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SABS-R3-projects / PKPD

A simple, graphical pharmacokinetic-pharmacodynamic modelling solution
GNU General Public License v3.0
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Speed up the model solve method #29

Closed DavAug closed 4 years ago

DavAug commented 4 years ago

model.solve()

The model class works properly but is too slow for useful inference times. This is likely because of unnecessary logs in the background of Myokit.

Currently solving the test one compartment model takes 0.745 sec.

more details:

>>> p = pstats.Stats('tests/model/profile_solve')
>>> p.sort_stats('cumulative').print_stats(50)
Wed Dec 18 12:19:03 2019    tests/model/profile_solve

         335637 function calls (324001 primitive calls) in 0.745 seconds

   Ordered by: cumulative time
   List reduced from 3297 to 50 due to restriction <50>

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
    676/1    0.005    0.000    0.746    0.746 {built-in method builtins.exec}
        1    0.000    0.000    0.746    0.746 tests/model/profile_solve.py:15(<module>)
        1    0.000    0.000    0.498    0.498 /Users/david/Workspace/sabs-r3/PKPD/PKPD/model/model.py:73(solve)
        1    0.000    0.000    0.487    0.487 /Users/david/Workspace/sabs-r3/PKPD/env/lib/python3.7/site-packages/myokit/_sim/cvodesim.py:82(__init__)
        1    0.000    0.000    0.486    0.486 /Users/david/Workspace/sabs-r3/PKPD/env/lib/python3.7/site-packages/myokit/_sim/__init__.py:88(_compile)
   507/21    0.000    0.000    0.410    0.020 <frozen importlib._bootstrap>:211(_call_with_frames_removed)
        1    0.000    0.000    0.339    0.339 /Users/david/Workspace/sabs-r3/PKPD/env/lib/python3.7/site-packages/setuptools/__init__.py:142(setup)
        1    0.000    0.000    0.327    0.327 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/core.py:57(setup)
        1    0.000    0.000    0.323    0.323 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/dist.py:960(run_commands)
     10/2    0.000    0.000    0.323    0.162 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/dist.py:970(run_command)
      8/5    0.000    0.000    0.322    0.064 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/cmd.py:308(run_command)
        1    0.000    0.000    0.287    0.287 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build.py:128(run)
        1    0.000    0.000    0.285    0.285 /Users/david/Workspace/sabs-r3/PKPD/env/lib/python3.7/site-packages/setuptools/command/build_ext.py:75(run)
        1    0.000    0.000    0.285    0.285 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py:278(run)
        1    0.000    0.000    0.284    0.284 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py:443(build_extensions)
        1    0.000    0.000    0.284    0.284 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py:471(_build_extensions_serial)
        1    0.000    0.000    0.284    0.284 /Users/david/Workspace/sabs-r3/PKPD/env/lib/python3.7/site-packages/setuptools/command/build_ext.py:193(build_extension)
        1    0.000    0.000    0.284    0.284 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py:486(build_extension)
   411/16    0.002    0.000    0.283    0.018 <frozen importlib._bootstrap>:978(_find_and_load)
   411/16    0.001    0.000    0.283    0.018 <frozen importlib._bootstrap>:948(_find_and_load_unlocked)
        2    0.000    0.000    0.282    0.141 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/ccompiler.py:909(spawn)
        2    0.000    0.000    0.282    0.141 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/spawn.py:16(spawn)
        2    0.000    0.000    0.282    0.141 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/spawn.py:88(_spawn_posix)
   387/20    0.001    0.000    0.280    0.014 <frozen importlib._bootstrap>:663(_load_unlocked)
        3    0.280    0.093    0.280    0.093 {built-in method posix.waitpid}
   325/19    0.001    0.000    0.279    0.015 <frozen importlib._bootstrap_external>:722(exec_module)
        1    0.000    0.000    0.243    0.243 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/ccompiler.py:511(compile)
        1    0.000    0.000    0.242    0.242 /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/unixccompiler.py:111(_compile)
   425/84    0.000    0.000    0.188    0.002 {built-in method builtins.__import__}
  371/368    0.001    0.000    0.158    0.000 <frozen importlib._bootstrap>:576(module_from_spec)
    41/39    0.000    0.000    0.151    0.004 <frozen importlib._bootstrap_external>:1040(create_module)
    41/39    0.150    0.004    0.151    0.004 {built-in method _imp.create_dynamic}

New execution time: 0.327 including initialization. Just solving the ODE after initialization is now much faster.

Progress: