[howto] install and run cudimot

A user asked us to install Cudimot. As this is the kind of software that can be installed by the user himself and which may interest the community, I post here the information.

Cudimot NODDI Bingham Installation

export CUDIMOT=${HOME}/cudimot
mkdir -p $CUDIMOT/bin
wget http://users.fmrib.ox.ac.uk/~moisesf/cudimot/NODDI_Bingham/CUDA_9.1/NODDI_Bingham.zip
unzip NODDI_Bingham.zip
cp NODDI_Bingham/bin/* $CUDIMOT/bin


Create a sbatch script as usual. As Cudimot needs or can use Cuda, you need to use a node with GPU.

#SBATCH --time=XXX # to adapt
#SBATCH --cpus-per-task=XX # to adapt.
#SBATCH --partition=shared-gpu-EL7
#SBATCH --gres=gpu:1

export CUDIMOT=${HOME}/cudimot

ml GCC/7.3.0-2.30  OpenMPI/3.1.1 FSL/5.0.11

srun $CUDIMOT/bin/Pipeline_NODDI_Bingham.sh [SubjectDirectory]

About the #SBATCH --cpus-per-task=X line, if unsure, start with 1, measure the run time. set it to 2, measure run time. If the run is almost twice as fast, you can continue to increase. If no, stick to 1.

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