Profiling

Profiling PyOP2 programs

Profiling a PyOP2 program is as simple as profiling any other Python code. You can profile the jacobi demo in the PyOP2 demo folder as follows:

python -m cProfile -o jacobi.dat jacobi.py

This will run the entire program under cProfile and write the profiling data to jacobi.dat. Omitting -o will print a summary to stdout, which is not very helpful in most cases.

Creating a graph

There is a much more intuitive way of representing the profiling data using the excellent gprof2dot to generate a graph. Install from PyPI with

sudo pip install gprof2dot

Use as follows to create a PDF:

gprof2dot -f pstats -n 1 jacobi.dat | dot -Tpdf -o jacobi.pdf

-f pstats tells gprof2dot that it is dealing with Python cProfile data (and not actual gprof data) and -n 1 ignores everything that makes up less than 1% of the total runtime - most likely you are not interested in that (the default is 0.5).

Consolidating profiles from different runs

To aggregate profiling data from different runs, save the following as concat.py:

"""Usage: concat.py PATTERN FILE"""

import sys
from glob import glob
from pstats import Stats

if len(sys.argv) != 3:
    print __doc__
    sys.exit(1)
files = glob(sys.argv[1])
s = Stats(files[0])
for f in files[1:]: s.add(f)
s.dump_stats(sys.argv[2])

With profiles from different runs named <basename>.*.part, use it as

python concat.py '<basename>.*.part' <basename>.dat

and then call gprof2dot as before.

Using PyOP2’s internal timers

PyOP2 automatically times the execution of certain regions:

  • Sparsity building

  • Plan construction

  • Parallel loop kernel execution

  • Halo exchange

  • Reductions

  • PETSc Krylov solver

To output those timings, call summary() in your PyOP2 program or run with the environment variable PYOP2_PRINT_SUMMARY set to 1.

To query e.g. the timer for parallel loop execution programatically, use the timing() helper:

from pyop2 import timing
timing("ParLoop compute")               # get total time
timing("ParLoop compute", total=False)  # get average time per call

To add additional timers to your own code, you can use the timed_region() and timed_function() helpers:

from pyop2.profiling import timed_region, timed_function

with timed_region("my code"):
    # my code

@timed_function("my function")
def my_func():
    # my func

Line-by-line profiling

To get a line-by-line profile of a given function, install Robert Kern’s line profiler and:

  1. Import the profile() decorator:

    from pyop2.profiling import profile

  2. Decorate the function to profile with @profile

  3. Run your script with kernprof.py -l <script.py>

  4. Generate an annotated source file with

    python -m line_profiler <script.py.lprof>

Note that kernprof.py injects the @profile decorator into the Python builtins namespace. PyOP2 provides a passthrough version of this decorator which does nothing if profile is not found in __builtins__. This means you can run your script regularly without having to remove the decorators again.

The profile() decorator also works with the memory profiler (see below). PyOP2 therefore provides the lineprof() decorator which is only enabled when running with kernprof.py.

A number of PyOP2 internal functions are decorated such that running your PyOP2 application with kernprof.py will produce a line-by-line profile of the parallel loop computation (but not the generated code!).

Memory profiling

To profile the memory usage of your application, install Fabian Pedregosa’s memory profiler and:

  1. Import the profile() decorator:

    from pyop2.profiling import profile

  2. Decorate the function to profile with @profile.

  3. Run your script with

    python -m memory_profiler <script.py>

    to get a line-by-line memory profile of your function.

  4. Run your script with

    memprof run --python <script.py>

    to record memory usage of your program over time.

  5. Generate a plot of the memory profile with memprof plot.

Note that memprof and python -m memory_profiler inject the @profile decorator into the Python builtins namespace. PyOP2 provides a passthrough version of this decorator which does nothing if profile is not found in __builtins__. This means you can run your script regularly without having to remove the decorators again.

The profile() decorator also works with the line profiler (see below). PyOP2 therefore provides the memprof() decorator which is only enabled when running with memprof.

A number of PyOP2 internal functions are decorated such that running your PyOP2 application with memprof run will produce a memory profile of the parallel loop computation (but not the generated code!).