You are missing the "Lm == xxx" and "Mm == xxx" lines from your /User/External/RomsInit_03_Jul1.in. Please compare it to say ocean_upwelling.in to make sure you have everything you need.
! Grid dimension parameters. See notes below in the Glossary for how to set
! these parameters correctly.
Lm == 248 ! Number of I-direction INTERIOR RHO-points
Mm == 294 ! Number of J-direction INTERIOR RHO-points
N == 31 ! Number of vertical levels
In matlab I would have a variable for a rho point with dimensions:
31x296x250
But for some reason it is not reading the dimensions right I get similar error:
Tile partition information for Grid 01: 0248x0000x0000 tiling: 001x001
tile Istr Iend Jstr Jend Npts
0 1 248 1 0 0
INP_PAR - domain decomposition error in input script file for grid: 1
The domain partition parameter, NtileJ = 1
is incompatible with grid size, Mm = 0
because it yields too small tile, Jstr = 1 Jend = 0
Decrease partition parameter: NtileJ
Elapsed CPU time (seconds):
Thread # 0 CPU: 0.018
Total: 0.018
Nonlinear model elapsed time profile:
Total: 0.000 0.0000
All percentages are with respect to total time = 0.018
ROMS/TOMS - Output NetCDF summary for Grid 01:
ROMS/TOMS - Partition error ......... exit_flag: 6
ERROR: Illegal domain partition.