Compute Canada

Computing Medial Surface

To compile and run skeltools on compute canada (CC) clusters you first need to load two modules itk and eigen. The current version of skeltools works with itk-5.4 and eigen-3.4. Before submitting a job to the cluster, ensure that you clone the reposity and compile the code.On CC clusters, there is no need to explicitly set the ITK_DIR variable in the CMakeLists.txt file, so it can be safetly commented out. Use the following commands to clone and compile skeltools on CC clusters:

$ git clone https://github.com/HaaPut/skeltools.git
$ cd skeltools
$ sed -i '10s/^/#/' CMakeLists.txt
$ mkdir -v build
$ cd build
$ module load itk/5.4
$ module load eigen/3.4
$ cmake -DCMAKE_BUILD_TYPE=Release ..
$ make -j

Create a job submission script (say skel-job.sh) based on the template below. Set the account variable to appropriate value and set mail-user to your email id.

#!/bin/bash

#SBATCH --account=def-pi
#SBATCH --time=00:05:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=8G
#SBATCH --job-name=medial-surface
#SBATCH --output=skeltools_%x_id_%j.log
#SBATCH --mail-user=user@mail.ca
#SBATCH --mail-type=ALL

module load itk/5.4
module load eigen/3.4


./skeltool -priority distance -surface -input ../data/dinosaur.tif -smooth 0.1  -fillholes -output ../results/dino_surface.tif -anchor aof -slow

Finally, submit the job using sbatch as follows

$ sbatch skel-job.sh