Linux and HPC

Ways of using Neurocommand in Linux and HPC

You can use the module files for Neurocontainers directly via CVMFS: /getting-started/neurocontainers/cvmfs/
Or you can install Neurocommand as described here.

Requirements

Python 3.6+: https://www.anaconda.com/docs/getting-started/miniconda/install#linux-terminal-installer
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 or HPC)

Load Singularity.

For optimal performance, ensure you are using Singularity version 3.x:
Terminal window
```
module load singularity/3.5.0
#or
module load singularity
#or
module load apptainer
```
If this doesn’t work it might already be loaded. Just run singularity and check.
Load aria2 (optional).

To speed up container downloads, you can optionally install or load aria2c:
Terminal window
```
module load aria2c
```
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 is recommended to perform this setup within a Python virtual environment (venv) or a Conda environment:
Terminal window
```
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.:

Search and install specific containers.

To search for containers that have “itksnap” in the name:
Terminal window
```
bash containers.sh itksnap
```
Install a specific version.

To install a specific version (e.g., itksnap version 4.0.2 from 20240117):
Terminal window
```
./local/fetch_containers.sh itksnap 4.0.2 20240117
```
To install all containers with that name:
Terminal window
```
bash containers.sh --itksnap
```
To download all containers (be careful, there are a lot of containers):
Terminal window
```
bash containers.sh --all
```

Add your containers to Lmod

To add each container to the module search path, run the following:
Terminal window
```
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. the output of:
Terminal window
```
echo "module use $PWD/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: use 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):
Terminal window
```
module --ignore_cache avail
```
Every time you start a new shell you need to run module use PathToYourContainers or add this command to your .bashrc file.

Some of our containers contain GPU-accelerated applications. Here is an example that runs the GPU accelerated program eddy in FSL:

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, to update the mrtrix3/3.0.2 module with the eddy_cuda fix:

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

Installation examples

We show a couple of specific examples on how Neurodesk can be installed on various HPC systems here.