I installed Neo4j on Ubuntu 12.04 using these instructions: http://www.neo4j.org/download/linux
wget -O - http://debian.neo4j.org/neotechnology.gpg.key | apt
As mentioned in this issue comment and fixed by this commit, since Neo4J 3.1,
you can add a line in
/etc/default/neo4j:NEO4J_ULIMIT_NOFILE=60000to set the ulimit setting (60000 open files) for the service.
There is no need anymore to use /etc/security/limits.conf on debian to set the number of open files.