To safely stop an ECFLOW server you should "halt", "check point" 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"