I need someone who is interested in ATLAS on Windows to take the lead in keeping ATLAS installing relatively smoothly on Windows. Will need to come to a pretty good understanding of the configure process in order to recommend needed changes to me.
I would start with simple installs, and build from there:
(1) Get serial ATLAS to install with all-gnu compilers in 32 bit cygwin
(2) Get parallel ATLAS to install with all-gnu compilers & pthreads in 32 bit cygwin
(3) Get serial ATLAS to install with gnu for kernels, but MSVC++ for interface compilers
(4) Get parallel code to work with windows threads & gnu compiler, despite gnu ABI violation
This would get the standard package working. We could then look at mechanisms to get a 64-bit install, which is currently impossible in cygwin (eg., we might need MinGW or something).
I simply don't have time to wrestle with Windows, so it may be literally a year or more before I can address this issue myself.