utils-fix-permissions

Set shared-readable permissions on an HPC directory tree.

When to use

• Another user reports "Permission denied".
• A shared conda env or data directory needs read access.
• A cross-user pipeline cannot read checkpoint, eval, or trace output.
• rsync or scp preserved 600/700 permissions.

What it does

scripts/permissions/fix_permissions.sh <dir> performs these passes:

Pass	Action
0	Ensure all ancestor directories up to / are traversable (o+x) — only touches dirs you own
1	Set all directories to 755 (rwxr-xr-x)
2	Set all files to 644 (rw-r--r--)
3	Restore 755 on executables in bin/ directories
4	Restore 755 on ELF binaries (detected by \x7f ELF magic header)
5	Restore 755 on shell scripts with shebang (#!)

Files remain owner-writable; collaborators receive read and execute.

How to invoke

SSH to the target cluster and run the script from the repo root:

# Leonardo example
ssh Leonardo 'cd $WORK/OpenThoughts-Agent && bash scripts/permissions/fix_permissions.sh /leonardo_work/AIFAC_5C0_290/bfeuer00'

# TACC example (large tree — run on a compute node if login node is loaded)
ssh TACCVista 'cd $SCRATCH/OpenThoughts-Agent && bash scripts/permissions/fix_permissions.sh $SCRATCH/eval_jobs'

# Jupiter example
ssh Jupiter 'cd $DCFT && bash scripts/permissions/fix_permissions.sh /p/home/../../public'

Large directories

For big trees, use an interactive compute node:

# TACC
ssh TACCVista 'srun -p gh-dev -N 1 -n 1 -t 08:00:00 --account=CCR24067 bash -c "cd $SCRATCH/OpenThoughts-Agent && bash scripts/permissions/fix_permissions.sh $SCRATCH/miniconda3"'

# Leonardo (idev or sbatch)
ssh Leonardo 'srun -p boost --account=AIFAC_5C0_290 --time=08:00:00 -N 1 bash -c "cd $WORK/OpenThoughts-Agent && bash scripts/permissions/fix_permissions.sh $WORK"'

Gotchas

• Use chmod -R g+w <dir> when shared editing is required.
• Rerun after pip install for a shared conda environment.
• Pass 0 changes only owned NFS directories.
• Safe to rerun; it is idempotent.