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There are a number of different philosophies for sizing the innodb_buffer_pool_size. On a dedicated server, MySQL recommends 70% of the available memory. If you are hosting Tomcat on the same server, then maybe that should be no more that 70% of the system memory minus the max Tomcat heap size.

Actual requirements depends on data shape and usage patterns - for the SDB layout, a good rule of thumb appears to be roughly 1G for every 5 million triples (rows in the Quads table)after accessing a number of different pages in VIVO and checking the free buffers, a good setting seems to be around 1MB for every 16,000 triples - e.g. 1.5GB for a 25million triple store. If you have the resources, increasing the buffer size doesn't hurt performance - in which case allocating at least 100MB per 1million triples would be a good idea.