I just installed Mothur in Ubuntu and the makefile was initially set for a 64 bit install when I unzipped the tar file.
This computer is not 64 bit, so I had to both change "64BIT_VERSION ?= " from yes to no and change the fortran compiler line to read this: “${FORTAN_COMPILER} -c -m32 *.f”, initially it had the -m64 option instead. If this is the intended functionality (ie, it is meant to be set by default to install as 64 bit) then the makefile wiki needs to be updated to reflect that (http://www.mothur.org/wiki/Makefile_options)
Or would the makefile somehow been set to 64bit install by other software prior to my looking at it (which was before I ever compiled anything)?