It is important to consider the memory requirements on the Essential Architecture Manager server as the number of instances in the model increases, to avoid Java Out Of Memory Exceptions.

If the server is reporting out of memory exceptions (see the logs in the <Protege_Install>/logs directory) then the MAX_MEMORY parameter in the server startup file (run_protege_server.bat or run_protege_server.sh) must be increased. It's worth starting this around -Xmx200M but when a large number (>1000) of instances are in the model, you may need to raise this, e.g. to -Xmx500M or above.