From 5759530a34b84aba95094c99996fd1629e7c3a0f Mon Sep 17 00:00:00 2001
From: Repo Updater <noreply@mpcdf.mpg.de>
Date: Fri, 1 Oct 2021 10:17:28 +0200
Subject: [PATCH] b10c604c polish pybind11 example, add README.md to f2py
example
---
.gitignore | 6 ++--
examples/cython/c_interface/README.md | 7 ++--
examples/cython/c_interface/setup.py | 3 +-
.../c_interface_shared_object/README.md | 6 ++--
.../libhello/Makefile | 4 +--
.../cython/c_interface_shared_object/setup.py | 4 +--
examples/cython/c_numpy/README.md | 2 +-
examples/cython/c_numpy/setup.py | 7 ++--
examples/f2py/README.md | 9 +++++
.../f2py/{fibonacci.py => test_fibonacci.py} | 0
examples/pybind11/README.md | 5 +++
examples/pybind11/setup.py | 5 +++
examples/pybind11/src/pybex.cpp | 30 +++++++++++++----
examples/pybind11/test_pybex.py | 33 +++++++++++++++++++
14 files changed, 95 insertions(+), 26 deletions(-)
create mode 100644 examples/f2py/README.md
rename examples/f2py/{fibonacci.py => test_fibonacci.py} (100%)
create mode 100644 examples/pybind11/README.md
create mode 100755 examples/pybind11/test_pybex.py
diff --git a/.gitignore b/.gitignore
index 5b28155..552d0b9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,11 +1,11 @@
# directories
-__pycache__
+#__pycache__
.unison
.ipynb_checkpoints
# files
-*.so
-*.o
+#*.so
+#*.o
*.lprof
*.tmp
diff --git a/examples/cython/c_interface/README.md b/examples/cython/c_interface/README.md
index af8026d..ef81727 100644
--- a/examples/cython/c_interface/README.md
+++ b/examples/cython/c_interface/README.md
@@ -2,11 +2,10 @@
## Features
-* Python module "foobar" lives in the directory "foobar" (has `__index__.py`)
+* Python module "foobar.hello" lives in the directory "foobar" (has `__index__.py`)
* `c_hello.c` contains a hello-world implementation in C
-* `hello.pyx` provides the sub-module 'foobar.hello' and contains the Python interface written in Cython
+* `hello.pyx` provides the module 'foobar.hello' and contains the Python interface written in Cython
* `setup.py` contains code to compile the extension, both the source files are compiled into the same shared object
-* `setup.py` demonstrates how to implement a clean command
## Usage
@@ -15,5 +14,5 @@
`python -c "from foobar import hello; hello.say_hello()"`
* or install the package, and run the extension from anywhere
`python setup.py install --user`
-* alternatively, run `test_foobar.py` to call the compiled code example
+* run `test_foobar.py` to call the compiled code example
diff --git a/examples/cython/c_interface/setup.py b/examples/cython/c_interface/setup.py
index 15a0b89..c8db113 100644
--- a/examples/cython/c_interface/setup.py
+++ b/examples/cython/c_interface/setup.py
@@ -2,7 +2,8 @@ import os
from setuptools import setup, Extension
ext = Extension("foobar.hello",
- sources=["foobar/hello.pyx", "foobar/c_hello.c"])
+ sources=["foobar/hello.pyx", "foobar/c_hello.c"]
+)
setup(name="foobar",
ext_modules=[ext],
diff --git a/examples/cython/c_interface_shared_object/README.md b/examples/cython/c_interface_shared_object/README.md
index dcffb69..8eb9e40 100644
--- a/examples/cython/c_interface_shared_object/README.md
+++ b/examples/cython/c_interface_shared_object/README.md
@@ -6,10 +6,10 @@
* `hello.pyx` contains the Python interface written in Cython
* `c_hello.c` contains a hello-world implementation in C, however, in contrast
to the previous simple example it is located in a different library (.so,
- shared object) in the directory `libhello`. Use `make` to generate the
- shared object.
+ shared object) in the directory `libhello`.
+ Use `make` to generate the shared object in that directory.
* `setup.py` contains code to compile the extension, demonstrating how to link
- the shared object in a stable way
+ the shared object in a stable way.
## Usage
diff --git a/examples/cython/c_interface_shared_object/libhello/Makefile b/examples/cython/c_interface_shared_object/libhello/Makefile
index e0f11f1..46f10f9 100644
--- a/examples/cython/c_interface_shared_object/libhello/Makefile
+++ b/examples/cython/c_interface_shared_object/libhello/Makefile
@@ -1,8 +1,8 @@
all: libhello.so
libhello.so: c_hello.c
- gcc -Wall -fPIC -c c_hello.c
- gcc -shared -o $@ c_hello.o
+ $(CC) -Wall -fPIC -c c_hello.c
+ $(CC) -shared -o $@ c_hello.o
.PHONY: clean
clean:
diff --git a/examples/cython/c_interface_shared_object/setup.py b/examples/cython/c_interface_shared_object/setup.py
index f19d9cf..1646a16 100644
--- a/examples/cython/c_interface_shared_object/setup.py
+++ b/examples/cython/c_interface_shared_object/setup.py
@@ -1,7 +1,6 @@
import os
from setuptools import setup, Extension
-
libhello_dir = os.path.abspath("./libhello")
# We need to specify the location of the include file.
@@ -19,7 +18,8 @@ ld_flags.append("-lhello") # link libhello
ext = Extension("wrap_libhello.hello",
sources=["wrap_libhello/hello.pyx"],
extra_link_args=ld_flags,
- include_dirs=include_dirs)
+ include_dirs=include_dirs
+)
setup(name="wrap_libhello",
ext_modules=[ext],
diff --git a/examples/cython/c_numpy/README.md b/examples/cython/c_numpy/README.md
index c3a6dbe..6ccd25c 100644
--- a/examples/cython/c_numpy/README.md
+++ b/examples/cython/c_numpy/README.md
@@ -2,7 +2,7 @@
## Features
-* Python module "ctonumpy" lives in the directory "ctonumpy" (has `__init__.py`)
+* Python module "ctonumpy.cube" lives in the directory "ctonumpy" (has `__init__.py`)
* `c_cube.c` contains a OMP parallel loop-based computation of the third power of an array
* `cube.pyx` contains the Python interface written in Cython
* `setup.py` contains code to compile the extension with optimizing compiler flags
diff --git a/examples/cython/c_numpy/setup.py b/examples/cython/c_numpy/setup.py
index 57009d0..0ee82e9 100644
--- a/examples/cython/c_numpy/setup.py
+++ b/examples/cython/c_numpy/setup.py
@@ -16,14 +16,15 @@ c_flags.append("-fopt-info")
include_dirs = []
include_dirs.append(np.get_include())
-# extra link flags are possible as well; we leave them empty here
-ld_flags = []
+# extra link flags are possible as well; here we use the same as for compilation to link to libgomp
+ld_flags = c_flags
ext = Extension("ctonumpy.cube",
sources=["ctonumpy/cube.pyx", "ctonumpy/c_cube.c"],
extra_compile_args=c_flags,
extra_link_args=ld_flags,
- include_dirs=[np.get_include()])
+ include_dirs=[np.get_include()]
+)
setup(name="ctonumpy",
ext_modules=[ext],
diff --git a/examples/f2py/README.md b/examples/f2py/README.md
new file mode 100644
index 0000000..1738f5f
--- /dev/null
+++ b/examples/f2py/README.md
@@ -0,0 +1,9 @@
+# Minimal example on how-to interface with Fortran code using 'f2py'
+
+Options:
+
+* compile on the command line using `f2py`, cf. 'compile_with_f2py.sh'
+* compile using 'setup.py', using the command `python setup.py build_ext --inplace`
+
+Run the module using 'test_fibonacci.py'.
+
diff --git a/examples/f2py/fibonacci.py b/examples/f2py/test_fibonacci.py
similarity index 100%
rename from examples/f2py/fibonacci.py
rename to examples/f2py/test_fibonacci.py
diff --git a/examples/pybind11/README.md b/examples/pybind11/README.md
new file mode 100644
index 0000000..4a8cf22
--- /dev/null
+++ b/examples/pybind11/README.md
@@ -0,0 +1,5 @@
+# Minimal example showing how to wrap C/C++ code into Python/Numpy using pybind11
+
+* you may need to run `pip install --user pybind11` if not yet installed
+* run `python test_pybex.py` to see the 'pybex' module in action
+
diff --git a/examples/pybind11/setup.py b/examples/pybind11/setup.py
index 5ef0a12..402e322 100644
--- a/examples/pybind11/setup.py
+++ b/examples/pybind11/setup.py
@@ -2,10 +2,15 @@ from setuptools import setup
# run `pip install --user pybind11` if not yet installed
from pybind11.setup_helpers import Pybind11Extension, build_ext
+# extra compile/link args may be injected, e.g. here for optimization and openmp with gcc
+extra_gcc_args=['-O3', '-march=native', '-fopenmp']
+
ext_modules = [
Pybind11Extension(
"pybex",
["src/pybex.cpp",],
+ extra_compile_args=extra_gcc_args,
+ extra_link_args=extra_gcc_args
),
]
diff --git a/examples/pybind11/src/pybex.cpp b/examples/pybind11/src/pybex.cpp
index 3700913..8f1f90b 100644
--- a/examples/pybind11/src/pybex.cpp
+++ b/examples/pybind11/src/pybex.cpp
@@ -1,29 +1,45 @@
// pybind11 example module 'pybex'
+#include <vector>
+#include <numeric>
+#include <functional>
+
#include <pybind11/pybind11.h>
#include <pybind11/numpy.h>
-namespace py = pybind11;
// C/C++ implementation of the function to be wrapped
void c_cube(const double * v_in, double * v_out, size_t n_elem) {
+ #pragma omp parallel for simd default(none) shared(v_in, v_out, n_elem)
for (size_t i=0; i<n_elem; ++i) {
v_out[i] = v_in[i] * v_in[i] * v_in[i];
}
}
+
+namespace py = pybind11;
+
// wrapper function, accepting a NumPy array as input and returning a NumPy array
-py::array_t<double> py_cube(py::array_t<double, py::array::c_style> v_in)
+py::array_t<double> py_cube(py::array_t<double, py::array::c_style> np_in)
{
- // allocate buffer to be returned as a NumPy array
- auto v_out = py::array_t<double>(v_in.size());
- double * v_out_ptr = (double*) v_out.request().ptr;
+ // obtain information about the input array
+ py::buffer_info pybuf_in = np_in.request();
+ auto shape = pybuf_in.shape;
+
+ // create output NumPy array of the same size and dimension
+ py::array_t<double, py::array::c_style> np_out(shape);
- c_cube(v_in.data(), v_out_ptr, v_in.size());
+ // call C/C++ function with proper arguments
+ double * pybuf_in_ptr = (double*) pybuf_in.ptr;
+ double * pybuf_out_ptr = (double*) np_out.request().ptr;
+ size_t count = std::accumulate(shape.begin(), shape.end(), 1, std::multiplies<size_t>());
+ c_cube(pybuf_in_ptr, pybuf_out_ptr, count);
- return v_out;
+ return np_out;
}
+
+// define Python module, expose py_cube function as "cube" to python
PYBIND11_MODULE(pybex, m) {
m.doc() = "pybind11 example module"; // module docstring
diff --git a/examples/pybind11/test_pybex.py b/examples/pybind11/test_pybex.py
new file mode 100755
index 0000000..932fa15
--- /dev/null
+++ b/examples/pybind11/test_pybex.py
@@ -0,0 +1,33 @@
+#!/usr/bin/env python
+
+import numpy as np
+from time import time
+from pybex import cube
+
+
+def test_pybex_cube(N=384):
+ v = np.full((N, N, N), fill_value=2.0)
+
+ # (1) compute the result using our C extension
+ t0 = time()
+ w_ext = cube(v)
+ dt0 = time() - t0
+
+ # (2) compute the result using NumPy, note the relative inefficiency
+ t0 = time()
+ w_ref = v * v * v
+ dt1 = time() - t0
+
+ # (3) compare both the results, be careful with NumPy temporary arrays
+ try:
+ assert(np.allclose(w_ext, w_ref))
+ #assert(np.allclose(w_ext[-1,-1,-1], w_ref[-1,-1,-1]))
+ except:
+ raise
+ else:
+ print("OK! t(C)=%f, t(NumPy)=%f" % (dt0, dt1))
+
+
+if __name__ == "__main__":
+ test_pybex_cube()
+
--
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