Linux and HPC

Ways of using Neurocommand in Linux and HPC:

1. You can use the module files for Neurocontainers directly via CVMFS: https://www.neurodesk.org/docs/getting-started/neurocontainers/cvmfs/
2. or you can install Neurocommand as described here:

Requirements:

• python 3.6+ https://docs.conda.io/en/latest/miniconda.html#linux-installers
• singularity https://docs.sylabs.io/guides/3.5/user-guide/quick_start.html
• git
• lmod https://lmod.readthedocs.io/en/latest/

Setup Instructions:

Install command line (e.g. running on Linux, HPC or CVL)

1. Load singularity For optimal performance, ensure you are using Singularity version 3.x:

module load singularity/3.5.0

2. Load aria2 (Optional) To speed up container downloads, you can optionally install or load aria2c:

module load aria2c

3. Clone and Set Up the Repository Clone the repository into a directory with enough storage and ensure you are not using a symbolic link (to be sure run cd `pwd -P`). It’s recommended to perform this setup within a Python virtual environment (venv) or a Conda environment:

git clone https://github.com/NeuroDesk/neurocommand.git 
cd neurocommand 
pip3 install -r neurodesk/requirements.txt --user 
bash build.sh --cli
bash containers.sh
export SINGULARITY_BINDPATH=`pwd -P`
# OR, depending on your installation:
export APPTAINER_BINDPATH=`pwd -P`

Install Containers

• If these steps are successful, the help will be displayed
• Install all or only specific containers by following the instructions, e.g.:

1. Search and Install Specific Containers To search for containers that have “itksnap” in the name:

bash containers.sh itksnap

2. Install a Specific Version To install a specific version, (e.g., itksnap version 4.0.2 from 20240117):

./local/fetch_containers.sh itksnap 4.0.2 20240117

To install all containers with that name:

bash containers.sh --itksnap

To download all containers (be careful - there are a lot of containers!):

bash containers.sh --all

Add your containers to lmod

• To add each container to the module search path, run the following:

module use $PWD/local/containers/modules/

• It may be a good idea to add this to your .bashrc if it works. When adding to your .bashrc you will need to replace $PWD to point to the correct path, i.e.

module use ~/neurocommand/local/containers/modules/

• It is very important to also set the SINGULARITY_BINDPATH or the APPTAINER_BINDPATH variable in your .bashrc. This variable must contain a comma-separated list of directories you want to access with the Neurodesk tools.

e.g.:

export SINGULARITY_BINDPATH=/scratch/,/data/
# OR, depending on your installation:
export APPTAINER_BINDPATH=/scratch/,/data/
#Note: User the correct line depending on your installation. Do not add a directory that does not exist, otherwise the containers will not start!

• Run ml avail to see the installed containers at the top of the list (neurodesk containers will take preference over system modules with the same name), run:

module --ignore_cache avail

• Every time you start a new shell you need to run module use PathToYourContainers or add this command to you .bashrc file.

module load fsl/6.0.5.1
export neurodesk_singularity_opts='--nv'
eddy_cuda9.1

mkdir -p $HOME/.config/menus
mkdir -p $HOME/.local/share/applications
mkdir -p $HOME/.local/share/desktop-directories
ln -sfn /PATH_TO_YOUR_INSTALLATION/neurocommand/local/xfce-applications.menu $HOME/.config/menus
ln -sfn /PATH_TO_YOUR_INSTALLATION/neurocommand/local/neurodesk-applications.menu $HOME/.config/menus
ln -sfn /PATH_TO_YOUR_INSTALLATION/neurocommand/local/applications $HOME/.local/share/applications/neurodesk
ln -sfn /PATH_TO_YOUR_INSTALLATION/neurocommand/local/desktop-directories $HOME/.local/share/desktop-directories/neurodesk

To update

1. Update the Neurocommand Repository

First, ensure your local repository is up to date by pulling the latest changes:

git pull

Next, rebuild Neurocommand by running:

bash build.sh

2. Update Containers

To update the containers, navigate to the neurodesktop directory and run:

bash containers.sh

3. Update Specific Modules

Choose the module you want to update for example you want to update mrtrix3/3.0.2 module with the eddy_cuda fix:

~/neurocommand/local/fetch_containers.sh mrtrix3 3.0.2 20221108 mrview $@