44 lines
2.1 KiB
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44 lines
2.1 KiB
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.. _developers-debugging:
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==============================
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Developers' Tips for Debugging
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==============================
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Memory errors: debugging Cython with valgrind
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=============================================
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While python/numpy's built-in memory management is relatively robust, it can
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lead to performance penalties for some routines. For this reason, much of
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the high-performance code in scikit-learn in written in cython. This
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performance gain comes with a tradeoff, however: it is very easy for memory
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bugs to crop up in cython code, especially in situations where that code
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relies heavily on pointer arithmetic.
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Memory errors can manifest themselves a number of ways. The easiest ones to
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debug are often segmentation faults and related glibc errors. Uninitialized
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variables can lead to unexpected behavior that is difficult to track down.
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A very useful tool when debugging these sorts of errors is
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`valgrind <http://valgrind.org>`_.
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Valgrind is a command-line tool that can trace memory errors in a variety of
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code. Follow these steps:
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1. Install valgrind from `valgrind.org <http://valgrind.org>`_.
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2 Download the python valgrind suppression file: `valgrind-python.supp <http://svn.python.org/projects/python/trunk/Misc/valgrind-python.supp>`_.
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3. Download the valgrind/python readme file:
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`README.valgrind <http://svn.python.org/projects/python/trunk/Misc/README.valgrind>`_.
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4. Follow the directions in the README file to set up your python
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suppressions.
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5. Run valgrind as follows::
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$> valgrind -v --suppressions=valgrind-python.supp python my_test_script.py
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The result will be a list of all the memory-related errors, which reference
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lines in the C-code generated by cython from your .pyx file. If you examine
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the referenced lines in the .c file, you will see comments which indicate the
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corresponding location in your .pyx source file. Hopefully the output will
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give you clues as to the source of your memory error.
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For more information on valgrind and the array of options it has, see the
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tutorials and documentation on the `valgrind web site <http://valgrind.org>`_.
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