Thanks Jim. I know we can compile and run from the executable, which I did. I got the inputs by running MWSWAT. But I am getting some errors like below:
[SWAT_Test.exe has triggered a breakpoint.
The thread 0x5cc has exited with code 24 (0x18).
The thread 0x520 has exited with code 24 (0x18).
The thread 0x53c has exited with code 24 (0x18).
The thread 0x172c has exited with code 24 (0x18).
The program '[4612] SWAT_Test.exe' has exited with code 24 (0x18).]
You are right, but actually I am going to use this model for larger scale like continental scale. And I think GUI version can not handle that large scale of data and may take longer time. And also, I am interested only in Stream flow output so, I am planning to exclude sediment, nutrient and other routines.