once neurodesktop is downloaded, leave the terminal open and check which server neurodesktop running on (Avoid pressing CTRL+C). ]

3. To access neurodesktop, open your web browser and type in one of the URLs provided in your terminal (e.g. http://127.0.0.1:8888/lab?token=your_unique_token).

4. Press on “Desktop Auto-Resolution” under “ALL CONNECTIONS”

5. If it is the first time you use Neurodesktop, wait until the desktop appears (it may take a few seconds). Otherwise, it should appear instantaneously.

6. Neurodesk is ready to use! See the tutorials page for advice on how to use Neurodesk.

7. For an optimal experience, switch your browser to full-screen mode by following the instructions for your browser here: https://www.thewindowsclub.com/open-chrome-edge-or-firefox-browser-in-full-screen-mode

Deleting neurodesktop:

When done processing your data it is important to stop and remove the container - otherwise the next start or container update will give an error ("… The container name “/neurodesktop” is already in use…")

1. Click on the terminal from which you ran neurodesktop

2. Press control-C

3. Type:

docker stop neurodesktop

4. Type:

docker rm neurodesktop

Using an Remote Desktop Protocol (RDP) Client

Startup Neurodesktop using the following command:

docker run \
--shm-size=1gb -it --privileged --user=root --name neurodesktop \
-v C:/neurodesktop-storage:/neurodesktop-storage \
-p 3390:3389 -p 8888:8888 \
-e NEURODESKTOP_VERSION=2024-03-27 vnmd/neurodesktop:2024-03-27

Open Windows Remote Desktop Connection and connect to Computer localhost:3390 as shown below.

Resolution and multi-monitor settings can be set from the Display tab.

Once ready, click Connect. This will take you to the following prompt

Use the following details to login

Session

Xorg

username

user

password

password

Using VNC

To enable VNC and disable RDP, startup Neurodesktop using the following command:

docker run --shm-size=1gb -it --privileged --user=root --name neurodesktop -v C:/neurodesktop-storage:/neurodesktop-storage -p 8888:8888 -e NEURODESKTOP_VERSION=2024-03-27 vnmd/neurodesktop:2024-03-27 --vnc 

Using a Virtual Network Computing (VNC) Client

Startup Neurodesktop using the following command:

docker run --shm-size=1gb -it --privileged --user=root --name neurodesktop -v C:/neurodesktop-storage:/neurodesktop-storage -p 5901:5901 -p 8888:8888 -e NEURODESKTOP_VERSION=2024-03-27 vnmd/neurodesktop:2024-03-27 --vnc 

Download the Tiger VNC client (vncviewer64-1.12.0.exe) from https://sourceforge.net/projects/tigervnc/files/stable/1.12.0/

Run the VNC Client and connect to localhost::5901

Enter password and click Ok.

5 - Play

Neurodesk Play

• Recommended if you want to quickly try out Neurodesktop without installing docker or signing in
• No login or sign-up required
• Does NOT preserve files from previous sessions

To use Neurodesk Play, choose the link below closest to your location:

• Australia
• US
• Europe

How to transfer data onto Neurodesk Play

We provide different ways from drag-and-drop, to cloud storage to transfer your files in and out of Neurodesk Play.

6 - Nectar Virtual Desktop Service

There are a few differences between the open-source version of Neurodesk and what’s hosted on Nectar VDI:

1. There is no /neurodesktop-storage folder (the folder on the Desktop does not lead anywhere).
2. Files uploaded via drag and drop do not get stored on the desktop but in /home/vdiuser/thinclient_drives/GUACFS

Instructions for use

1. Go to https://desktop.rc.nectar.org.au/

2. Click on “Sign in”.

3. Choose the AAF option.

4. Choose your institution from the list.

5. Provide your email address and password.

6. Click on create a Workspace (you only need to do this when you sign in for the first time).

7. Fill form ‘Apply for new Workspace’ and submit.

8. Click on “EXPLORE”.

9. Click “VIEW DETAILS” under Neurodesktop:

10. Click “CREATE DESKTOP +” button on the top right corner.

11. Choose the desired availability zone.

12. Wait until everything is completed:

13. Click “OPEN DESKTOP ->”:

14. For a general guide on using the ARDC virtual desktops, click here: https://tutorials.rc.nectar.org.au/virtual-desktop-service/01-overview

15. For a specific explanation on how to launch the various applications available in the Neurodesktop desktop, follow the instructions here: https://www.neurodesk.org/docs/getting-started/neurodesktop/

7 - Cloud

Options for Running Neurodesk on cloud computing resources

There are a couple of ways how Neurodesktop can be run on cloud computing resources:

1. The first and easiest option is to provision a virtual Linux machine and run docker on this machine similar to a local Linux setup: https://www.neurodesk.org/docs/getting-started/neurodesktop/linux/
2. Another option is to use Windows VMs and some groups have had success with that. Here is a detailed instructions on this setup: https://github.com/NeuroDesk/neurodesk.github.io/blob/main/static/docs/getting-started/neurodesktop/Neurodesk_Windows_Technion.pdf
3. The third and most scalable solution is to run Neurodesk via Kubernetes. This setup is a bit more complex, but can handle many simultaneous users and is ideal for research groups and workshops. The easiest way to deploy Neurodesk on Kubernetes is to use Zero to Jupyterhub (https://z2jh.jupyter.org/en/stable/) - then you can use the Neurodesk image like any other jupyterhub image. If you do not want to run a privileged container you need to deploy the cvmfs setup on Kubernetes as well (https://github.com/cvmfs-contrib/cvmfs-csi).

8 - Data Storage

Drag and Drop

Uploading files

You can drag-and-drop files into the browser window to get files into Neurodesktop. This will then start a file upload:

Downloading files

To download files from the desktop using the same mechanism you will need to open the guacamole settings by pressing CTRL-ALT-SHIFT (Control-Command-Shift on Mac). This will open a menu on the side:

where you can click on “Shared Drive”:

a click (or double click on Mac) on the file will start the download.

You can browse into folders in the shared drive by clicking (double clicking on Mac) on them. To get back to the base of the shared drive, press on the drive icon in the top left of the side menu (just below the “Shared Drive” title).

To close the side menu, click on CTRL-ALT-SHIFT once more (Control-Command-Shift on Mac).

Note that it is only possible to upload or download one file at a time through this interface. If you have multiple files in a directory we recommend zipping the directory and then transferring one zip archive:

zip files.zip files/

Local storage

If you are running Neurodesktop on your own hardware there will be a direct connection between the “Storage” folder on the Desktop, which is a link between “/neurodesktop-storage” in neurodesktop and the “neurodesktop-storage” folder on your C-drive (Windows) or home directory (Mac/Linux). This connection can be used for data processing and data transfer.

Mounting external storage on your host-computer

The -v C:/neurodesktop-storage:/neurodesktop-storage part of the docker command links the directory “neurodesktop-storage” on the “C drive” of your Windows computer to the directory /neurodesktop-storage inside the Desktop environment. Everything you store in there will be available inside the desktop and on the host computer. You can also mount additional directories by adding another -v parameter set (e.g. -v D:/moredata:/data) - this will mount the directory moredata from your D drive to /data inside neurodesktop. Important: the mountpoint inside neurodesktop needs to be named /data, otherwise the applications will not see the files without modifying the SINGULARITY_BINDPATH variable in your .bashrc.

If you are using the NeurodeskApp, you can set an additional storage location through the settings

If you are starting Neurodesk through the command line, here is an example for Windows adding another storage directory:

docker run --shm-size=1gb -it --privileged --user=root --name neurodesktop -v C:/neurodesktop-storage:/neurodesktop-storage -v D:/moredata:/data -p 8888:8888 -e NEURODESKTOP_VERSION=2024-03-27 vnmd/neurodesktop:2024-03-27

Note for Windows users: Connecting network shares from Windows to Neurodesk can cause problems, so be careful when attempting this. Also, be aware that processing large amounts of files stored on a Windows filesystem inside Neurodesk will come with a performance penality due to the file system translation in the background. One option to get around these problems is to directly accessing your storage infrastructure inside Neurodesk.

Cloud storage

Another way to get your data into Neurodesktop is to use a cloud storage provider like Dropbox, OneDrive, OwnCloud, Nextcloud or more general tools like rclone or davfs2. Another good option could be to utilize Globus for large amounts of data.

Nextcloud and Owncloud desktop clients

Under the menu item “Accessories” you can find “Nextcloud” and “ownCloud” desktop sync clients that you can configure with your cloud service accounts.

Mounting webdav storage using davfs2

Another option is to directly mount webdav storage. Here is an example how to mount OwnCloud Storage into Neurodesktop:

sudo mount -t davfs https://yourOwnCloudInstance.com/plus/remote.php/webdav/ /data/

It then asks you for a username and password, which you can generate in the settings: yourOwnCloudInstance/plus/settings/personal?sectionid=security

Rclone

Rclone is a command line tool that enables interaction with various cloud services. Here is an example how to setup rclone with an OwnCloud account:

• start the configuration in a terminal window rclone config
• Create a new remote: n
• Provide a name for the remote: OwnCloud
• For the “Storage” option choose: webdav
• As “url” set: https://yourOwnCloudInstance.com/plus/remote.php/webdav/
• As “vendor” set OwnCloud: 2
• Set your OwnCloud username after generating an access token yourOwnCloudInstance/plus/settings/personal?sectionid=security
• Choose to type in your own password: y
• Enter the Password / Token from the OwnCloud App passwords page and confirm it again:
• Leave blank the bearer_token: <hit Enter>
• No advanced config necessary: <hit Enter>
• accept the configuration: <hit Enter>
• Quit the config: q
• Now we can download data to the HPC easily: rclone copy --progress --transfers 8 OwnCloud:/raw-data-for-science-paper .
• or upload data to OwnCloud: rclone copy --progress --transfers 8 . OwnCloud:/data-processed

Globus

We also provide the globus client, so you can transfer large amounts of data between globus endpoints and Neurodesktop. You can configure it by running the following commands in the Neurodesktop environment:

ml globus
# First run the setup:
globusconnectpersonal -setup

#Follow the instructions in the terminal: 
#1) copy the URL into a browser and generate the Native App Authorization Code
#2) then copy this code and paste it in the terminal
#3) then name the endpoint, e.g. Neurodesktop

# Then start the GUI:
globusconnectpersonal -gui

# If the connection fails, reset the permissions on the key file:
chmod 600 /home/jovyan/.globusonline/lta/relay-anonymous-key.pem

# If the connection still fails, start the client like this to get more information
globusconnectpersonal -debug

Then add the directories you want to share with globus, by opening File -> Preferences:

and then add the paths required and hit Save:

Then you can go to the globus file-manager https://app.globus.org/file-manager and your neurodesktop instance will be an endpoint for globus. You can change the path to any location you specified in the Preferences:

Mount volume using SSHFS

It is theoretically possible to mount an SSH target inside Neurodesktop, but it’s not a very reliable way of mounting storage:

sshfs -o allow_root USER@TARGET_HOST:TARGET_PATH SOURCE_PATH

A better option is to use scp and copy data from an SSH endpoint:

scp /neurodesk/myfile user@remoteserver:/data/

An alternative is to mount the SSHFS target into a parent directory on your local machine or VM and then use the -v option in the docker run command to bind the parent directory of the SSHFS mount. NOTE: the SSHFS has to be mounted to a subdirectory inside a parent directory which is then bound to the docker container. If you directly bind to the mounted directory itself, your Neurodesktop container will stop being able to access it if the SSHFS mount disconnects and will not be able to access it again without restarting the Neurodesktop container.

For example, on a local Linux machine or VM:

sshfs -o allow_root USER@TARGET_HOST:TARGET_PATH/MyData SOURCE_PATH/SSHFS_Mounts/MyData

Then add the following line to the docker run command when starting Neurodesktop (note the rshared flag):

-v /SSHFS_Mounts:/data:rshared \

TIP: If you use key pair authentication instead of password for your SSHFS mount, you can use the reconnect flag to reconnect automatically if the connection drops:

sshfs -o IdentityFile=~/.ssh/id_rsa,allow_root,ServerAliveInterval=5,ServerAliveCountMax=3 USER@TARGET_HOST:TARGET_PATH/MyData SOURCE_PATH/SSHFS_Mounts/MyData