The most basic forms of filesystem protection are file permissions and filesystem encryption.
Any portion of the filesystem that contains sensitive data should be accessible only to the account used to run the server. In a default PingDirectory software installation, all components of the server reside within the instance root. When the software is extracted, which should be done using the account that will be used to run the software, the instance root directory will have filesystem permissions of 0700, preventing any access by other accounts on the system other than those exempt from file permission restrictions, like the root account. Directories used to hold database files are also given permissions of 0700 by default, and log files are written with default permissions of 0600. If the server is configured to access other areas of the filesystem outside of the instance root, take care to set file permissions and ownership on the paths that contain that content.
Some operating systems offer mechanisms beyond the basic file permissions. For example, Linux systems offer getfacl and setfacl commands that can define more fine-grained access controls for files and directories. Consider using those mechanisms to provide greater protection from unauthorized access.
Filesystem auditing software can help identify questionable use of file permissions. It can also keep a record of all filesystem permission and content changes. Although this is not useful for content that changes frequently like database and log files, it can be very helpful for detecting changes to other content, like server binaries and configuration. We also recommend using this auditing for the operating system binaries and configuration.
PingDirectory software provides support for encrypting database contents, backups, LDIF exports, and other content. You can also gain additional protection by enabling filesystem encryption to help protect against unauthorized access to the underlying storage.
The use of filesystem encryption might not offer much additional protection for a mounted filesystem because it appears unencrypted to the users and applications that interact with it.