📋 HPC Batch Job Instructions

✅ Unzip the dataset now (this dataset is small, you don't need interactive mode):

✅ Rename the dataset to mri_practice. Navigate to the directory:

This directory contains the fully BIDS compliant subdirectory data with a single subject, sub-CAM003.

Ensure runbet.sh is in your bin directory

runbet.sh is available from /groups/dkp/neuroimaging/scripts if you do not already have it in your ~/bin directory, copy it now:
cp /groups/dkp/neuroimaging/scripts/runbet.sh ~/bin

Ensure runbet.sh is executable

Confirm that runbet.sh has executable permissions (x)
ls -l ~/bin
-rwxr-xr-x. 1 dkp dkp 1514 Dec 15 2022 runbet.sh

Ensure your copy of runbet.sh is in the path BEFORE /groups/dkp/neuroimaging/scripts/runbet.sh

Use which to ensure the correct script is found
$ which runbet.sh
~/bin/runbet.sh

pathdump

You can use pathdump to view the order in which paths are searched (to make sure your home bin directory is in the path BEFORE my scripts directory). This will show you paths you have added to the search path in addition to paths the system provides.

$ pathdump
/groups/dkp/neuroimaging/fsl_6073/share/fsl/bin
/home/u7/dkp/.pyenv/bin
/groups/dkp/neuroimaging/fsl/share/fsl/bin
/home/u7/dkp/miniconda3/condabin
.
/opt/ohpc/pub/sbin
/opt/ohpc/pub/bin
/usr/local/bin
/usr/bin
/usr/local/sbin
/usr/sbin
/home/u7/dkp/bin
/groups/dkp/neuroimaging/scripts
/groups/dkp/neuroimaging/bin
/groups/dkp/neuroimaging/bin/Mango
/groups/dkp/neuroimaging/bin/workbench/bin_rh_linux64
/groups/dkp/neuroimaging/fsl/bin
/groups/dkp/neuroimaging/bin/dsi-studio

✅ Open the batch job file runbet.sh in the OOD editor (runbet.sh should be in your home bin directory AND it should be executable):

✅ Modify the account, e.g., change --account=dkp to your own account name, e.g., --account=akielar.

Group account name not username!

The account to be charged is your PI

✅ Modify #SBATCH --mail-user=dkp@arizona.edu to use your email address instead of mine.

SLURM is not Bash!

Any command in the script that starts with #SBATCH is a command to the SLURM job software. These commands must start with the initial #.
This is different than Bash where the # means the line is a comment.

✅ Modify the line that begins export MRIS. It should point to the mri_practice directory you just identified with pwd. For example, my test run now reads:

nodes-busy

You can check each cluster when you switch to it to see how busy it is with the nodes-busy command.

🟢 HPC 3: Pr (10)