Path: blob/master/doc/en/developer/coding_in_cython.rst
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.. _chapter-cython:
================
Coding in Cython
================
This chapter discusses Cython, which is a
compiled language based on Python.
The major advantage it has over Python is that code can be
much faster (sometimes orders of magnitude).
Cython also allows Sage to interface with C and C++, as well
as other languages. See the Python documentation at
http://www.python.org/doc/ for more details. In particular, the
section "Extending and Embedding the Python Interpreter", available at
http://docs.python.org/ext/ext.html, describes how to write C or
C++ modules for use in Python.
Cython is a compiled version of Python. It is based on Pyrex
(http://www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex/). To a
large degree, Cython has changed based on what Sage's developers
needed; Cython has been developed in concert with Sage. However, it is
an independent project now, which is used beyond the scope of Sage.
As such, it is a young, but developing language, with young, but
developing documentation. See its web page,
http://www.cython.org/, for the most up-to-date information.
Python is an interpreted language and has no declared data types for
variables. These features make it easy to write and debug, but Python
code can sometimes be slow. Cython code can look a lot like Python,
but it gets translated into C code (often very efficient C code) and
then compiled. Thus it offers a language which is familiar to Python
developers, but with the potential for much greater speed.
Writing Cython code in Sage
===========================
There are several ways to create and build Cython code in Sage.
#. In the Sage Notebook, begin any cell with ``%cython``. When you
evaluate that cell,
#. It is saved to a file.
#. Cython is run on it with all the standard Sage libraries
automatically linked if necessary.
#. The resulting ``.so`` file is then loaded into your running
instance of Sage.
#. The functionality defined in that cell is now available for you
to use in the notebook. Also, the output cell has a link to the C
program that was compiled to create the ``.so`` file.
#. Create an ``.spyx`` file and attach or load it from the command
line. This is similar to creating a ``%cython`` cell in the
notebook but works completely from the command line (and not from
the notebook).
#. Create a ``.pyx`` file and add it to the Sage library.
#. First, add a listing for the Cython extension to the variable
``ext_modules`` in the file
``SAGE_ROOT/devel/sage/module_list.py``. See the
``distutils.extension.Extension`` class for more information on
creating a new Cython extension.
#. Then, if you created a new directory for your ``.pyx`` file, add
the directory name to the ``packages`` list in the file
``SAGE_ROOT/devel/sage/setup.py``. (See also the section on
"Creating a new directory" in :ref:`chapter-python`.)
#. Run ``sage -b`` to rebuild Sage.
For example, the file
``SAGE_ROOT/devel/sage/sage/graphs/chrompoly.pyx`` has the lines
::
Extension('sage.graphs.chrompoly',
sources = ['sage/graphs/chrompoly.pyx']),
in ``module_list.py``. In addition, ``sage.graphs`` is included in
the ``packages`` list under the Distutils section of ``setup.py``
since ``chrompoly.pyx`` is contained in the directory
``sage/graphs``.
Special pragmas
===============
If Cython code is either attached or loaded as a ``.spyx`` file or
loaded from the notebook as a ``%cython`` block, the following
pragmas are available:
* clang --- may be either c or c++ indicating whether a C or C++
compiler should be used.
* clib --- additional libraries to be linked in, the space separated
list is split and passed to distutils.
* cinclude --- additional directories to search for header files. The
space separated list is split and passed to distutils.
* cfile -- additional C or C++ files to be compiled
* cargs -- additional parameters passed to the compiler
For example::
#clang C++
#clib givaro
#cinclude /usr/local/include/
#cargs -ggdb
#cfile foo.c
Attaching or loading .spyx files
================================
The easiest way to try out Cython without having to learn anything
about distutils, etc., is to create a file with the extension
``spyx``, which stands for "Sage Pyrex":
#. Create a file ``power2.spyx``.
#. Put the following in it:
::
def is2pow(n):
while n != 0 and n%2 == 0:
n = n >> 1
return n == 1
#. Start the Sage command line interpreter and load the ``spyx`` file
(this will fail if you do not have a C compiler installed).
.. skip
::
sage: load "power2.spyx"
Compiling power2.spyx...
sage: is2pow(12)
False
Note that you can change ``power2.spyx``, then load it again and it
will be recompiled on the fly. You can also attach ``power2.spyx`` so
it is reloaded whenever you make changes:
.. skip
::
sage: attach "power2.spyx"
Cython is used for its speed. Here is a timed test on a 2.6 GHz
Opteron:
.. skip
::
sage: %time [n for n in range(10^5) if is2pow(n)]
[1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096, 8192, 16384, 32768, 65536]
CPU times: user 0.60 s, sys: 0.00 s, total: 0.60 s
Wall time: 0.60 s
Now, the code in the file ``power2.spyx`` is valid Python, and if we
copy this to a file ``powerslow.py`` and load that, we get the
following:
.. skip
::
sage: load "powerslow.py"
sage: %time [n for n in range(10^5) if is2pow(n)]
[1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096, 8192, 16384, 32768, 65536]
CPU times: user 1.01 s, sys: 0.04 s, total: 1.05 s
Wall time: 1.05 s
By the way, we could gain even a little more speed with the Cython
version with a type declaration, by changing ``def is2pow(n):`` to
``def is2pow(unsigned int n):``.
.. _section_sig_on:
Interrupt and signal handling
===============================================
(This section was written by Jeroen Demeyer.)
When writing Cython code for Sage, special care must be taken to ensure
the code can be interrupted with ``CTRL-C``.
Since Cython optimizes for speed,
Cython normally does not check for interrupts.
For example, code like the following cannot be interrupted:
.. skip
::
sage: cython('while True: pass') # DON'T DO THIS
While this is running, pressing ``CTRL-C`` has no effect. The only
way out is to kill the Sage process.
On certain systems, you can still quit Sage by typing ``CTRL-\``
(sending a Quit signal) instead of ``CTRL-C``.
Using ``sig_on()`` and ``sig_off()``
------------------------------------
.. highlight:: cython
To enable interrupt handling, use the ``sig_on()`` and ``sig_off()`` functions.
You should put ``sig_on()`` *before* and ``sig_off()`` *after* any Cython code
which could potentially take a long time.
These two *must always* be called in **pairs**, i.e. every
``sig_on()`` must be matched by a closing ``sig_off()``.
In practice your function will probably look like::
def sig_example():
# (some harmless initialization)
sig_on()
# (a long computation here, potentially calling a C library)
sig_off()
# (some harmless post-processing)
return something
You can put ``sig_on()`` and ``sig_off()`` in all kinds of Cython functions:
``def``, ``cdef`` or ``cpdef``.
You cannot put them in pure Python code (i.e. files with extension ``.py``).
It is possible to put ``sig_on()`` and ``sig_off()`` in different functions,
provided that ``sig_off()`` is called before the function which calls
``sig_on()`` returns.
The following code is *invalid*::
# INVALID code because we return from function foo()
# without calling sig_off() first.
cdef foo():
sig_on()
def f1():
foo()
sig_off()
But the following is valid::
cdef int foo():
sig_off()
return 2+2
def f1():
sig_on()
return foo()
For clarity however, it is best to avoid this.
One good example where the above makes sense is the ``new_gen()``
function in :ref:`section-pari-library`.
A common mistake is to put ``sig_off()`` towards the end of a
function (before the ``return``) when the function has multiple
``return`` statements.
So make sure there is a ``sig_off()`` before *every* ``return``
(and also before every ``raise``).
.. WARNING::
The code inside ``sig_on()`` should be pure C or Cython code.
If you call Python code, an interrupt is likely to mess up Python.
Also, when an interrupt occurs inside ``sig_on()``, code execution
immediately stops without cleaning up.
For example, any memory allocated inside ``sig_on()`` is lost.
See :ref:`advanced-sig` for ways to deal with this.
When the user presses ``CTRL-C`` inside ``sig_on()``, execution will jump back
to ``sig_on()`` (the first one if there is a stack) and ``sig_on()``
will raise ``KeyboardInterrupt``. These can be handled just like other
Python exceptions::
def catch_interrupts():
try:
sig_on() # This MUST be inside the try
# (some long computation)
sig_off()
except KeyboardInterrupt:
# (handle interrupt)
Certain C libraries in Sage are written in a way that they will raise
Python exceptions: NTL and PARI are examples of this.
NTL can raise ``RuntimeError`` and PARI can raise ``PariError``.
Since these use the ``sig_on()`` mechanism,
these exceptions can be caught just like the ``KeyboardInterrupt``
in the example above.
It is possible to stack ``sig_on()`` and ``sig_off()``.
If you do this, the effect is exactly the same as if only the outer
``sig_on()``/``sig_off()`` was there. The inner ones will just change
a reference counter and otherwise do nothing. Make sure that the number
of ``sig_on()`` calls equal the number of ``sig_off()`` calls::
def stack_sig_on():
sig_on()
sig_on()
sig_on()
# (some code)
sig_off()
sig_off()
sig_off()
Extra care must be taken with exceptions raised inside ``sig_on()``.
The problem is that, if you do not do anything special, the ``sig_off()``
will never be called if there is an exception.
If you need to *raise* an exception yourself, call a ``sig_off()`` before it::
def raising_an_exception():
sig_on()
# (some long computation)
if (something_failed):
sig_off()
raise RuntimeError, "something failed"
# (some more computation)
sig_off()
return something
Alternatively, you can use ``try``/``finally`` which will also catch
exceptions raised by subroutines inside the ``try``::
def try_finally_example():
sig_on()
try:
# (some long computation, potentially raising exceptions)
finally:
sig_off()
return something
Other signals
-------------
Apart from handling interrupts, ``sig_on()`` provides more general
signal handling.
Indeed, if the code inside ``sig_on()`` would generate
a segmentation fault or call the C function ``abort()``
(or more generally, raise any of SIGSEGV, SIGILL, SIGABRT, SIGFPE, SIGBUS),
this is caught by the interrupt framework and a ``RuntimeError`` is raised::
cdef extern from 'stdlib.h':
void abort()
def abort_example():
sig_on()
abort()
sig_off()
.. code-block:: python
sage: abort_example()
Traceback (most recent call last):
...
RuntimeError: Aborted
This exception can then be caught as explained above.
This means that ``abort()`` can be used
as an alternative to exceptions within ``sig_on()``/``sig_off()``.
A segmentation fault unguarded by ``sig_on()`` would simply terminate Sage.
Instead of ``sig_on()``, there is also a function ``sig_str(s)``,
which takes a C string ``s`` as argument.
It behaves the same as ``sig_on()``, except that the string ``s``
will be used as a string for the exception.
``sig_str(s)`` should still be closed by ``sig_off()``.
Example Cython code::
cdef extern from 'stdlib.h':
void abort()
def abort_example_with_sig_str():
sig_str("custom error message")
abort()
sig_off()
Executing this gives:
.. code-block:: python
sage: abort_example_with_sig_str()
Traceback (most recent call last):
...
RuntimeError: custom error message
With regard to ordinary interrupts (i.e. SIGINT), ``sig_str(s)``
behaves the same as ``sig_on()``:
a simple ``KeyboardInterrupt`` is raised.
.. _advanced-sig:
Advanced functions
------------------
There are several more specialized functions for dealing with interrupts.
The function ``sig_check()`` behaves exactly as ``sig_on(); sig_off()``
(except that ``sig_check()`` is faster since it does not involve a ``setjmp()`` call).
``sig_check()`` can be used to check for pending interrupts.
If an interrupt happens outside of a ``sig_on()``/``sig_off()`` block,
it will be caught by the next ``sig_check()`` or ``sig_on()``.
The typical use case for ``sig_check()`` is within tight loops doing
complicated stuff
(mixed Python and Cython code, potentially raising exceptions).
It gives more control, because a ``KeyboardInterrupt``
can *only* be raised during ``sig_check()``::
def sig_check_example():
for x in foo:
# (one loop iteration which does not take a long time)
sig_check()
As mentioned above, ``sig_on()`` makes no attempt to clean anything up
(restore state or freeing memory) when an interrupt occurs.
In fact, it would be impossible for ``sig_on()`` to do that.
If you want to add some cleanup code, use ``sig_on_no_except()``
for this. This function behaves *exactly* like ``sig_on()``, except that
any exception raised (either ``KeyboardInterrupt`` or ``RuntimeError``)
is not yet passed to Python. Essentially, the exception is there, but
we prevent Cython from looking for the exception.
Then ``cython_check_exception()`` can be used to make Cython look
for the exception.
Normally, ``sig_on_no_except()`` returns 1.
If a signal was caught and an exception raised, ``sig_on_no_except()``
instead returns 0.
The following example shows how to use ``sig_on_no_except()``::
def no_except_example():
if not sig_on_no_except():
# (clean up messed up internal state)
# Make Cython realize that there is an exception.
# It will look like the exception was actually raised
# by cython_check_exception().
cython_check_exception()
# (some long computation, messing up internal state of objects)
sig_off()
There is also a function ``sig_str_no_except(s)``
which is analogous to ``sig_str(s)``.
.. NOTE::
See the file :file:`SAGE_ROOT/devel/sage/sage/tests/interrupt.pyx`
for more examples of how to use the various ``sig_*()`` functions.
Testing interrupts
------------------
.. highlight:: python
When writing :ref:`section-docstrings`,
one sometimes wants to check that certain code can be interrupted in a clean way.
In the module ``sage.tests.interrupt``, there is a function
``interrupt_after_delay(ms_delay = 500)`` which can be used to test interrupts.
That function simulates a ``CTRL-C`` (by sending SIGINT)
after ``ms_delay`` milliseconds.
The following is an example of a doctest demonstrating that
the function ``factor()`` can be interrupted::
sage: import sage.tests.interrupt
sage: try:
... sage.tests.interrupt.interrupt_after_delay()
... factor(10^1000 + 3)
... except KeyboardInterrupt:
... print "ok!"
ok!