I would like to compile and then use the scientific project BASS, which is distributed as c++ source code on github. I've set up a conda environment bass to hold everything related to BASS, and I'd like to compile BASS into this environment (so that if I delete the environment, it's cleanly removed).
I don't know if I should be using conda-build or make to do this. There is a Makefile distributed with the project, but I think it might have an error.
My latest try is the following: (the source files are in code/ and gsl seems to be a dependency):
conda create -n bass
conda activate bass
conda install make
conda install gsl
cd code/
make
I get the following:
gcc -c main.cpp -I../Libs/GSL/include/ -I./
main.cpp:19:10: fatal error: 'gsl/gsl_statistics.h' file not found
#include <gsl/gsl_statistics.h>
^~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [Makefile:11: main.o] Error 1
My questions:
should I be doing this with make?
do I need gcc/g++/cxx-compiler installed in my conda env?
is the Makefile correct where it says "-I../Libs/GSL/include/"
Thank you!
Here's a very basic Conda recipe for the package. Make a folder (say recipe) and put the following two files in it:
meta.yaml
package:
name: bass
version: 0.1 # this is totally arbitrary (there are no versions)
source:
git_url: https://github.com/judyboon/BASS.git
requirements:
build:
- {{ compiler('cxx') }}
host:
- gsl
run:
- gsl
about:
home: https://github.com/judyboon/BASS
license: GPL-3.0-only
license_file: COPYING
license_family: GPL
build.sh
#!/bin/bash
## change to source dir
cd ${SRC_DIR}/code
## compile
${CXX} -c main.cpp *.cpp -I./ ${CXXFLAGS}
## link
${CXX} *.o -o BASS -lgsl -lgslcblas -lm ${LDFLAGS}
## install
mkdir -p $PREFIX/bin
cp BASS ${PREFIX}/bin/BASS
You can then build this with conda build ., run from in that directory.
Installing
After successful build, you can create an environment with this package installed using
conda create -n foo --use-local bass
Since I'm on an Intel architecture, and this tool uses CBLAS, I would further specify to use MKL:
conda create -n foo --use-local bass blas=*=*mkl
Now if you activate the environment foo (that's an arbitrary name), the software will be on PATH, under the binary BASS.
Additional Notes
I verified this works on osx-64 platform with the conda-forge channel prioritized.
The Makefile accompanying the code isn't very generic. Here we just have it compile all .cpp files and subsequently link all .o files.
There aren't any releases on the repository, so the versioning in the meta.yaml is arbitrary.
The build.sh defines the final output binary as BASS - that could be changed, and differs from the original Makefile which outputs the binary as main.
Based on what you write, the correct way is to build a conda recipe. By writing a recipe the conda knows what to delete, when you delete the environment.
The recipe is a text file (the meta.yaml file), where you write some metadata describing the package, define dependencies and write a short build script that executes the make file and installs the binaries to correct location. Defining the compilation environment may not be trivial and you should follow the documentation for the package you are trying to install. If there are problems with the package code (that includes the makefile) that's something conda can't help you with.
See the documentation on how to write the recipe:
https://docs.conda.io/projects/conda-build/en/latest/concepts/recipe.html
When you've got the recipe complete, then you would run the conda build and conda install -c [path to the build] [the package name] (I'm writing this because it took me ages to realize how to correctly install a local package.)
Is there any solution to make compilation with g++-8.2 for the project using Hazelcast C++ client library ?
If I compile it with g++-8.2, it shows a lot of errors "undefined reference ...".
While using g++-4.9, it works well.
The issue is a bit like the discussion in this google group forum, which indicated the compilation errors are because of the wrong version of a compiler.
However, the compiler g++-4.9 is too old for me to build my big project.
The sample code can be found in the official org website, if someone needs to give it a try.
I finally solved it by upgrading the library from 3.10 to 3.11.
The 3.11 library is built manually using g++-8.2 from Hazelcast source code in Github.
Because there is no make install after building hazelcast-cpp-clienet package, so I use some scripts to arrange header files together in one directory (hazelcast-cpp-client/include) so that a program can easily link the library and headers.
Build script:
#!/bin/bash
# Package Requirements:
# - asio
mkdir hazelcast-cpp-client ; cd hazelcast-cpp-client
# Build
git clone https://github.com/hazelcast/hazelcast-cpp-client.git
mv hazelcast-cpp-client tmp
cd tmp
git checkout v3.11
mkdir release ; cd release
cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_BUILD_TYPE=Release ..
make
# Back to 'hazelcast-cpp-client' directory
cd ../..
# Copy .a library out from tmp/
cp tmp/release/*.a .
# Arrange all header files in an one directory
cp -r tmp/hazelcast/include .
cp -r tmp/hazelcast/generated-sources/include/hazelcast/client/protocol ./include/hazelcast/client
rm tmp/external/include/*.md # We don't need readme file
cp -r tmp/external/include/* ./include
# Delete tmp directory
rm -rf tmp
Compilation command is like:
g++ -std=c++11 \
-I/path/to/hazelcast-cpp-client/include \
hz_test.cpp \
/path/to/hazelcast-cpp-client/libHazelcastClient3.11_64.a \
-lpthread
Thanks for reporting this problem. We did not test with the g++-8.2 compiler. I opened an issue to solve the problems: https://github.com/hazelcast/hazelcast-cpp-client/issues/494
Can you tell me also your OS environment? What distribution and version is it?
I'm trying to compile alpha_encoder) (little utility of The WebM Project, under webm-tools).
I have a previous installation of msys2 (downloaded and configured by build_locally_with_various_option_prompts.bat) under c:\FFcompiler. It took its time, but I managed to compile ffmpeg, so I decided to use it (I think it will do). That's what I've done till now.
First, I cloned webm-tools under /cygdrive/c/FFcompiler/ffmpeg_local_builds/sandbox/win32/libvpx-1.4.0/third_party/. There's a Makefile so I tried to run make:
$ cd /cygdrive/c/FFcompiler/ffmpeg_local_builds/sandbox/win32/libvpx-1.4.0/third_party/
$ git clone https://chromium.googlesource.com/webm/webm-tools.git
$ cd webm-tools/alpha_encoder/
$ make
But g++ complains mkvparser.hpp doesn't exist. The command is
g++ -c -W -Wall -O3 -g -I../../libwebm alpha_encoder.cc -o alpha_encoder.o
After searching the web, it seems that webm-tools depends on libwebm, and expect finding it as a sibling folder of webm-tools. So...
$ cd ../..
$ git clone https://chromium.googlesource.com/webm/libwebm.git
$ cd libwebm
Now, what? README.libwebm tells that 'to cross compile libwebm for Windows using mingw-w64' first I must run cmake like this cmake -DCMAKE_TOOLCHAIN_FILE=path/to/libwebm/build/mingw-w64_toolchain.cmake path/to/libwebm. In my case:
cmake -DCMAKE_TOOLCHAIN_FILE=build/mingw-w64_toolchain.cmake .
And cmake cannot find i686-w64-mingw32-g++. After googling more, it seems the easiest way to fix this is to add bin of mingw-w64-i686 to PATH.
$ export PATH=/cygdrive/c/FFcompiler/ffmpeg_local_builds/sandbox/cross_compilers/mingw-w64-i686/bin:$PATH
After this, now cmake finishes successfully and creates a Makefile, but make stops with an error:
/cygdrive/c/FFcompiler/ffmpeg_local_builds/sandbox/win32/libvpx-1.4.0/third_part
y/libwebm/common/file_util.cc:44:39: error: 'tmpnam_s' was not declared in this
scope
errno_t err = tmpnam_s(tmp_file_name);
^
I've searched about the error but I'm stuck. What am I missing?
I get the error message:
make[2]: g++: Command not found
which I know means it cannot find the C++ compiler. However, in Netbeans if I go to the configuration to choose my C++ compiler it shows the following being in /usr/bin:
g++4.6
g++4.7
g++4.8
but it doesn't have just g++.
Tried sudo aptitude install g++ but it didnt work.
If I do g++ --version I get:
The program 'g++' can be found in the following packages:
* g++
* pentium-builder
1) Verify you can run "g++" from the command line,
2) type whereis g++ to get the path,
3) Make sure you have the NetBeans C++ plugin installed
Go to Tools->Options->C++->Build Tools
4) Configure the path in NetBeans
Usually, /usr/bin/g++ is a symlink to some /usr/bin/g++-4.7 (or g++-4.8 etc...); just make it again (which is usually provided by the g++ virtual package on Debian or Ubuntu), e.g.
% sudo -s
# cd /usr/bin
# ln -sv g++-4.8 g++
Above % and # are shell prompts that you should not type.
Of course, don't forget the sudo apt-get install g++ etc...
BTW, you might put that link from $HOME/bin/g++ to /usr/bin/g++-4.8 and you don't need root permission for that.
(sometimes, these symlinks go indirectly thru /etc/alternatives etc...)
Your issue is a sysadmin issue; you should rather ask it (with a big lot more details) on askubuntu or superuser; it is off-topic on Stack Overflow.
BTW, NetBeans is not a compiler, but an editor (sometimes called IDE). You could use something better/simpler (e.g. emacs or vim) with e.g. make as a builder (to be run inside a terminal). Before using NetBeans ensure that g++ -v is working alone in some terminal
How does boost.python deal with Python 3? Is it Python 2 only?
Newer versions of Boost should work fine with Python V3.x. This support has been added quite some time ago, I believe after a successful Google Summer of Code project back in 2009.
The way to use Python V3 with Boost is to properly configure the build system by adding for instance:
using python : 3.1 : /your_python31_root ;
to your user-config.jam file.
libboostpython needs to be built with python3 in order to do this. This doesn't work with boost 1.58 (which comes with Ubuntu 16.04), so make sure you download the latest boost distribution. I just did this with boost_1_64_0.
As mentioned above, find the file "user-config.jam" in you boost code distribution, and copy it to $HOME.
cp /path/to/boost_1_64_0/tools/build/example/user-config.jam $HOME
Then edit the python line (the last line) so that is says:
using python : 3.5 : /usr/bin/python3 : /usr/include/python3.5m : /usr/lib ;
This is correct for Ubuntu 16.04. You can use pkg-config to find the correct include directory.
user#computer > pkg-config --cflags python3
-I/usr/include/python3.5m -I/usr/include/x86_64-linux-gnu/python3.5m
And you only need the first include directory.
Then build boost from scratch. (Sorry.) I install it to /usr/local
cd /path/to/boost_1_64_0
./bootstrap.sh --prefix=/usr/local
./b2
sudo ./b2 install
Now jump into the python example directory, and build the tutorial
cd /path/to/boost_1_64_0/libs/python/example/tutorial
bjam
This will not build correctly if you have a system install of boost, because, under the hood, bjam is linking to libboostpython using the g++ parameter "-lboost". But, on Ubuntu 16.04, this will just go and find "/usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0", and then the python bindings will fail to load. In fact, you'll get his error:
ImportError: /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0: undefined symbol: PyClass_Type
If you want to see the g++ commands that bjam is using, do this:
user#computer > bjam -d2 -a | grep g++
g++ -ftemplate-depth-128 -O0 -fno-inline -Wall -g -fPIC -I/usr/include/python3.5m -c -o "hello.o" "hello.cpp"
g++ -o hello_ext.so -Wl,-h -Wl,hello_ext.so -shared -Wl,--start-group hello.o -Wl,-Bstatic -Wl,-Bdynamic -lboost_python -ldl -lpthread -lutil -Wl,--end-group
Here we see the problem, you need "-L/usr/includ/lib" just before "-lboost_python". So execute this to link the shared library correctly:
g++ -o hello_ext.so -Wl,-h -Wl,hello_ext.so -shared -Wl,--start-group hello.o -Wl,-Bstatic -Wl,-Bdynamic -L/usr/local/lib -lboost_python -ldl -lpthread -lutil -Wl,--end-group
You may need to rerun ldconfig (or reboot)
sudo ldconfig
And you are finally ready to go:
user#computer > python3
Python 3.5.2 (default, Nov 17 2016, 17:05:23)
[GCC 5.4.0 20160609] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import hello_ext
>>> hello_ext.greet()
'hello, world'
>>> exit()
Yes this question is super old, but I had to do something that wasn't specified in any of the answers here (though it was built off some of the suggestions), so I'll quickly jot down my entire process:
Download boost_X_Y_Z.tar.bz2 (I used boost 1.68.0)
tar --bzip2 -xf boost_1_68_0.tar.bz2 (where you want folder to be temporarily)
cd boost_1_68_0
./bootstrap.sh --with-python-version=3.6 --prefix=/usr/local
./b2
sudo ./bjam install
cp tools/build/example/user-config.jam $HOME, then modify the contents of this file to say using python : 3.6 : /usr/bin/python3 : /usr/include/python3.6m : /usr/lib ; (or whatever folders are appropriate for your environment)
Given this C++ source file BoostPythonHelloWorld.cpp:
#include <boost/python.hpp>
char const* say_hi()
{
return "Hi!";
}
BOOST_PYTHON_MODULE(BoostPythonHelloWorld)
{
boost::python::def("say_hi", say_hi);
}
And this Python script BoostPythonHelloWorld.py:
import BoostPythonHelloWorld
print(BoostPythonHelloWorld.say_hi())
It can be compiled and ran as such:
gcc -c -fPIC -I/path/to/boost_1_68_0 -I/usr/include/python3.6 /other_path/to/BoostPythonHelloWorld.cpp
gcc -shared -Wall -Werror -Wl,--export-dynamic BoostPythonHelloWorld.o -L/path/to/boost_1_68_0/stage/lib -lboost_python36 -o BoostPythonHelloWorld.so
python3 BoostPythonHelloWorld.py
The part that was different for me was -Wl,--export-dynamic BoostPythonHelloWorld.o, I had not seen that anywhere else, and I was getting a Python error concerning an undefined symbol until I added that.
Hope this helps someone down the line!
If you get "error: No best alternative for /python_for_extension" be sure to have
using python : 3.4 : C:\\Python34 : C:\\Python34\\include : C:\\Python34\\libs ;
only in user-config.jam in your home path and nowhere else.
Use double backslashes when compiling under windows with mingw (toolset=gcc) or MSVC (toolset=msvc).
Compile with cmd, not msys, and if you also have python 2.7 installed remove that from PATH in that shell.
First do
bootstrap.bat gcc/msvc
assuming you have the gcc/msvc tools available via PATH (/ for the alternatives, but use only one, or leave away)
Afterward you can also do
booststrap.sh --with-bjam=b2
in msys to generate a project-config.jam, but need to edit it to remove the "using python" and "/usr",..
Then the following
b2 variant=debug/shared link=static/shared toolset=gcc/msvc > b2.log
With static the python quickstart examples did not work for me, although I would prefer to do without the boost_python dll.
I did not try on linux, but it should be more straightforward there.
You can even specify the python distribution via
./bootstrap.sh --with-python=<path to your python binary>
e.g.
./bootstrap.sh --with-python=python3
for your system's python3 or
./bootstrap.sh --with-python=$VIRTUAL_ENV/bin/python
for the python version of your currently active virtual env python.
Refer this to know how to build boost with python. It shows the way to build with python2 with Visual Studio 10.0 (2010). But I go through the same procedure for a project that I am currently working on and it works fine with python 3.5 and Visual Studio 14.1 (2017).
If you get this error when building your python boost project, just add BOOST_ALL_NO_LIB value to Preprocessor Definitions (inside C\C++ > preprocessor tab) in your project properties.
And also, do not forget to add boost .dll files location to your system path.
When the path to Python contains spaces, you will be in for quite a ride. After a whole lot of trial and error, I finally managed to get something that works. Behold my user-config.jam (which has to be in my home directory for bjam to find it):
import toolset : using ;
using python : 3.6
: \"C:\\Program\ Files\ (x86)\\Microsoft\ Visual\ Studio\\Shared\\Python36_64\\python.exe\"
: C:\\Program\ Files\ (x86)\\Microsoft\ Visual\ Studio\\Shared\\Python36_64\\include
: C:\\Program\ Files\ (x86)\\Microsoft\ Visual\ Studio\\Shared\\Python36_64\\libs
;
The inconsistent quoting is intended and seems to be required. With this I can build boost-python and use it as Boost::python36 in my CMakeLists.txt. Still, one issue remains: I have to link to python manually viz
target_link_libraries(MyTarget
Boost::boost Boost::python36
"C:/Program Files (x86)/Microsoft Visual Studio/Shared/Python36_64/libs/python36.lib")
target_include_directories(MyTarget PRIVATE
"C:/Program Files (x86)/Microsoft Visual Studio/Shared/Python36_64/include")
In my case adding "Using Python : 3 etc." into user-config.jam in my home directory didn't work. I had to add the line into project-config.jam instead, which resides in the root directory of unpacked boost.
Specifically the line was:
using python : 3.9 : /usr/bin/python3 : /usr/include/python3.9 : /usr/lib ;
and the version of boost was 1_78_0