Develop Reference

Boost Python Basic function returning int: SIGSEGV

I successfully used Boost Python to write C++ functions with Numpy array arguments.
But I'm struggling with a very basic case: when my function has to return a value. There's no problem until I try to read the int returned by my function.
I strongly suspect my setup has something to do with this, but I'm not sure where to begin. I commented my CMakeLists.txt to explain how I did setup all the libs.
I tried to play with return_value_policy but it seems irrelevant for simple scalar values.
Environment:
MacOS 11.0.1 (20B50)
CLion for C++ edition and build
Pycharm to run Python code, configured using conda environment with Python 3.8
Boost setup described in CMakeLists.txt
C++ code:
int testFunction() {
std::cout << "Test Function 1\n";
return 1;
}
void testFunction2() {
std::cout << "Test Function 2\n";
}
BOOST_PYTHON_MODULE (mylib) {
np::initialize();
py::def("test_function", testFunction);
py::def("test_function_2", testFunction2);
}
My CMakeLists.txt:
cmake_minimum_required(VERSION 3.17)
project(mylib_project)
set(CMAKE_VERBOSE_MAKEFILE ON)
set(CMAKE_CXX_STANDARD 20)
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE Release)
endif()
set(CMAKE_CXX_FLAGS "-Wall -Wextra")
set(CMAKE_CXX_FLAGS_DEBUG "-g")
set(CMAKE_CXX_FLAGS_RELEASE "-O3")
find_package(PythonInterp 3)
find_package(PythonLibs 3)
# Standard boost installation
# Download boost https://www.boost.org/users/download/ and unzip
# Inside boost dir:
# ./bootstrap.sh
# ./b2
# ./b2 install
# Other (brew / macports) install will have all chances to fail (at the time of writing)
# Components should be found in path with name libboost_NAME.dylib, eg: /usr/local/lib/libboost_numpy38.dylib
# This is additional to standard boost installation
# For both python38 and numpy38 to be produced, you have to:
# - be in the right python environment (conda python 3.8 for example)
# - install numpy: pip install numpy
# - inside boost dir:
# ./bootstrap.sh --with-libraries=python
# ./b2
# ./b2 install
find_package(Boost 1.75.0 COMPONENTS python38 numpy38 REQUIRED)
# Python library, will produce a mylib.so file
python_add_module(mylib python-mylib.cpp)
target_include_directories(mylib PRIVATE ${PYTHON_INCLUDE_DIRS})
target_include_directories(mylib PRIVATE ${Boost_INCLUDE_DIRS})
target_link_libraries(mylib ${PYTHON_LIBRARY})
target_link_libraries(mylib ${Boost_PYTHON_LIBRARY})
target_link_libraries(mylib ${Boost_LIBRARIES})
I'm then producing a mylib.so that I provide to the path of my python code.
Python code:
if __name__ == '__main__':
mylib.test_function_2()
result = mylib.test_function()
print(result)
Output:
Test Function 2
Test Function 1
Process finished with exit code 139 (interrupted by signal 11: SIGSEGV)
My naive question is: how to avoid this crash ?
But after some further investigations (see comments) I'd rather ask: how can I proceed to find (and then probably fix) the cause of this issue in my setup ?

How to (hermetically) include Python interpreter in Bazel to build Python library (sdist)

How can I (hermetically) include python as an (executable) input to my genrule?
Conceptually, I'm aware of the following approaches:
include a python interpreter in the source repo at third_party/python
have Bazel fetch python ala rules-go
There also seem to be a couple methods for doing so:
py_runtime
py_toolchain (doesn't seem to be available yet)
py_distribution_package (doesn't seem to be available yet)
genrules.tools
genrules.toolchains
Example:
I have a python library:
myproject
- setup.py
- mylibrary
- __init__.py
- myfunction.py
I'd like to produce a pip install-able distribution with Bazel so that I can do:
pip install <path/to/distribution>
python
>>> from mylibrary.myfunction import helloworld
>>> helloworld()
I added a (empty) WORKSPACE file at myproject/WORKSPACE and followed the example in this medium article:
# myproject/BUILD
genrule(
name = "mylibrary_sdist",
srcs = glob(["**/*.py"]),
outs = ["mylibrary.tar.gz"],
cmd = "python setup.py sdist && mv dist/mylibrary*.tar.gz $(location mylibrary.tar.gz)"
)
This works (ie. produces bazel-genfiles/mylibrary.tar.gz), but I'm shelling out to python.
How can I (hermetically) include python as an (executable) input to my genrule?

Unless I'm misunderstanding your question, this should just be a matter of passing the actual path to your target python executable. I would check the python executable into the third_party dir and instead of invoking your genrule using simply python I'd pass the relative path to that executable relative to WORKSPACE.

Cython Compilation Error: dynamic module does not define module export function

I am building a package in Cython. I am using the following as the structure for setup.py:
from distutils.core import setup
from distutils.extension import Extension
from Cython.Build import cythonize
import numpy
import scipy
extensions = [
Extension("xxxxx",["xxxx/xxxxx.pyx"],
include_dirs=[numpy.get_include(),"."]),
Extension("nnls",["xxxxx/xxxxx.pyx"],
include_dirs=[numpy.get_include(),"."]),
]
setup(
name='xxxxxx',
version='0.0.0',
description='''********''',
url='xxxxxxx',
author='xxxxx',
author_email='xxxxx',
packages=[
'xxxxx',
],
install_requires=[
'cython',
'numpy',
'scipy',
],
ext_modules=cythonize(extensions),
)
However, I am getting an error upon installation in Python 3. It is working in Python 2 however, it is not compiling in Python 3 having the following error:
dynamic module does not define module export function
How can I solve this problem? Is the structure of the setup.py the reason why this is not compiling?

You need to call setup.py with Python 3 (python3 setup.py build_ext, maybe --inplace). It's because Python 3 defines a different name for the init function called when the module starts, and so you need to build it using Python 3 to ensure the correct name is generated.
See dynamic module does not define init function (PyInit_fuzzy) and How to specify Python 3 source in Cython's setup.py? for slightly more detail (it's bordering on a duplicate of these questions, but isn't quite in my view)

I experienced this and found that I had to use the same name of .pyx as the module name, e.g.
makefile:
# (default)
# INSTALL_DIR:=/usr/lib/python3.6/site-packages
# (my venv)
INSTALL_DIR:=/home/<username>/python3_venv/lib/python3.6/site-packages
all:
sudo python3 setup_myproj.py install --install-lib ${INSTALL_DIR}
setup_myproj.py
from distutils.core import setup, Extension
from Cython.Build import cythonize
ext = Extension("myproj",
sources=["myproj.pyx", "myCppProjFacade.cpp"],
<etc>
language="c++"
)
setup(name="myproj",
version="0.0.1",
ext_modules=cythonize(ext))
client module, run after installing to venv
import myproj as myCppProjWrapper
...
I also found that if the "myproj" names are different, under <python-lib-dir>/<python-vers>/site-packages the .so and .egg-info names are different and the client fails to load it.
In addition I found that the client's environment does not need to have the cython package installed.

I had the same error for torchvision. FIxed it by downgrading the installation versions:
pip install torch==1.2.0+cu92 torchvision==0.4.0+cu92 -f https://download.pytorch.org/whl/torch_stable.html

Error installing/compiling grpc on Ubuntu

I have protobuf compiler version 3.0 and need to install grpc and grpc python plugin. Following the tutorial, I added deb http://http.debian.net/debian jessie-backports main to my sources.list file and did sudo apt-get update and sudo apt-get install libgrpc-dev which returned
Package libgrpc-dev is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
E: Package 'libgrpc-dev' has no installation candidate
So, I decided to compile it from source as mentioned in INSTALL notes and did:
$ git clone https://github.com/grpc/grpc.git
$ cd grpc
$ git submodule update --init
$ make
$ [sudo] make install
However, on the make step, I get
[MAKE] Generating cache.mk
make: Circular /home/vagrant/grpc2/grpc/libs/opt/libboringssl.a <- /home/vagrant/grpc2/grpc/libs/opt/libboringssl.a dependency dropped.
[C] Compiling third_party/boringssl/crypto/bio/connect.c
third_party/boringssl/crypto/bio/connect.c: In function 'split_host_and_port':
third_party/boringssl/crypto/bio/connect.c:127:17: error: declaration of 'close' shadows a global declaration [-Werror=shadow]
cc1: all warnings being treated as errors
make: *** [/home/vagrant/grpc2/grpc/objs/opt/third_party/boringssl/crypto/bio/connect.o] Error 1
On switching to the release-0_11 branch, running make results in
[HOSTCXX] Compiling src/compiler/csharp_generator.cc
src/compiler/csharp_generator.cc:47:43: error: 'google::protobuf::compiler::csharp::GetUmbrellaClassName' has not been declared
src/compiler/csharp_generator.cc: In function 'void grpc_csharp_generator::{anonymous}::GenerateServiceDescriptorProperty(grpc::protobuf::io::Printer*, const ServiceDescriptor*)':
src/compiler/csharp_generator.cc:237:62: error: 'GetUmbrellaClassName' was not declared in this scope
make: *** [/home/vagrant/grpc2/grpc/objs/opt/src/compiler/csharp_generator.o] Error 1
I can't figure out how to install this. Any help would be appreciated.

For me the issue got fixed after i made change in the file as:
diff --git a/src/compiler/csharp_generator.cc
b/src/compiler/csharp_generator.cc
index 7b497df..5a8746d 100644
--- a/src/compiler/csharp_generator.cc
+++ b/src/compiler/csharp_generator.cc
## -44,7 +44,7 ##
using google::protobuf::compiler::csharp::GetFileNamespace;
using google::protobuf::compiler::csharp::GetClassName;
-using google::protobuf::compiler::csharp::GetUmbrellaClassName;
+using google::protobuf::compiler::csharp::GetReflectionClassName;
using grpc::protobuf::FileDescriptor;
using grpc::protobuf::Descriptor;
using grpc::protobuf::ServiceDescriptor;
## -234,7 +234,7 ## void GenerateServiceDescriptorProperty(Printer* out, const ServiceDescriptor *se
out->Print("public static global::Google.Protobuf.Reflection.ServiceDescriptor Descriptor\n");
out->Print("{\n");
out->Print(" get { return $umbrella$.Descriptor.Services[$index$]; }\n",
- "umbrella", GetUmbrellaClassName(service->file()), "index",
+ "umbrella", GetReflectionClassName(service->file()), "index",
index.str());
out->Print("}\n");
out->Print("\n");
More specifically, please open the file src/compiler/csharp_generator.cc and replace all references of GetUmbrellaClassName by GetReflectionClassName

Working backwards:
for release-0_11: it looks like you're trying to compile against the most recent protobuf. Since we're both in development right now there's occasional breakage - but grpc does track the version of protobuf it's tested against in third_party/protobuf. Try checking out and installing that version. I filed https://github.com/grpc/grpc/issues/4697 to update to the latest protobuf 3.0 version.
for master from github: which compiler and OS are you using? I recently checked in the boringssl integration work, so it's fresh, and not nearly as battle-tested. I'd like to get it battle-tested. That said, if you do a 'make EMBED_OPENSSL=false' then things should work out for you.
for the debian package problem: I'm not sure what's going on. I'm happy to try and spin up a VM with your OS and repro if you can let me know which OS it is.

bjam `Unable to find file or target named 'libboost_python'`

What am I missing in my Boost.Python configuration/installation?
I'm trying to compile tutorial example, and I get error with libboost_python not found
cd /usr/share/doc/libboost1.42-doc/examples/libs/python/example/tutorial
bjam
error: Unable to find file or target named
error: 'libboost_python'
error: referred from project at
error: '.'
But the library is there, ldconfig.real has been run:
/usr/lib/libboost_python.a -> libboost_python-py27.a
/usr/lib/libboost_python-mt-py26.a -> libboost_python-py26.a
/usr/lib/libboost_python-mt-py26.so -> libboost_python-py26.so.1.42.0
/usr/lib/libboost_python-mt-py27.a -> libboost_python-py27.a
/usr/lib/libboost_python-mt-py27.so -> libboost_python-py27.so.1.42.0
/usr/lib/libboost_python-py26.a
/usr/lib/libboost_python-py26.so -> libboost_python-py26.so.1.42.0
/usr/lib/libboost_python-py26.so.1.42.0
/usr/lib/libboost_python-py27.a
/usr/lib/libboost_python-py27.so -> libboost_python-py27.so.1.42.0
/usr/lib/libboost_python-py27.so.1.42.0
/usr/lib/libboost_python.so -> libboost_python-py27.so
I'm using default libboost packages from Ubuntu 11.04.
My user-config.jam is
using python : 2.7 ;

I had a similar problem on ubuntu 12.04 where I installed all the boost libraries as a package. I found the solution here:
http://jayrambhia.wordpress.com/2012/06/25/configuring-boostpython-and-hello-boost/
It turns out that you do not need to use bjam at all. A makefile suffices. I will repeat the the solution from the above link here:
1.) Install the libboost-python package
2.) Create a hello world source file called 'hello_ext.c':
char const* greet()
{
return "hello, world";
}
#include<boost/python.hpp>
BOOST_PYTHON_MODULE(hello_ext)
{
using namespace boost::python;
def("greet",greet);
}
3.) Create a makefile:
PYTHON_VERSION = 2.7
PYTHON_INCLUDE = /usr/include/python$(PYTHON_VERSION)
# location of the Boost Python include files and library
BOOST_INC = /usr/include
BOOST_LIB = /usr/lib
# compile mesh classes
TARGET = hello_ext
$(TARGET).so: $(TARGET).o
g++ -shared -Wl,--export-dynamic $(TARGET).o -L$(BOOST_LIB) -lboost_python -L/usr /lib/python$(PYTHON_VERSION)/config -lpython$(PYTHON_VERSION) -o $(TARGET).so
$(TARGET).o: $(TARGET).c
g++ -I$(PYTHON_INCLUDE) -I$(BOOST_INC) -fPIC -c $(TARGET).c
4.) make
make
5.) Ready to use. In python:
import hello_ext
print hello_ext.greet()

Still not sure it that's the proper way, seems little hackish, but following helped:
In Jamroot file replaced
project
: requirements <library>libboost_python ;
with
project
: requirements <library>/usr/lib/libboost_python.so ;

You could have a site-config file with something like the following ;
using boost : 1.48 : <include>/usr/include/boost-1_48 <library>/usr/lib ;
(you need the < library > bit, not sure why)
then you can do stuff like.
project foo
: <library>/boost//python
Makes things easier in the long run, as you inevitably will have to change boost version at some point.