If there is no other workaround you could remove -ffast-math
partially, it's a combination of a few more specific math-related
options.
Correct for gcc whose documentation clearly lists all the flags but then moving to clang is a guess work…
Anyway, I tried another approach: identifying the exact point of failure and coding a workaround: commit 24207.
Actually adding this option was quite an important decision, given
that it violates language standards, disallows NaNs, etc. And all this
is propagated to other projects that are built with libtbx/scons.
By default, the cctbx will crash on you if NaN’s are produced, not because of -ffast-math but because of the way we set the FP flags. Do you unset them in the CCP4?