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Sewer model calibration tend to be very different from water distribution system calibration. The focus is often more on loading than on hydraulic properties. Flow metering at key locations is essential but a lot more expensive than simply using a pressure gage.
For dry weather flow, the focus is mainly on matching loading patterns with the metered flows. If you find a location where the depth is much high than expected but the flows match, the cause is more likely blockage (e.g. sediment, FOG, dead rat, roots) than the wrong Manning n. It’s best to perform a CCTV and correct the problem rather than try to adjust the pipe roughness.
Wet weather flows can be a bigger challenge. They have much more to do with hydrology than hydraulics. You would pair a rain gage up with each catchment. For sanitary sewer I&I (Inflow and Infiltration), the preference would typically be to use the RTK method to convert rainfall into sewer flow. You would adjust R if the magnitude of flow is wrong and T if the timing of the peak is wrong.
Usually the problems you’re working on occur in the downstream end of the system and the small upstream pipes aren’t important in that analysis. One trick is to not model anything upstream of the most upstream flow meters. You can make those pipes upstream of the flow meter inactive or not include them in the first place. You can directly input the hydrograph at the flow meter for each event or model that entire area as a single catchment in RTK, rather than trying to model smaller catchments which can't be calibrated. You may want to load the dry weather flow separate from the wet weather. You can always go back in and make the upstream pipes active after you get the downstream system straightened out.
The above are just a few suggestions. Calibration can be an art.
Starting with the V8i SELECTseries 4 release of SewerGEMS, the SCADAConnect tool is included. This tool allows you to connect to SCADA data sources so you can view measured field data along with your model data. A manual calibration could then be performed based on the differences. See the link below for more.
Chapter 9 of the book Wastewater Collection System Modeling and Design covers the topic of sewer model calibration in more detail.
(Help Topic) Adding Hydrographs Based On the RTK Method
(Book) Wastewater Collection System Modeling and Design - Chapter 9 (Model Calibration)
SCADAConnect in SewerGEMS