[cctbxbb] pyyaml - iotbx.pdb incompatibility

James Stroud xtald00d at gmail.com
Mon Apr 15 21:32:12 PDT 2013

Hello All,

Below shows how to reproduce the error directly.


chernev 314% cctbx.python
Enthought Python Distribution -- www.enthought.com
Version: 7.3-2 (64-bit)

Python 2.7.3 |EPD 7.3-2 (64-bit)| (default, Apr 12 2012, 11:14:05)
[GCC 4.0.1 (Apple Inc. build 5493)] on darwin
Type "credits", "demo" or "enthought" for more information.
py> inf = 1e300
py> inf * inf
py> from iotbx import pdb
py> inf * inf
show_stack(1): <stdin>(1) <module>
libc backtrace (13 frames, most recent call last):
  14  python2.7                           0x0000000100000f54 start + 52
  13  Python                              0x0000000100108576 Py_Main + 3318
  12  Python                              0x00000001000f2c6e PyRun_AnyFileExFlags + 126
  11  Python                              0x00000001000f2b2e PyRun_InteractiveLoopFlags + 78
  10  Python                              0x00000001000f28eb PyRun_InteractiveOneFlags + 379
  9   Python                              0x00000001000cd2c6 PyEval_EvalCode + 54
  8   Python                              0x00000001000ccfc5 PyEval_EvalCodeEx + 1733
  7   Python                              0x00000001000c7ea0 PyEval_EvalFrameEx + 11200
  6   Python                              0x0000000100010af8 PyNumber_Multiply + 40
  5   Python                              0x000000010000c569 binary_op1 + 137
  4   ???                                 0x0000000000000002 0x0 + 2
  3   libsystem_c.dylib                   0x00007fff84b0ccfa _sigtramp + 26
  2   boost_python_meta_ext.so            0x00000001007013c0 initboost_python_meta_ext + 0
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):
                This will NOT solve the problem, just mask it, but
                may allow you to proceed in case it is not critical.

On Apr 15, 2013, at 9:24 PM, James Stroud wrote:

> Hello All,
> There is a strange incompatibility between pyyaml and iotbx.pdb that depends on the order of import. If yaml is imported first, there is no problem. If iotbx.pdb is imported first, then importing yaml crashes. This is the yaml that comes with enthought python, but I don't think it's using libyaml, which is the C implementation. So the yaml, from what I can tell, is pure python.
> I'm wondering if anyone else can reproduce this error.
> James

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