HPC

Ways of using Neurocommand in Linux:

1. You can use Neurocontainers (i.e., download Singularity containers) directly via CVMFS: https://www.neurodesk.org/docs/getting-started/neurocontainers/cvmfs/
2. or you can install Neurocommand as described here:

Requirements:

Required

• 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

Optional

• lmod https://lmod.readthedocs.io/en/latest/

NB: Your HPC will likely have lmod and Singularity already installed - check with your sysadmin

Command line mode (e.g. running on an HPC or CVL)

• Load singularity and for best performance it should be 3.x e.g.

module load singularity/3.5.0

• Load or install aria2 to optimize the download performance of our containers (THIS IS OPTIONAL)

module load aria2c

• To install the repository, run the following (make sure to clone this to a directory with enough storage, write permissions and NOT a symbolic link (to be sure run cd `pwd -P`)!)

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=$PWD
export APPTAINER_BINDPATH=$PWD

Containers

• If these steps were successful, all Neurodesk containers will be listed
• Copy and paste the line for your desired container(s)

Adding your containers to lmod

• To add each container to 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 this is working. 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 set the SINGULARITY_BINDPATH variable in your .bashrc as well. This variable needs to contain all directories you want to access with the Neurodesk tools:

e.g.:

export SINGULARITY_BINDPATH=/scratch/,/data/

• 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 load --ignore_cache avail

Starting a new shell

• Every time you start a new shell you will need to run conda activate neurocommand. Unless you added it to your .bashrc, you will also need to run module use PathToYourContainers.

To update

Run

git pull
bash build.sh

• this updates the neurocommand but not the modules
• install.sh does not need to be run again to update containers go into the neurodesktop directory and run

bash containers.sh

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 $@

To download all containers

Run

bash containers.sh --all