That is not the correct command for running an mpi process
The impi_intel_win folder does not compile with the OpenMP libraries, just the MPI libraries. If you want both you need to compile in the the omp folder for windows. OpenMP however imposes substantial penalties in being able to optimize the code. If you have 48 cores you are likely better off using more than 12 mpi processes than using 12 mpi processes with OpenMP threads.
If you are running your own version of FDS from the command you would set the OpenMP threads using the environmental variable OMP_NUM_THREADS and you would set the number of mpi processes by running mpiexec:
mpiexec -n mpi_processes fds_exectuable_file.exe jobname.fds where fds_executable_file and jobname.fds are your compiled fds and input file. If your compiled fds directory is not in your path then you need to give the path as well.