Category: cPanel

When a cPanel server experiences file permission issues-after a migration, manual file operations, or a misbehaving script-websites may become inaccessible, emails may fail, or security might be at risk. This script automates the process of fixing file ownership and permissions for one or more cPanel users, ensuring everything is back to a secure and functional state.

Use Case

You may need to run this script when:

• Website files show 403 Forbidden errors
• Email delivery fails due to etc/ permissions
• Files were copied or restored without --preserve flags
• CageFS directories have incorrect modes

How to run the script

for i in `ls -A /var/cpanel/users` ; do ./fixperms $i ; done

The Script (save as ./fixperms and chmod +x fixperms)

#!/bin/bash
# Script to fix permissions and ownerships for one or more cPanel users

if [ "$#" -lt "1" ]; then
  echo "Must specify at least one user"
  exit 1
fi

USERS=$@

for user in $USERS; do
  HOMEDIR=$(getent passwd "$user" | cut -d: -f6)

  if [ ! -f /var/cpanel/users/"$user" ]; then
    echo "User file missing for $user, skipping"
    continue
  elif [ -z "$HOMEDIR" ]; then
    echo "Could not determine home directory for $user, skipping"
    continue
  fi

  echo "Fixing ownership and permissions for $user"

  # Ownership
  chown -R "$user:$user" "$HOMEDIR" >/dev/null 2>&1
  chmod 711 "$HOMEDIR" >/dev/null 2>&1
  chown "$user:nobody" "$HOMEDIR/public_html" "$HOMEDIR/.htpasswds" 2>/dev/null
  chown "$user:mail" "$HOMEDIR/etc" "$HOMEDIR/etc/"*/shadow "$HOMEDIR/etc/"*/passwd 2>/dev/null

  # File permissions (parallel)
  find "$HOMEDIR" -type f -print0 2>/dev/null | xargs -0 -P4 chmod 644 2>/dev/null
  find "$HOMEDIR" -type d ! -name cgi-bin -print0 2>/dev/null | xargs -0 -P4 chmod 755 2>/dev/null
  find "$HOMEDIR" -type d -name cgi-bin -print0 2>/dev/null | xargs -0 -P4 chmod 755 2>/dev/null

  chmod 750 "$HOMEDIR/public_html" 2>/dev/null

  # CageFS fixes
  if [ -d "$HOMEDIR/.cagefs" ]; then
    chmod 775 "$HOMEDIR/.cagefs" 2>/dev/null
    chmod 700 "$HOMEDIR/.cagefs/tmp" "$HOMEDIR/.cagefs/var" 2>/dev/null
    chmod 777 "$HOMEDIR/.cagefs/cache" "$HOMEDIR/.cagefs/run" 2>/dev/null
  fi

done

This is a improved script from: https://www.casbay.com/guide/kb/script-to-fix-cpanel-account-permissions-2

When a cPanel server experiences catastrophic failure without any valid backups, restoring websites and databases manually becomes the only option. In my case, the server had completely failed and could only be accessed via a rescue environment. No backups were available in /backup, and the system was non-bootable due to critical library corruption.

To recover, I mounted the failed system, manually transferred essential directories such as /var/lib/mysql and /home to a freshly installed cPanel server using rsync, and fixed ownership and permissions. This restored websites and database files physically, but cPanel/WHM did not recognize the MySQL databases or users.

Problem: cPanel Doesn’t Recognize Existing MySQL Databases

Although the database folders were correctly placed in /var/lib/mysql/ and all MySQL users were present in the mysql.user table, cPanel GUI showed no databases or users associated with any account.

This is expected behavior — cPanel stores mappings between accounts, databases, and MySQL users in its own internal metadata files, which were not recoverable.

Solution: Rebuild cPanel MySQL Mapping Using dbmaptool

To restore MySQL database and user associations for each cPanel account without recreating them manually, I used the official cPanel utility:

/usr/local/cpanel/bin/dbmaptool

I created a script that:

• Loops through all cPanel users (found in /var/cpanel/users)
• For each user, finds all MySQL databases starting with the user’s prefix (e.g. user_db1)
• Finds all MySQL users belonging to that prefix (e.g. user_dbuser1)
• Automatically maps them using dbmaptool

#!/bin/bash

for user in $(ls /var/cpanel/users); do
  dbs=$(mysql -N -e "SHOW DATABASES LIKE '${user}\_%';" | tr '\n' ',' | sed 's/,\$//')
  dbusers=$(mysql -N -e "SELECT User FROM mysql.user WHERE User LIKE '${user}\_%';" | tr '\n' ',' | sed 's/,\$//')

  if [[ -n "$dbs" || -n "$dbusers" ]]; then
    echo "Mapping for user: $user"
    /usr/local/cpanel/bin/dbmaptool "$user" --type 'mysql' --dbs "$dbs" --dbusers "$dbusers"
  fi
done

Final Cache Refresh

After running the script, I executed:

/scripts/update_db_cache
/scripts/updateuserdatacache

This forced cPanel to reload and re-index the updated metadata, and all previously invisible databases and MySQL users reappeared in the cPanel UI for each respective account.

Even in total system failure scenarios with no backups, if the /home and /var/lib/mysql directories are intact and MySQL users are present, it’s entirely possible to recover a cPanel environment manually. The key is to re-establish metadata associations using dbmaptool, which tells cPanel which databases and users belong to which accounts.