[cctbxbb] iotbx::pdb and boost::unit_test::framework
vanv0059 at umn.edu
vanv0059 at umn.edu
Wed Dec 14 07:00:50 PST 2011
Here is what I have found on both Linux (an ancient version of SUSE Linux
Enterprise) and Mac OS X 10.6.8 using their respective build toolchains
(without any tweaks).
Steps to reproduce:
* Download the 2011_09_03_0448 tarball for cctbx
* Replace the cctbx_sources/boost directory with the 1_48_0 release of boost
* Build the Boost Test library using the default values
** ./bootstrap.sh --with-libraries=test
** ./b2 --with-test
* Follow the cctbx documentation to build iotbx
** python ../cctbx_sources/libtbx/configure.py
--build-boost-python-extensions=False
** source setpaths.sh
** make
** On Mac OS X, create the shared library by hand
* Create a simple boost test that does nothing more than:
** Create a test function
** Create an uninitialized (or initialized if you prefer) iotbx::pdb::input
variable/object in the test function
This results (on both systems):
An invalid free/delete for a checked array that it appears the Boost Test
module is trying to free (and it was already freed by iotbx::pdb::input)
This problem appears to be resolved by compiling iotbx with threads
(i.e. configuring with the --enable-boost-threads flag).
I'm hoping that this enabling threads will not adversely affect my python
extension modules that use iotbx.pdb. Are there any issues that I should be
aware of when enabling the threads for iotbx.pdb (other than Mac OS X's
buggy implementations of core system components such as pthreads, polling,
etc.)?
--Jeff
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