What are the reasons for abnormally long simulation time?

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You mention you have two buildings. Split it into two different models.

378000 m2 is enormous, and if built they would be the 5th and 6th largest buildings in the world if the two buildings are of equal size. Energyplus just isn't going to be fast if it has to run convergence on HVAC systems across 1288 zones and 3496 surfaces. Ideal loads is faster because it doesn't have to resolve the operation of the plant equipment; it meets the zone loads exactly.

The number of zones that you have may be the culprit. You can try setting you numberOfTimestepsPerHour to 1 to try and reduce the simulation time.

Also, as for the warmupconvergence error, it can be either you have really complex constructions or you have errors in your geometry. Each zone normally has at least 6 surfaces, but currently, you have an average of 2.7 surfaces per zone. I would argue that the export from DesignBuilder failed.

You definitely have a very large amount of zones. What I have done, which is also the recommendation in the manual, is to reduce the number of zones. If an office block for example has 22 cubicles, rather have just one zone for the whole office block, than try to simulate each individual cubicle. In some cases it is best to have a single zone per floor in a multi storey building and to approximate loads and occupancies across that.

Another thing you could try is to not simulate an entire year in one go, but to set up multiple simulations for different months. You could potentially speed up simulations by a factor of 12 if you simulate one month at a time.

I am honestly surprised that your simulation even completes at all with that many severe errors.