Dear colleagues,
I recently discovered that normalize() function of scitbx::vec3<double> is not safe, i.e. this case
scitbx::vec3<double> a(0,0,0);
a.normalize();
it will produce division by zero and fail. If function contains this being called from python the traceback would be rather vague:
<...>
Floating-point error (Python and libc call stacks above)
This crash may be due to a problem in any imported
Python module, including modules which are not part
of the cctbx project. To disable the traps leading
to this message, define these environment variables
(e.g. assign the value 1):
BOOST_ADAPTBX_FPE_DEFAULT
BOOST_ADAPTBX_SIGNALS_DEFAULT
This will NOT solve the problem, just mask it, but
may allow you to proceed in case it is not critical.
The code that generates this error sits in scitbx/vec3.h, lines 143-153 with a comment that this was done intentionally and a pointer to an appropriate function to do safe normalization. This function is not wrapped to be available in python directly.
Similar functionality (but coded in a different place) accessible via python by:
>>> from scitbx import matrix
>>> b = matrix.col([0,0,0])
>>> b.normalize()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/net/anaconda/raid1/olegs/phenix_queue/modules/cctbx_project/scitbx/matrix/__init__.py", line 270, in normalize
return self / abs(self)
File "/net/anaconda/raid1/olegs/phenix_queue/modules/cctbx_project/scitbx/matrix/__init__.py", line 158, in __truediv__
return rec([e/other for e in self.elems], self.n)
ZeroDivisionError: float division by zero
Fast grepping shows that normalize() is widely used in xfel, smtbx, rstbx, dxtbx, mmtbx/hydrogens, scitbx/rigid_body, and in some other places.
My questions to CCTBX community are:
1. Were you aware of this issue?
2. Should we do something about it:
- make the function more safe and slow;
- leave it like it is and let everybody know about the issue and let developers deal with it individually;
3. Any other input on the matter?
Best regards,
Oleg Sobolev.