In order to run ALYA, you need at least the following input files per execution: X.dom.dat X.typ.dat X.geo.dat X.bcs.dat X.inflow_profile.bcs X.ker.dat X.nsi.dat X.dat In our case, there are 2 different inputs, so X={1_1p1mill,3_27p3mill} To execute a simulation, you must be inside the input directory and you should submit a job like: mpirun Alya.x 1_1p1mill or mpirun Alya.x 3_27p3mill