Script

runbet.sh is available from /groups/dkp/neuroimaging/scripts.

✅ If you do not already have runbet.sh in your ~/bin directory, copy it now:

✅ Confirm that runbet.sh has executable permissions (x)

✅ Ensure your copy of runbet.sh is in the path

pathdump

You can use pathdump to view the order in which paths are searched. 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):

✅ In the open runbet.sh file, 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 #.
Bash sees lines starting with an initial # as comments, which is good, because these lines are not for Bash to read, they are for SLURM to read!

✅ 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 (e.g. puma, ocelote, elgato) when you switch to it to see how busy it is with the nodes-busy command.

🟢 HPC 6: Pr (10 pts): Batch jobs