Not a secret, from IEEE:

The NNSA—which oversees Lawrence Livermore as well as Los Alamos National Laboratory and Sandia National Laboratories—plans to use El Capitan to “model and predict nuclear weapon performance, aging effects, and safety,”

There's no real secret about nuclear weapons simulations. Sure the software they use is protected and "secret", but the real secret computing facilities are likely there to break encryption and spy on everyone. Nuclear weapons simulations don't really give the US a tactical advantage, but breaking encryption does, and so that kind of compute power would be kept secret.