From 6cbd155ad974d1d7c90a2e7060776db88d15d67f Mon Sep 17 00:00:00 2001
From: Robin De Schepper <robin.deschepper93@gmail.com>
Date: Thu, 7 Oct 2021 13:40:15 +0200
Subject: [PATCH] Expose profiler to Python (#1688)
Adds the `profiler_initialize(ctx)` and `profiler_summary()` functions to the Python module and the `profiling` key to `arbor.config()`. closes #1685.
---
.gitignore | 4 +-
doc/install/build_install.rst | 23 ++++++-
doc/python/profiler.rst | 16 +++++
python/config.cpp | 5 ++
python/profiler.cpp | 13 ++++
python/test/unit/runner.py | 3 +
python/test/unit/test_profiling.py | 107 +++++++++++++++++++++++++++++
7 files changed, 168 insertions(+), 3 deletions(-)
create mode 100644 python/test/unit/test_profiling.py
diff --git a/.gitignore b/.gitignore
index cb17f702..f2c26f5f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,6 +10,9 @@
# intermediate python files
*.pyc
+# python dev env files
+.python-version
+
# graphviz files generated by executables
*.dot
@@ -83,4 +86,3 @@ dist
# generated image files by Python examples
python/example/*.svg
-
diff --git a/doc/install/build_install.rst b/doc/install/build_install.rst
index 8fcf077b..95a75fa4 100644
--- a/doc/install/build_install.rst
+++ b/doc/install/build_install.rst
@@ -285,6 +285,12 @@ CMake parameters and flags, follow links to the more detailed descriptions below
cmake -DARB_VECTORIZE=ON -DCMAKE_INSTALL_PREFIX=/opt/arbor
+.. topic:: `Release <buildtarget_>`_ mode with profiling enabled
+
+ .. code-block:: bash
+
+ cmake -DARB_WITH_PROFILING=ON
+
.. _buildtarget:
Build target
@@ -459,7 +465,7 @@ use ``ARB_PYTHON_LIB_PATH`` to specify the location where the Python module is t
The location of libraries under a prefix in only guaranteed to be standard for Python's global library location.
Therefore, correct installation of the Python package to any other location using ``CMAKE_INSTALL_PREFIX``,
such as user directory (e.g. `~/.local`), a Python or Conda virtual environment, may result in installation to a wrong path.
-
+
``python3 -m site --user-site`` (for user installations) or a path from ``python3 -c 'import site; print(site.getsitepackages())'``
(for virtual environment installation) can be used in combination with ``ARB_PYTHON_LIB_PATH``.
@@ -551,6 +557,20 @@ component ``neuroml``. The corresponding CMake library target is ``arbor::arbori
# ...
target_link_libraries(myapp arbor::arborio)
+.. install-profiling:
+
+Profiling
+---------
+
+Arbor has built in profiling that can report the time spent in each step during
+the simulation that can be toggled with the ``-DARB_WITH_PROFILING`` CMake option:
+
+.. code-block:: bash
+
+ cmake .. -DARB_WITH_PROFILING=ON
+
+By default ``ARB_WITH_PROFILING=OFF``.
+
.. _install:
@@ -871,4 +891,3 @@ need to be `updated <install-downloading_>`_.
git submodule update
Or download submodules recursively when checking out:
git clone --recurse-submodules https://github.com/arbor-sim/arbor.git
-
diff --git a/doc/python/profiler.rst b/doc/python/profiler.rst
index 9df7a77b..6940682c 100644
--- a/doc/python/profiler.rst
+++ b/doc/python/profiler.rst
@@ -5,6 +5,22 @@
Profiler
========
+If Arbor is built with :ref:`profiling support <install-profiling>` the profiler
+can be initialized after the context is created and a summary is available after
+the simulation has concluded:
+
+.. code-block:: python
+
+ arbor.profiler_initialize(context)
+ simulation.run(tfinal)
+ summary = arbor.profiler_summary()
+ print(summary)
+
+
+
+Meter manager
+=============
+
Arbor's python module :py:mod:`arbor` has a :class:`meter_manager` for measuring time (and if applicable memory) consumptions of regions of interest in the python code.
Users manually instrument the regions to measure.
diff --git a/python/config.cpp b/python/config.cpp
index 69188a7a..3de7f86d 100644
--- a/python/config.cpp
+++ b/python/config.cpp
@@ -33,6 +33,11 @@ pybind11::dict config() {
dict[pybind11::str("vectorize")] = pybind11::bool_(true);
#else
dict[pybind11::str("vectorize")] = pybind11::bool_(false);
+#endif
+#ifdef ARB_PROFILE_ENABLED
+ dict[pybind11::str("profiling")] = pybind11::bool_(true);
+#else
+ dict[pybind11::str("profiling")] = pybind11::bool_(false);
#endif
dict[pybind11::str("version")] = pybind11::str(ARB_VERSION);
dict[pybind11::str("source")] = pybind11::str(ARB_SOURCE_ID);
diff --git a/python/profiler.cpp b/python/profiler.cpp
index e08b4402..31fe6b06 100644
--- a/python/profiler.cpp
+++ b/python/profiler.cpp
@@ -4,6 +4,8 @@
#include <pybind11/stl.h>
#include <arbor/profile/meter_manager.hpp>
+#include <arbor/profile/profiler.hpp>
+#include <arbor/version.hpp>
#include "context.hpp"
#include "strprintf.hpp"
@@ -52,6 +54,17 @@ void register_profiler(pybind11::module& m) {
"manager"_a, "context"_a)
.def("__str__", [](arb::profile::meter_report& r){return util::pprintf("{}", r);})
.def("__repr__", [](arb::profile::meter_report& r){return "<arbor.meter_report>";});
+
+#ifdef ARB_PROFILE_ENABLED
+ m.def("profiler_initialize", [](context_shim& ctx) {
+ arb::profile::profiler_initialize(ctx.context);
+ });
+ m.def("profiler_summary", [](){
+ std::stringstream stream;
+ stream << arb::profile::profiler_summary();
+ return stream.str();
+ });
+#endif
}
} // namespace pyarb
diff --git a/python/test/unit/runner.py b/python/test/unit/runner.py
index 3b12c402..75550dee 100644
--- a/python/test/unit/runner.py
+++ b/python/test/unit/runner.py
@@ -18,6 +18,7 @@ try:
import test_event_generators
import test_identifiers
import test_morphology
+ import test_profiling
import test_schedules
import test_spikes
import test_tests
@@ -32,6 +33,7 @@ except ModuleNotFoundError:
from test.unit import test_event_generators
from test.unit import test_identifiers
from test.unit import test_morphology
+ from test.unit import test_profiling
from test.unit import test_schedules
from test.unit import test_spikes
# add more if needed
@@ -45,6 +47,7 @@ test_modules = [\
test_event_generators,\
test_identifiers,\
test_morphology,\
+ test_profiling,\
test_schedules,\
test_spikes,\
] # add more if needed
diff --git a/python/test/unit/test_profiling.py b/python/test/unit/test_profiling.py
new file mode 100644
index 00000000..bd0a99b5
--- /dev/null
+++ b/python/test/unit/test_profiling.py
@@ -0,0 +1,107 @@
+# -*- coding: utf-8 -*-
+#
+# test_schedules.py
+
+import unittest
+
+import arbor as arb
+import functools
+
+# to be able to run .py file from child directory
+import sys, os
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../../')))
+
+try:
+ import options
+except ModuleNotFoundError:
+ from test import options
+
+"""
+all tests for profiling
+"""
+
+def lazy_skipIf(condition, reason):
+ """
+ Postpone skip evaluation until test is ran by evaluating callable `condition`
+ """
+ def inner_decorator(f):
+ @functools.wraps(f)
+ def wrapped(*args, **kwargs):
+ if condition():
+ raise unittest.SkipTest(reason)
+ else:
+ return f(*args, **kwargs)
+
+ return wrapped
+
+ return inner_decorator
+
+class a_recipe(arb.recipe):
+ def __init__(self):
+ arb.recipe.__init__(self)
+ self.props = arb.neuron_cable_properties()
+ self.trains = [
+ [0.8, 2, 2.1, 3],
+ [0.4, 2, 2.2, 3.1, 4.5],
+ [0.2, 2, 2.8, 3]]
+
+ def num_cells(self):
+ return 3
+
+ def cell_kind(self, gid):
+ return arb.cell_kind.spike_source
+
+ def connections_on(self, gid):
+ return []
+
+ def event_generators(self, gid):
+ return []
+
+ def global_properties(self, kind):
+ return self.the_props
+
+ def probes(self, gid):
+ return []
+
+ def cell_description(self, gid):
+ return arb.spike_source_cell("src", arb.explicit_schedule(self.trains[gid]))
+
+def skipWithoutSupport():
+ return not bool(arb.config().get("profiling", False))
+
+class TestProfiling(unittest.TestCase):
+ def test_support(self):
+ self.assertTrue("profiling" in arb.config(), 'profiling key not in config')
+ profiling_support = arb.config()["profiling"]
+ self.assertEqual(bool, type(profiling_support), 'profiling flag should be bool')
+ if profiling_support:
+ self.assertTrue(hasattr(arb, "profiler_initialize"), 'missing profiling interface with profiling support')
+ self.assertTrue(hasattr(arb, "profiler_summary"), 'missing profiling interface with profiling support')
+ else:
+ self.assertFalse(hasattr(arb, "profiler_initialize"), 'profiling interface without profiling support')
+ self.assertFalse(hasattr(arb, "profiler_summary"), 'profiling interface without profiling support')
+
+ @lazy_skipIf(skipWithoutSupport, "run test only with profiling support")
+ def test_summary(self):
+ context = arb.context()
+ arb.profiler_initialize(context)
+ recipe = a_recipe()
+ dd = arb.partition_load_balance(recipe, context)
+ arb.simulation(recipe, dd, context).run(1)
+ summary = arb.profiler_summary()
+ self.assertEqual(str, type(summary), 'profiler summary must be str')
+ self.assertTrue(summary, 'empty summary')
+
+def suite():
+ # specify class and test functions in tuple (here: all tests starting with 'test' from classes RegularSchedule, ExplicitSchedule and PoissonSchedule
+ suite = unittest.TestSuite()
+ suite.addTests(unittest.makeSuite(TestProfiling, ('test')))
+ return suite
+
+def run():
+ v = options.parse_arguments().verbosity
+ runner = unittest.TextTestRunner(verbosity = v)
+ runner.run(suite())
+
+if __name__ == "__main__":
+ run()
--
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