The info I caught stated that the sub burned for a full day before being contained. (The Early Show, CBS)
EDIT: ...and the reactor was off-line and shut down. The munitions were removed before going into drydock.
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Pretty much SOP for any warship going into the docks, nuclear or otherwise. You guys should have seen the cluster-fuck that is disarming and rearming an Arleigh Burke before she enters the drydock and after she leaves. If you got a competent handling crew, then MAYBE it can all happen in one day.
As for the fire itself, I'm honestly not surprised that it got as bad as it did. With the ship in drydock, they probably have assloads of paint, solvents, and lubricants... and all of it of the most flammable variety. The cause will probably be because some dumbass was sneaking a smoke break - pretty much the same thing that happened to the USS George Washington (CVN-73) on its way to Yokosuka. Someone took a smoke break during an underway replenishment evolution... and they did so in a fan room that had a bunch of improperly stowed HAZMAT. And that being a fan room, the fire quickly spread to every compartment it serviced. Ouch.
...here's the weird thing: They stated on the news that it was the rubber muffling material that burned.
(I'll give you this much: That stuff doesn't matter.)
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Hrm.... Probably petroleum based rubber then. That shit burns like boiling oil, only without having to be brought to 'boiling' first.