.. _howtouse:
How to use Choclo
=================
The simplest case
-----------------
Using Choclo is very simple, but it requires some work from our side. Let's say
we need to compute the upward component of the gravitational acceleration that
a single rectangular prism produces on a single computation point. To do so we
can just call the :func:`choclo.prism.gravity_u` function:
.. jupyter-execute::
import numpy as np
from choclo.prism import gravity_u
# Define a single computation point
easting, northing, upward = 0.0, 0.0, 10.0
# Define the boundaries of the prism as a list
prism = [-10.0, 10.0, -7.0, 7.0, -15.0, -5.0]
# And its density
density = 400.0
# Compute the upward component of the grav. acceleration
g_u = gravity_u(easting, northing, upward, *prism, density)
g_u
But this case is very simple: we usually deal with multiple sources and
multiple computation points.
Multiple sources and computation points
---------------------------------------
In case we have a collection of prisms with certain densities:
.. jupyter-execute::
prisms = np.array([
[-10.0, 0.0, -7.0, 0.0, -15.0, -10.0],
[-10.0, 0.0, 0.0, 7.0, -25.0, -15.0],
[0.0, 10.0, -7.0, 0.0, -20.0, -13.0],
[0.0, 10.0, 0.0, 7.0, -12.0, -8.0],
])
densities = np.array([200.0, 300.0, -100.0, 400.0])
And a set of observation points:
.. jupyter-execute::
easting = np.linspace(-50.0, 50.0, 21)
northing = np.linspace(-40.0, 40.0, 21)
easting, northing = np.meshgrid(easting, northing)
upward = 10 * np.ones_like(easting)
coordinates = (easting.ravel(), northing.ravel(), upward.ravel())
And we want to compute the gravitational acceleration that those prisms
generate on each observation point, we need to write some kind of loop that
computes the effect of each prism on each observation point and adds it to
a running result.
A possible solution would be to use Python *for loops*:
.. jupyter-execute::
def gravity_upward_slow(coordinates, prisms, densities):
"""
Compute the upward component of the acceleration of a set of prisms
"""
# Unpack coordinates of the observation points
easting, northing, upward = coordinates[:]
# Initialize a result array full of zeros
result = np.zeros_like(easting, dtype=np.float64)
# Compute the upward component that every prism generate on each
# observation point
for i in range(len(easting)):
for j in range(prisms.shape[0]):
result[i] += gravity_u(
easting[i], northing[i], upward[i], *prisms[j, :], densities[j]
)
return result
We use this function to compute the field on every point of the grid:
.. jupyter-execute::
g_u = gravity_upward_slow(coordinates, prisms, densities)
And plot the results:
.. jupyter-execute::
import matplotlib.pyplot as plt
plt.pcolormesh(easting, northing, g_u.reshape(easting.shape), shading='auto')
plt.gca().set_aspect("equal")
plt.colorbar()
plt.show()
*For loops* are known to be slow, and in case we are working with very large
models and a large number of computation points these calculations could take
too long. So this solution is not recommended.
.. important::
Using Python *for loops* to run Choclo's functions is not advisable!
We can write a much faster and efficient solution relying on :mod:`numba`.
Since every function in Choclo is being JIT compiled, we can safely include
calls to these functions inside other JIT compiled functions. So we can write
an alternative function by adding a ``@numba.jit`` decorator:
.. jupyter-execute::
import numba
@numba.jit(nopython=True)
def gravity_upward_jit(coordinates, prisms, densities):
"""
Compute the upward component of the acceleration of a set of prisms
"""
# Unpack coordinates of the observation points
easting, northing, upward = coordinates[:]
# Initialize a result array full of zeros
result = np.zeros_like(easting, dtype=np.float64)
# Compute the upward component that every prism generate on each
# observation point
for i in range(len(easting)):
for j in range(prisms.shape[0]):
result[i] += gravity_u(
easting[i],
northing[i],
upward[i],
prisms[j, 0],
prisms[j, 1],
prisms[j, 2],
prisms[j, 3],
prisms[j, 4],
prisms[j, 5],
densities[j],
)
return result
g_u = gravity_upward_jit(coordinates, prisms, densities)
plt.pcolormesh(easting, northing, g_u.reshape(easting.shape), shading='auto')
plt.gca().set_aspect("equal")
plt.colorbar()
plt.show()
Let's benchmark these two functions to see how much faster the decorated
function runs:
.. jupyter-execute::
%timeit gravity_upward_slow(coordinates, prisms, densities)
.. jupyter-execute::
%timeit gravity_upward_jit(coordinates, prisms, densities)
From these numbers we can see that we have significantly reduced the
computation time by several factors by just decorating our function.
.. note::
The benchmarked times may vary if you run them in your system.
.. seealso::
Check `How to measure the performance of Numba?
`__
to learn more about how to properly benchmark jitted functions.
Parallelizing our runs
----------------------
We have already shown how we can reduce the computation times of our forward
modelling by decorating our functions with ``@numba.jit(nopython=True)``. But
this is just the first step: all the computations were being run in *serial* in
a single CPU. We can harness the full power of our modern multiprocessors CPUs
by parallelizing our runs. To do so we need to use the :func:`numba.prange`
instead of the regular Python ``range`` function and slightly change the
decorator of our function by adding a ``parallel=True`` argument:
.. jupyter-execute::
@numba.jit(nopython=True, parallel=True)
def gravity_upward_parallel(coordinates, prisms, densities):
"""
Compute the upward component of the acceleration of a set of prisms
"""
# Unpack coordinates of the observation points
easting, northing, upward = coordinates[:]
# Initialize a result array full of zeros
result = np.zeros_like(easting, dtype=np.float64)
# Compute the upward component that every prism generate on each
# observation point
for i in numba.prange(len(easting)):
for j in range(prisms.shape[0]):
result[i] += gravity_u(
easting[i],
northing[i],
upward[i],
prisms[j, 0],
prisms[j, 1],
prisms[j, 2],
prisms[j, 3],
prisms[j, 4],
prisms[j, 5],
densities[j],
)
return result
g_u = gravity_upward_parallel(coordinates, prisms, densities)
plt.pcolormesh(easting, northing, g_u.reshape(easting.shape), shading='auto')
plt.gca().set_aspect("equal")
plt.colorbar()
plt.show()
With :func:`numba.prange` we can specify which loop we want to run in parallel.
Since we are updating the values of ``results`` on each iteration, it's
advisable to parallelize the loop over the observation points.
By setting ``parallel=True`` in the decorator we are telling Numba to
parallelize this function, otherwise Numba will reinterpret the
``numba.prange`` function as a regular ``range`` and run this loop in serial.
.. note::
In some applications it's desirable that our forward models are run in
serial. For example, if they are part of larger problem that gets
parallelized at a higher level. The ``parallel`` parameter in the
``numba.jit`` decorator allows us to change this behaviour at will without
having to modify the function code.
Let's benchmark this function against the non-parallelized
``gravity_upward_jit``:
.. jupyter-execute::
%timeit gravity_upward_jit(coordinates, prisms, densities)
.. jupyter-execute::
%timeit gravity_upward_parallel(coordinates, prisms, densities)
By distributing the load between multiple processors we were capable of
lowering the computation time by a few more factors.
----
.. grid:: 2
.. grid-item-card:: :jupyter-download-script:`Download Python script `
:text-align: center
.. grid-item-card:: :jupyter-download-nb:`Download Jupyter notebook `
:text-align: center