Profiling

profile

Python has a profile module to help you find the places in the code where the time is spent.

Let’s say you have a script script.py that you want to run through the profiler. This is what you do:

>>> import profile
>>> profile.run('import script', 'prof')

This will run your script and generate a profile in the file prof. You can also generate the profile by inserting a line like this in your script:

...
import profile
profile.run('atoms.get_potential_energy()', 'prof')
...

To analyse the results, you do this:

>>> import pstats
>>> pstats.Stats('prof').strip_dirs().sort_stats('time').print_stats(20)
Tue Oct 14 19:08:54 2008    prof

        1093215 function calls (1091618 primitive calls) in 37.430 CPU seconds

  Ordered by: internal time
  List reduced from 1318 to 20 due to restriction <20>

  ncalls  tottime  percall  cumtime  percall filename:lineno(function)
   37074   10.310    0.000   10.310    0.000 :0(calculate_spinpaired)
    1659    4.780    0.003    4.780    0.003 :0(relax)
  167331    3.990    0.000    3.990    0.000 :0(dot)
    7559    3.440    0.000    3.440    0.000 :0(apply)
     370    2.730    0.007   17.090    0.046 xc_correction.py:130(calculate_energy_and_derivatives)
   37000    0.780    0.000    9.650    0.000 xc_functional.py:657(get_energy_and_potential_spinpaired)
   37074    0.720    0.000   12.990    0.000 xc_functional.py:346(calculate_spinpaired)
     ...
     ...

The list shows the 20 functions where the most time is spent. Check the pstats documentation if you want to do more fancy things.

Tip

Since the profile module does not time calls to C-code, it is a good idea to run the code in debug mode - this will wrap calls to C-code in Python functions:

$ python3 -d script.py

Tip

There is also a quick and simple way to profile a script:

$ pyhton script.py --profile=prof

This will produce a file called prof.0000 where 0000 is the rank number (if your run the script in parallel, there will be one file per rank).

Use:

$ python3 script.py --profile=-

to write the report directly to standard output.