# 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:
```bash
$ 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.
```bash
#!/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

```bash
$ sbatch skel-job.sh
```