Distributed processing using C + OpenMP for MODIS and Landsat, the more thread number enabled in your CPU (Check your BIOS settings for enabling HyperTransport for example), the fastest this will run.
1 - Download MODIS tiles you like in one of the 1_HDF subdirectories
2 - run the gdal_import_xxx.sh script located in the subdirectory
3 - go to 2_PreProcessed or 3_Products to collect the data
4 - choose any of the relevant prog_XXX to run on your dataset
5 - Move on to collect your final product of interest
6 - Get to work and use the data generated for your goal