Linux
Minimum System Requirements
- At least 3GB free space for neurodesktop base image
- Docker requirements. Details found under https://docs.docker.com/get-docker/
Quickstart
1. Install Docker/Podman
Install Docker from here: https://docs.docker.com/get-docker/. Additional information available below. Neurodesk also works with Podman.
2. Run Neurodesktop
Before the first run, create a local folder where the downloaded applications will be stored, e.g. ~/neurodesktop-storage
Then 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
- Open a terminal, and type the following command to automatically download the neurodesktop container and run it
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=2023-09-20 vnmd/neurodesktop:2023-09-20
If you get errors in neurodesktop then check if the ~/neurodesktop-storage directory is writable to all users. Otherwise run:
chmod a+rwx ~/neurodesktop-storage
- Once neurodesktop is downloaded, leave the terminal open and check which server neurodesktop is running on (Avoid pressing CTRL+C).
- 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
).
If using Chrome, a pop-up may open with the text:
"http://127.0.0.1:8888 wants to
See text and images copied to the clipboard".
Press “Allow” to access your clipboard from within Neurodesktop.
Press on “Desktop Auto-Resolution” under “ALL CONNECTIONS”
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.
Neurodesk is now ready to use! See the tutorials page for advice on how to use Neurodesk.
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…")
Note
Notice that any data that were saved outside of /neurodesktop-storage would be lost. Please make sure to move all your data to that folder before deleting neurodesktop.Click on the terminal from which you ran neurodesktop
Press
Ctrl-C
Run:
docker stop neurodesktop
- 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 $USER
sudo chown root:docker /var/run/docker.sock
newgrp docker
Ubuntu/Debian (apt-based)
Refer to https://docs.docker.com/engine/install/ubuntu/
One example to install docker in a apt-based distribution could look like this:
sudo apt-get update
sudo apt-get install apt-transport-https ca-certificates curl gnupg lsb-release
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg
echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/ubuntu \
$(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
sudo apt-get update
sudo apt-get install docker-ce docker-ce-cli containerd.io
GPU support
RHEL/CentOS (yum-based)
sudo yum install nvidia-container-toolkit -y
Running neurodesktop container with GPU
sudo docker run \
--shm-size=1gb -it --privileged --user=root --name neurodesktop \
-v ~/neurodesktop-storage:/neurodesktop-storage \
-e NB_UID="$(id -u)" -e NB_GID="$(id -g)" \
--gpus all \
-p 8888:8888 -e NEURODESKTOP_VERSION=2023-09-20 \
vnmd/neurodesktop:2023-09-20
Running tensorflow (w/ GPU)
Using tensorflow (python)
conda install tensorflow-gpu
python
import tensorflow as tf
print("Num GPUs Available: ", len(tf.config.list_physical_devices('GPU')))
Using tensorflow (singularity container in neurodesktop)
singularity pull docker://tensorflow/tensorflow:latest-gpu
singularity run --nv tensorflow_latest-gpu.sif
python
import tensorflow as tf
print("Num GPUs Available: ", len(tf.config.list_physical_devices('GPU')))
Using an RDP Client
Startup Neurodesktop using the following command:
sudo docker run \
--shm-size=1gb -it --privileged --user=root --name neurodesktop \
-v ~/neurodesktop-storage:/neurodesktop-storage \
-e NB_UID="$(id -u)" -e NB_GID="$(id -g)" \
-p 8888:8888 -p 3390:3389 \
-e NEURODESKTOP_VERSION=2023-09-20 vnmd/neurodesktop:2023-09-20
Open your RDP client and connect to Computer localhost:3390
Use the following details to login if prompted
- username
- user
- password
- password
Using VNC
To enable VNC and disable RDP, startup Neurodesktop using the following command:
sudo docker run \
--shm-size=1gb -it --privileged --user=root --name neurodesktop \
-v ~/neurodesktop-storage:/neurodesktop-storage \
-e NB_UID="$(id -u)" -e NB_GID="$(id -g)" \
-p 8888:8888 \
-e NEURODESKTOP_VERSION=2023-09-20 vnmd/neurodesktop:2023-09-20 --vnc
To enable both VNC and RDP, startup Neurodesktop using the following command:
sudo docker run \
--shm-size=1gb -it --privileged --user=root --name neurodesktop \
-v ~/neurodesktop-storage:/neurodesktop-storage \
-e NB_UID="$(id -u)" -e NB_GID="$(id -g)" \
-p 8888:8888 \
-e NEURODESKTOP_VERSION=2023-09-20 vnmd/neurodesktop:2023-09-20 --vnc --rdp
Using a VNC Client
Startup Neurodesktop using the following command:
sudo docker run \
--shm-size=1gb -it --privileged --user=root --name neurodesktop \
-v ~/neurodesktop-storage:/neurodesktop-storage \
-e NB_UID="$(id -u)" -e NB_GID="$(id -g)" \
-p 8888:8888 -p 5901:5901 \
-e NEURODESKTOP_VERSION=2023-09-20 vnmd/neurodesktop:2023-09-20 --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.