I just compiled on bluewaters and received output
Done creating cactus_simO3. All done ! Building utilities for simO3 Building utilities for simO3 ... Creating hdf5_recombiner in /mnt/a/u/sciteam/rhaas/ET_trunk/exe/simO3 from /mnt/a/u/sciteam/rhaas/ET_trunk/configs/simO3/build/CarpetIOHDF5/hdf5_recombiner.o mkdir: cannot create directory `/tmp/1399318629': File exists mkdir: cannot create directory `/tmp/1399318629': File exists
with the full (last part of) the log in the attached file.
So it seems as if we have a race condition in the make system that causes it to try and build the utilities twice (in parallel).
On bluewaters simfactory (which I used) builds Cactus using 16 processes.