To safely stop an ECFLOW server you should "halt", "checkpoint" and then "terminate" the server. This can be done either through GUI (right-click on the server) or directly by the CLI commands "halt", "check_pt" and "terminate".
# halt server, write out the in memory definition as a check* # point file, then terminate the server* # The 'yes' bypasses the prompt # ecflow_client --group="halt=yes; check_pt; terminate=yes"