The warning message
Execution of parallel task failed: grayComponent.frdat could not be opened because there are too many open files appears once running the FineReader Engine 12 application.
The reason for this issue could be that during processing FineReader Engine 12 tries to open more temporary files than allowed by the operating system.
This is a known issue, and for FineReader Engine 12 for Linux, the following note is included in the Developer's Guide article Specifications → System requirements:
For multi-page documents synthesis and export, please set the open files limit to be no less than 2000. Run
ulimit -n [limit_size] to change it.