I am building a QWSAT model over a DEM of around 18,000,000 cells. The process is working nice but the model is currently running the "Creating HRUs" module since 15 hours. Does it need so much time or is the program stuck?
The answer is it shouldn't take this long. I believe the watershed processing went ok for you. Hence, I don't think it is the number fo cells in your DEM that causes the issue. Check your soil map and land use map for any issue. If you believe these maps are error free then reduce the number of sub-basin and try to create the HRUs. If this takes too long I suggest you follow Arun's suggestion.
I believe the maps are free from errors, the number of sub watershed is 55 (the threshold was taken from a previous study).
The only hot spot may be the dem. I build it myself by fillinng the void in a 30 m raster with the data from a 90 m full dem (that are SRTM 1 arcsec and SRTM 3 arcsec resampled). Anyway the dem reacts well to the hydrological terrain elaboration and the final watershed model runs fast and without issues.
By the way the three raster (dem, land use and soils) are aligned on the same grid.
SWAT run could be faster with better computing and RAM. With 18 million cells and routing, I recommend running it on a different machine with better capability. This might reduce the computation time. Remember, there are lots of hydrological processes and routing performed for each time step. It is common to see such long time lengths for large river basins. Changing threshold setting for delineation might also help but depends on the problem you are simulating.
Based on the number of cells and resolution, i estimate the total area for your DEM is about 16000 km2. So for such large area I think it is common for the process to take long time, like Timothy said. I am currently working on a watershed about the same size and it did take about 10 hours or more in a new desktop with 16GB RAM depending on how much I am using the computer for other purposes. It is always a good practice to check your dataset for any error or inconsistency but the issue you have is not uncommon.