I was unable to make any change to alloc.c that would fix the GC_MARK_STACK
problem without later crashes in the build while compiling the lisp
files.

However, I suspect the attached change to src/s/gnu-linux.h is
approprate.  This produces a working emacs (for me) on a amd64
gnu-linux system (SuSE 9.1), although it sidesteps the problem in
alloc.c.