Q1: I get strange errors of inexistent haloes or trees. Why? A1: Try doing a clean of the post-simulation pipeline, ./project make clean-post-simulation or of the full pipeline. In principle, ./project make clean-pipeline should clean out all the files that might be problematic. Try removing other temporary built files in the .build/ subdirectories with cosmological calculations, which in order are: n-body-init/ haloes/ galaxies/ mergertrees/ voids/ Q2: The .mk files carry out calculations that I think are unnecessary since they have already been done. Why? A2: You can understand the exact reasoning used by 'make' if you add the --debug option to your ./project command, e.g. ./project make create-galaxies --debug But best store all output in a log file, e.g. (./project make create-galaxies --debug 2>&1) | tee mylogfile.1 See also Q1/A1.