The sys admins had recently changed the timeout on the firewalls to a fairly low value to deal with the excessive connections issue. This was causing an issue with the mysql servers as the nightly etl and scripts were failing with stale connection issue. Googled around to find a way to set the connection timeout in mysql settings but couldn't find any lead. One of our sys admins suggested we change the tcp timeout on the mysql boxes and that seems to have resolved the issue. here's the command:
sudo /sbin/sysctl net.ipv4.tcp_keepalive_time=90
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