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line_profiler and kernprof

line_profiler is a module for doing line-by-line profiling of functions. kernprof is a convenient script for running either line_profiler or the Python standard library's cProfile or profile modules, depending on what is available.

They are available under a BSD license.

Installation

Source releases and any binaries can be downloaded from the PyPI link.

http://pypi.python.org/pypi/line_profiler

The current release of the kernprof.py script may be downloaded separately here:

http://packages.python.org/line_profiler/kernprof.py

To check out the development sources, you can use Mercurial:

$ hg clone https://bitbucket.org/robertkern/line_profiler

You may also download source tarballs of any snapshot from that URL.

Source releases will require a C compiler in order to build line_profiler. In addition, Mercurial checkouts will also require Cython >= 0.10. Source releases on PyPI should contain the pregenerated C sources, so Cython should not be required in that case.

kernprof.py is a single-file pure Python script and does not require a compiler. If you wish to use it to run cProfile and not line-by-line profiling, you may copy it to a directory on your PATH manually and avoid trying to build any C extensions.

In order to build and install line_profiler, you will simply use the standard build and install for most Python packages:

$ python setup.py install

line_profiler

The current profiling tools supported in Python 2.5 and later only time function calls. This is a good first step for locating hotspots in one's program and is frequently all one needs to do to optimize the program. However, sometimes the cause of the hotspot is actually a single line in the function, and that line may not be obvious from just reading the source code. These cases are particularly frequent in scientific computing. Functions tend to be larger (sometimes because of legitimate algorithmic complexity, sometimes because the programmer is still trying to write FORTRAN code), and a single statement without function calls can trigger lots of computation when using libraries like numpy. cProfile only times explicit function calls, not special methods called because of syntax. Consequently, a relatively slow numpy operation on large arrays like this,

a[large_index_array] = some_other_large_array

is a hotspot that never gets broken out by cProfile because there is no explicit function call in that statement.

LineProfiler can be given functions to profile, and it will time the execution of each individual line inside those functions. In a typical workflow, one only cares about line timings of a few functions because wading through the results of timing every single line of code would be overwhelming. However, LineProfiler does need to be explicitly told what functions to profile. The easiest way to get started is to use the kernprof.py script.

If you use "kernprof.py [-l/--line-by-line] script_to_profile.py", an instance of LineProfiler will be created and inserted into the __builtins__ namespace with the name "profile". It has been written to be used as a decorator, so in your script, you can decorate any function you want to profile with @profile.

@profile
def slow_function(a, b, c):
    ...

The default behavior of kernprof is to put the results into a binary file script_to_profile.py.lprof . You can tell kernprof to immediately view the formatted results at the terminal with the [-v/--view] option. Otherwise, you can view the results later like so:

$ python -m line_profiler script_to_profile.py.lprof

For example, here are the results of profiling a single function from a decorated version of the pystone.py benchmark (the first two lines are output from pystone.py, not kernprof):

Pystone(1.1) time for 50000 passes = 2.48
This machine benchmarks at 20161.3 pystones/second
Wrote profile results to pystone.py.lprof
Timer unit: 1e-06 s

File: pystone.py
Function: Proc2 at line 149
Total time: 0.606656 s

Line #      Hits         Time  Per Hit   % Time  Line Contents
==============================================================
   149                                           @profile
   150                                           def Proc2(IntParIO):
   151     50000        82003      1.6     13.5      IntLoc = IntParIO + 10
   152     50000        63162      1.3     10.4      while 1:
   153     50000        69065      1.4     11.4          if Char1Glob == 'A':
   154     50000        66354      1.3     10.9              IntLoc = IntLoc - 1
   155     50000        67263      1.3     11.1              IntParIO = IntLoc - IntGlob
   156     50000        65494      1.3     10.8              EnumLoc = Ident1
   157     50000        68001      1.4     11.2          if EnumLoc == Ident1:
   158     50000        63739      1.3     10.5              break
   159     50000        61575      1.2     10.1      return IntParIO

The source code of the function is printed with the timing information for each line. There are six columns of information.

  • Line #: The line number in the file.
  • Hits: The number of times that line was executed.
  • Time: The total amount of time spent executing the line in the timer's units. In the header information before the tables, you will see a line "Timer unit:" giving the conversion factor to seconds. It may be different on different systems.
  • Per Hit: The average amount of time spent executing the line once in the timer's units.
  • % Time: The percentage of time spent on that line relative to the total amount of recorded time spent in the function.
  • Line Contents: The actual source code. Note that this is always read from disk when the formatted results are viewed, not when the code was executed. If you have edited the file in the meantime, the lines will not match up, and the formatter may not even be able to locate the function for display.

If you are using IPython, there is an implementation of an %lprun magic command which will let you specify functions to profile and a statement to execute. It will also add its LineProfiler instance into the __builtins__, but typically, you would not use it like that. For IPython 0.10, you can install it by editing the IPython configuration file ~/.ipython/ipy_user_conf.py to add the following lines:

# These two lines are standard and probably already there.
import IPython.ipapi
ip = IPython.ipapi.get()

# These two are the important ones.
import line_profiler
ip.expose_magic('lprun', line_profiler.magic_lprun)

For IPython 0.11+, you can install it by editing the IPython configuration file ~/.ipython/profile_default/ipython_config.py to add the 'line_profiler' item to the extensions list:

c.TerminalIPythonApp.extensions = [
    'line_profiler',
]

To get usage help for %lprun, use the standard IPython help mechanism:

In [1]: %lprun?

These two methods are expected to be the most frequent user-level ways of using LineProfiler and will usually be the easiest. However, if you are building other tools with LineProfiler, you will need to use the API. There are two ways to inform LineProfiler of functions to profile: you can pass them as arguments to the constructor or use the add_function(f) method after instantiation.

profile = LineProfiler(f, g)
profile.add_function(h)

LineProfiler has the same run(), runctx(), and runcall() methods as cProfile.Profile as well as enable() and disable(). It should be noted, though, that enable() and disable() are not entirely safe when nested. Nesting is common when using LineProfiler as a decorator. In order to support nesting, use enable_by_count() and disable_by_count(). These functions will increment and decrement a counter and only actually enable or disable the profiler when the count transitions from or to 0.

After profiling, the dump_stats(filename) method will pickle the results out to the given file. print_stats([stream]) will print the formatted results to sys.stdout or whatever stream you specify. get_stats() will return LineStats object, which just holds two attributes: a dictionary containing the results and the timer unit.

kernprof

kernprof also works with cProfile, its third-party incarnation lsprof, or the pure-Python profile module depending on what is available. It has a few main features:

  • Encapsulation of profiling concerns. You do not have to modify your script in order to initiate profiling and save the results. Unless if you want to use the advanced __builtins__ features, of course.
  • Robust script execution. Many scripts require things like __name__, __file__, and sys.path to be set relative to it. A naive approach at encapsulation would just use execfile(), but many scripts which rely on that information will fail. kernprof will set those variables correctly before executing the script.
  • Easy executable location. If you are profiling an application installed on your PATH, you can just give the name of the executable. If kernprof does not find the given script in the current directory, it will search your PATH for it.
  • Inserting the profiler into __builtins__. Sometimes, you just want to profile a small part of your code. With the [-b/--builtin] argument, the Profiler will be instantiated and inserted into your __builtins__ with the name "profile". Like LineProfiler, it may be used as a decorator, or enabled/disabled with enable_by_count() and disable_by_count(), or even as a context manager with the "with profile:" statement in Python 2.5 and 2.6.
  • Pre-profiling setup. With the [-s/--setup] option, you can provide a script which will be executed without profiling before executing the main script. This is typically useful for cases where imports of large libraries like wxPython or VTK are interfering with your results. If you can modify your source code, the __builtins__ approach may be easier.

The results of profile script_to_profile.py will be written to script_to_profile.py.prof by default. It will be a typical marshalled file that can be read with pstats.Stats(). They may be interactively viewed with the command:

$ python -m pstats script_to_profile.py.prof

Such files may also be viewed with graphical tools like kcachegrind through the converter program pyprof2calltree or RunSnakeRun.

Frequently Asked Questions

  • Why the name "kernprof"?

    I didn't manage to come up with a meaningful name, so I named it after myself.

  • Why not use hotshot instead of line_profile?

    hotshot can do line-by-line timings, too. However, it is deprecated and may disappear from the standard library. Also, it can take a long time to process the results while I want quick turnaround in my workflows. hotshot pays this processing time in order to make itself minimally intrusive to the code it is profiling. Code that does network operations, for example, may even go down different code paths if profiling slows down execution too much. For my use cases, and I think those of many other people, their line-by-line profiling is not affected much by this concern.

  • Why not allow using hotshot from kernprof.py?

    I don't use hotshot, myself. I will accept contributions in this vein, though.

  • The line-by-line timings don't add up when one profiled function calls another. What's up with that?

    Let's say you have function F() calling function G(), and you are using LineProfiler on both. The total time reported for G() is less than the time reported on the line in F() that calls G(). The reason is that I'm being reasonably clever (and possibly too clever) in recording the times. Basically, I try to prevent recording the time spent inside LineProfiler doing all of the bookkeeping for each line. Each time Python's tracing facility issues a line event (which happens just before a line actually gets executed), LineProfiler will find two timestamps, one at the beginning before it does anything (t_begin) and one as close to the end as possible (t_end). Almost all of the overhead of LineProfiler's data structures happens in between these two times.

    When a line event comes in, LineProfiler finds the function it belongs to. If it's the first line in the function, we record the line number and t_end associated with the function. The next time we see a line event belonging to that function, we take t_begin of the new event and subtract the old t_end from it to find the amount of time spent in the old line. Then we record the new t_end as the active line for this function. This way, we are removing most of LineProfiler's overhead from the results. Well almost. When one profiled function F calls another profiled function G, the line in F that calls G basically records the total time spent executing the line, which includes the time spent inside the profiler while inside G.

    The first time this question was asked, the questioner had the G() function call as part of a larger expression, and he wanted to try to estimate how much time was being spent in the function as opposed to the rest of the expression. My response was that, even if I could remove the effect, it might still be misleading. G() might be called elsewhere, not just from the relevant line in F(). The workaround would be to modify the code to split it up into two lines, one which just assigns the result of G() to a temporary variable and the other with the rest of the expression.

    I am open to suggestions on how to make this more robust. Or simple admonitions against trying to be clever.

  • Why do my list comprehensions have so many hits when I use the LineProfiler?

    LineProfiler records the line with the list comprehension once for each iteration of the list comprehension.

  • Why is kernprof distributed with line_profiler? It works with just cProfile, right?

    Partly because kernprof.py is essential to using line_profiler effectively, but mostly because I'm lazy and don't want to maintain the overhead of two projects for modules as small as these. However, kernprof.py is a standalone, pure Python script that can be used to do function profiling with just the Python standard library. You may grab it and install it by itself without line_profiler.

  • Do I need a C compiler to build line_profiler? kernprof.py?

    You do need a C compiler for line_profiler. kernprof.py is a pure Python script and can be installed separately, though.

  • Do I need Cython to build line_profiler?

    You should not have to if you are building from a released source tarball. It should contain the generated C sources already. If you are running into problems, that may be a bug; let me know. If you are building from a Mercurial checkout or snapshot, you will need Cython to generate the C sources. You will probably need version 0.10 or higher. There is a bug in some earlier versions in how it handles NULL PyObject* pointers.

  • What version of Python do I need?

    Both line_profiler and kernprof have been tested with Python 2.4-2.7. It might work with Python 2.3, but does not currently work with Python 3.x.

  • I get negative line timings! What's going on?

    There was a bug in 1.0b1 on Windows that resulted in this. It should be fixed in 1.0b2. If you are still seeing negative numbers, please let me know.

To Do

cProfile uses a neat "rotating trees" data structure to minimize the overhead of looking up and recording entries. LineProfiler uses Python dictionaries and extension objects thanks to Cython. This mostly started out as a prototype that I wanted to play with as quickly as possible, so I passed on stealing the rotating trees for now. As usual, I got it working, and it seems to have acceptable performance, so I am much less motivated to use a different strategy now. Maybe later. Contributions accepted!

Bugs and Such

If you find a bug, or a missing feature you really want added, please post to the enthought-dev mailing list or email the author at <robert.kern@enthought.com>.

Changes

1.0b3

  • ENH: Profile generators.
  • BUG: Update for compatibility with newer versions of Cython. Thanks to Ondrej Certik for spotting the bug.
  • BUG: Update IPython compatibility for 0.11+. Thanks to Yaroslav Halchenko and others for providing the updated imports.

1.0b2

  • BUG: fixed line timing overflow on Windows.
  • DOC: improved the README.

1.0b1

  • Initial release.

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