This paper presents using GDAL utilities and GRASS GIS for topographic analysis of the raster grids based on GEBCO DEM as NetCDF file at 15 arc-second intervals. The focus study area encompasses the area around Okinawa Trough, Ryukyu trench-arc system, southern Japan, East China Sea and the Philippine Sea, West Pacific Ocean. Several GDAL utilities were applied for data processing: gdaldem, gdalwarp, gdalinfo, gdal_translate. The data were imported to GRASS GIS via r.in.gdal. Data visualization highlighted high resolution and accuracy of GEBCO grid, enabling topographic modelling at the advanced level. The algorithm of DEM processing, implemented in GDAL utility gdaldem, was used for generating multi-purpose topographic models: aspect, hillshade, roughness and topographic indices, such as Topographic Position Index (TPI), Terrain Ruggedness Index (TRI). Thematic maps (topography, geoid, marine free-air gravity) were visualized using GRASS GIS modules for raster (d.rast, r.colors, r.contour) and vector (d.vect, v.in.region, d.legend) data processing. The results demonstrated smoother bathymetry in the East China Sea and rugged relief in the Philippine Sea which corresponds to their different geological and geophysical settings. The presented methodology of the topographic analysis based on DEM demonstrated technical aspects of GDAL and GRASS as scripting approach of advanced cartography.