The first message can be neglected. There is no sediment at one location where there is erosion, but this is negligible (O(-14)). 

The second message cannot be neglected. A bed level change in one time step larger than 5% of the water depth is something to check. In, accuracy if this happens is low. Maybe the water depth is very small and the message can be neglected. Double check what the limit water depth is for allowing sediment computation in flag <sedthr> in the mor-file (chech the value used in the computation in the dia-file). If the water depth is not very small or the threshold is large enough, there may have been an issue with the flow leading to large changes in bed level. How does the solution look like?

The model run didn't give any solution as the error showed up at the start of morphological development.   I used the default 0.1 value for <sedthr>. I found an equation showing the relation between Thet, h1, SedThr, HMaxTH and ThetSD in the manual but I am not sure how it will give the proper SedThr valuefor the model. 

Hi, 

I don't see any error in your message above, only warnings. There is no 'proper' value of <sedthr> or any equation to compute it. It is a threshold which is model dependent. The essence of the threshold is that you do not want that locations with 'very small' flow depth drag your computational time or become a source of unrealistic bed level changes due to poorly resolved flow fields. What 'very small' is depends on the application. In a flume model it will be different than in a model of a large river. 0.1 m sounds a reasonable value for your case. Just check at which locations you find changes in bed level that you find unreallistic and check whether these occur at locations with very shallow flows. 

Thank you. I also thought the same thing because it is working fine and giving reasonable result in a whole run. My concern is about the simulation time it is taking after those messages. The unpartitioned run takes about 7 days to complete and gives a complete result. But the partitioned run is working and giving these messages too but the estimated time changes from 3 days to 30days. I am not sure if it is just for the instant and changes overtime but there was no progress in the model run for a long time. And the solver iteration is above 10 when the model is working fine but after those messages, it is generally 1 to 4. But it is not giving any error while running, just these messages and warnings. Is this an expected condition during morphodynamic runs? I am new to this so trying to learn more on this. Thanks.    

You are facing a stalling simulation. I expect that there has been an unreallistic change in bed level which has caused an unreallistic flow field (e.g., a location with a very large flow velocity). Then, the time step tends to 0 and the flow solver finds the solution in just one iteration. The simulation does not technically crash, but it does not proceed, as the time step is very small. 

You say that the same morphodynamic simulation runs in sequential but not in parallel. Can you confirm that I understand this correctly? Is it the exact same simulation? And does the stalling occur after a while or at the beginning (i.e., it is related to initial condition)? 

Yeah. I am using the same files for both runs. I am using 2s as the maximum computation timestep and 0.5s as the initial computation  time step. The stalling occurs right at the beginning for the parallel run. For the sequential run, it also gives similar messages but the estimated time remains the same and the model progresses according to the regular estimated time.