It seems that there're some conflicts on CUDA 9.0 and GCC 6.x, (discussed here). So I decide to use gcc 5.5 to setup python package.
According to the answer https://stackoverflow.com/a/25595274/5634636, and https://stackoverflow.com/a/16737696/5634636, I tried to run setup.py as follow:
CC=gcc-5 CXX=g++-5 python setup.py install --user
which raise the error (I only paste part of it because it's too long):
/usr/include/c++/6/tuple: In instantiation of ‘static constexpr bool
std::_TC<, _Elements>::_MoveConstructibleTuple() [with
_UElements = {std::tuple};
It seems that python is still using g++ 6 (/usr/include/c++/6/tuple) library on compiling. How to avoid using g++ 6?
It seems that there are two places where gcc is used. One is python setup itself, the other is nvcc. The environment variable CC and CXX only specific the gcc version for python, but it didn't change the gcc version for nvcc.
To change the gcc version cuda used by default, do as follows:
sudo unlink /usr/local/cuda/bin/gcc
sudo ln -s /usr/bin/gcc-5 /usr/local/cuda/bin/gcc
There /usr/bin/gcc-5 can be any path to the gcc you want to use.
Related
So I'm about to throw my laptop through the window, out the window, and go and burn Apple HQ.
See Updates Below:
I can't get python3, boost-python and clang to work with each other. The error I'm stuck at is running:
clang++ <FLAGS/INCLUDES> -o hello.so hello.cpp
Invokes the response:
Undefined symbols for architecture x86_64:
"__Py_NoneStruct", referenced from:
boost::python::api::object::object() in hello-0c512e.o
"_main", referenced from:
implicit entry/start for main executable
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [hello] Error 1
Any help would be greatly, greatly appreciated. I think I have included everything necessary. Let me know if you require extra information.
The setup:
OSX 10.11.6 (El Capi-s##%)
Must use Xcode 7.3 (and appropriate CLT): Requirement of NVIDIA for CUDA programming (installed).
Must use Python3 (Homebrew installed)
brew install python3
which python -> /usr/bin/python
/usr/local/Cellar/python3/3.5.2_3/Frameworks/Python.framework/Versions/3.5/include/python3.5m
I set up an alias for python3.5 (see below).
Using Boost-Python (Homebrew installed)
brew install boost
brew install boost-python --with-python3 --without-python
/usr/local/Cellar/boost-python/1.62.0/
Using LLVM 3.9.0 (Homebrew installed)
brew install llvm --universal
Now a few helpful things that you may ask for:
Clang++:
Apple LLVM version 7.3.0 (clang-703.0.29)
Target: x86_64-apple-darwin15.6.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
FLAGS and INCLUDES in makefile:
CPPFLAGS = -g -Wall -std=c++11 -stdlib=libc++
LDHEADERS = -I/usr/local/opt/llvm/include
LDLIBS = -L/usr/local/opt/llvm/lib
BOOSTHEADERS = -I/usr/local/Cellar/boost/1.62.0/include/boost
BOOSTLIBS = -L/usr/local/Cellar/boost-python/1.62.0/lib
PYTHONHEADERS = -I/usr/local/Cellar/python3/3.5.2_3/Frameworks/Python.framework/Versions/3.5/include/python3.5m
PYTHONLIBS = -L/usr/local/Cellar/python3/3.5.2_3/Frameworks/Python.framework/Versions/3.5/lib
And finally, the code I am trying to compile:
hello.cpp
#include <boost/python.hpp>
struct World
{
void set(std::string msg) { this->msg = msg; }
std::string greet() { return msg; }
std::string msg;
};
using namespace boost::python;
BOOST_PYTHON_MODULE(hello)
{
class_<World>("World")
.def("greet", &World::greet)
.def("set", &World::set)
;
};
After much heartache and pain, I HAVE THE ANSWER!
To all those using OSX and homebrew, here's how you do it.
brew install python3 Python3 has UCS4 native (Unicode) which is an essential part of this process. If you need Python2, then make sure it is configured for UCS4 as it is natively UCS2.
brew install boost Install general boost first.
brew install boost-python --with-python3 --without-python This installs boost-python for Python3 WITHOUT Python2. You can change these options if you need Python2.
brew install llvm --universal Make sure you have llvm installed, this should have clang++ included in it which is the compiler we will use (not the Xcode one).
Create a makefile (see below) that includes the directories for all your python and boost headers/libraries, AND includes the libraries you want to use. (This is what tripped me up, I had the directories but did not specify which library in that directory the compiler should use).
My makefile:
# compiler flags:
# -g adds debugging information to the executable file
# -Wall turns on most, but not all, compiler warnings
COMPILER = /usr/local/Cellar/llvm/3.9.0/bin/clang++
CPPFLAGS = -g -Wall -std=c++11 -stdlib=libc++
# Python and BoostPython links.
BOOSTHEADERS = -I/usr/local/Cellar/boost/1.62.0/include/boost
BOOSTLIBRARIES = -L/usr/local/Cellar/boost-python/1.62.0/lib/
# This is the boost library we want to use, there are also libraries for multithreading etc.
# All we do is find the file libboost_python3.a and link it by taking away the 'lib' and '.a'.
BOOSTLIB = -lboost_python3
PYTHONHEADERS = -I/usr/local/Cellar/python3/3.5.2_3/Frameworks/Python.framework/Versions/3.5/include/python3.5m
PYTHONLIBRARIES = -L/usr/local/Cellar/python3/3.5.2_3/Frameworks/Python.framework/Versions/3.5/lib
# Link to python3.5 library, the same as we did for boost.
PYTHONLIB = -lpython3.5
# Collect links.
LIBRARIES = $(BOOSTLIBRARIES) $(PYTHONLIBRARIES) $(PYTHONLIB) $(BOOSTLIB)
HEADERS = $(BOOSTHEADERS) $(PYTHONHEADERS)
# Build target.
TARGET = hello
# BEGIN MAKE
all: $(TARGET)
$(TARGET): $(TARGET).cpp
# Note that '-shared' creates a library that is accessible.
$(COMPILER) -shared $(LIBRARIES) $(HEADERS) $(TARGET).cpp -o $(TARGET).so
clean:
$(RM) $(TARGET)
Then all you need to do is run your makefile with all the inclusions and everything should be sweet :) I hope this helps someone and removes the pain I had of trying to get insertProfanity boost working.
Not enough points to comment so unfortunately I'll have to post as an answer since not too long ago I was going through this same linker error stuff with Boost.
My guess is that this appears to be a Python linker problem, as opposed to a Boost linker problem. I see that you've added the Python includes to your CXX_INCLUDE_PATH, but what about your Python library?
If the path you've mentioned above (that long path in your CXX_INCLUDE_PATH variable) is where your includes are then [that_long_path]/Versions/3.5/lib should be where your Python libraries are. Include this library when you run your build command by using
clang++ -g -v -std=c++11 -stdlib=libc++ -L/[that_long_path]/Versions/3.5/lib -lpython3.5m hello.cpp -o hello.so
The -L flag tells the compiler to include that directory, while the -l flag tells the compiler to include the following library. Alternatively you can just append this lib path to your current CXX_INCLUDE PATH, which would then look like this:
export CXX_INCLUDE_PATH="/usr/local/Cellar/python3/3.5.2_3/Frameworks/Python.framework/Versions/3.5/include/python3.5m:/usr/local/Cellar/python3/3.5.2_3/Frameworks/Python.framework/Versions/3.5/lib"
Also make sure you are including any relevant boost include paths and library paths when you run the build command to avoid any more linker errors (if boost is not installed in a default location like usr/local/[some_place].
Then run this new build command (may be able to do without the -std and -stdlib flags:
clang++ -g -v -std=c++11 -stdlib=lib++ -lpython3.5m -o hello.so hello.cpp
In summary:
1) Include your python header files (which you seem to have done)
2) Include your python library file(s) (which you seem to be missing)
3) Include any relevant boost libraries and the boost include directory (which is a bit out of the scope of this question but still worth noting)
Hope this helps.
I tried to install graph-tool on Mac OSX 10.10 using homebrew. The brew build process works fine, but when I try to import graph-tool I get the error described in this question.
Another problem with homebrew is that I always builds graph-tool for python2.7 and it installs the packages in the Python 2.7 sit-packages folder. But I want to use it with Python 3.4. These are the reasons why I tried to build graph-tool from source.
The ./configure command automatically uses Python 2.7, too. So I passed it the desired Python version with ./configure PYTHON=python3.4
It then detects the correct version as well as the related paths but crash with the following error:
configure: error:
Could not link test program to Python. Maybe the
main Python library has been installed in some non-standard library
path. If so, pass it to configure, via the LDFLAGS environment
variable.
Example: ./configure LDFLAGS="-L/usr/non-standard-path/python/lib"
======================================================================
ERROR!
You probably have to install the development version of the
Python package for your distribution. The exact name of this package varies
among them.
======================================================================
The error occurs with and without PYTHON variable set.
From the output of ./configure I can see that everything works fine except for the last line, which says:
checking consistency of all components of python development
environment... no
Whats does the above line mean and how do I properly install graph-tool on my maschine?
The error message is explaining exactly what needs to be done. Since python was installed in a non-standard path, you need to pass the flag LDFLAGS="-L/usr/non-standard-path/python/lib" pointing to the directory where the python libraries are located. This is most likely "/usr/local/lib", if you are using homebrew.
I was getting this error when I was trying to install graph-tool using outdated an autoconf / automake / pkg-config combination (installed using yum in CentOS 5.10). Installing those packages from source fixed the problem... although I'm not sure how this related to my python installation....
It worked for me by passing the variable PYTHON_EXTRA_LDFLAGS="-Wl,-stack_size,1000000 -F/usr/local/Cellar/python3/3.6.3/Frameworks -framework CoreFoundation".
In your case, it would be the path to the homebrew installation of python3.4.
The way I found out is that in the config.log, the error message shows the following:
configure:19023: checking python extra libraries
configure:19030: result: -ldl -framework CoreFoundation
configure:19037: checking python extra linking flags
configure:19044: result: -Wl,-stack_size,1000000 -framework CoreFoundation Python.framework/Versions/3.6/Python
configure:19051: checking consistency of all components of python development environment
configure:19079: gcc -o conftest -g -O2 -DNDEBUG -I/usr/local/Cellar/python3/3.6.3/Frameworks/Python.framework/Versions/3.6/include/python3.6m -F/usr/local/Cellar/python3/3.6.3/Frameworks/ -Wl,-stack_size,1000000 -framework CoreFoundation Python.framework/Versions/3.6/Python conftest.c -L/usr/local/opt/python3/Frameworks/Python.framework/Versions/3.6/lib -lpython3.6m -ldl -framework CoreFoundation -ldl -framework CoreFoundation >&5
clang: error: no such file or directory: 'Python.framework/Versions/3.6/Python'
The error seems to be path 'Python.framework/Versions/3.6/Python', that in a homebrew installation does not exist. I search for the same path in the config.log and I found this line:
PYTHON_EXTRA_LDFLAGS="-Wl,-stack_size,1000000 -framework CoreFoundation Python.framework/Versions/3.6/Python"
So, the solution for me was to pass this variable with the right path.
I want to install the pyvlfeat package. It requires Boost.Python.
When I run the command
python.exe setup.py build
I receive the following message:
C:\Users\alex\Anaconda\Scripts\gcc.bat -DMS_WIN64 -mdll -O -Wall -IC:\Users\A
lexkow\AppData\Roaming\Python\Python27\site-packages\numpy\core\include -Ivlfeat
/ -IC:\Users\alex\Anaconda\include -IC:\Users\alex\Anaconda\PC -c vlfeat/m
ser/vl_erfill.cpp -o build\temp.win-amd64-2.7\Release\vlfeat\mser\vl_erfill.o -m
sse2 -O2 -fPIC -w
In file included from vlfeat/mser/vl_erfill.cpp:7:0:
vlfeat/mser/../py_vlfeat.h:18:28: fatal error: boost/python.hpp: No such file or
directory
Which tells me Boost.Python is not installed correctly on my computer, or that I don't launch the python install command correctly.
The package INSTALL instructions are :
Building the Module on a Unix System --
The C++ wrappers require Boost.Python to be installed:
$ sudo apt-get install boost-python1.35-dev
pyvlfeat uses distutils, so to build the library:
$ python setup.py build
As I am on Windows I can't sudo apt-get, so I downloaded boost 1.57.0 and extracted it into
C:\Program Files\boost\boost_1_57_0
It did not change the result. And now I don't know what I should do:
When I read the documentation
The section 3: "No-Install Quick Start" explains how to build an extension module called extending and test it by running a Python script called test_extending.py. I don't think that is what I want to achieve and it seems outdated because it talks about the bjam build driver.
The section 4: "Installing Boost.Python on your system" looks more interresting, but it says the information is in the Getting Started Guide, and it is not.
How to install Boost.Python on Windows 7 in order to install a python package ? ?
I am looking at the setup.py file. It looks like you can set BOOST_PATH at the top. You should set that to the correct path to the Boost you downloaded, I think.
I want to use python consistently in a variety of environments. One of those environments is cygwin. One of the components I want to use is gevent (http://www.gevent.org/intro.html). Under cygwin, I have python 2.7 running (built locally, with the one line change described here, which is required for it to build: http://www.gossamer-threads.com/lists/python/python/976956).
gevent requires libevent (http://libevent.org/).
libevent seems to build just fine under cygwin (./configure && make && make install).
However, when building gevent (pip install gevent), it fails because libevent built static libraries (such as /usr/local/lib/libevent.a) and the gevent build wants shared libraries. Thus:
gcc -shared -Wl,--enable-auto-image-base build/temp.cygwin-1.7.13-i686-2.7/gevent/core.o -L/usr/local/lib/python2.7/config -levent -lpython2.7 -o build/lib.cygwin-1.7.13-i686-2.7/gevent/core.dll
/usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld: cannot find -levent
Meanwhile, if I try to get gevent to link statically (CFLAGS='-static' pip install gevent), -levent still fails, along with numerous warnings about how dereferencing type-punned pointer will break strict-aliasing rules and some additional ld failures:
gevent/core.c:21835: warning: dereferencing type-punned pointer will break strict-aliasing rules
....
gevent/core.c:21836: warning: dereferencing type-punned pointer will break strict-aliasing rules
gcc -shared -Wl,--enable-auto-image-base -static build/temp.cygwin-1.7.13-i686-2.7/gevent/core.o -L/usr/local/lib/python2.7/config -levent -lpython2.7 -o build/lib.cygwin-1.7.13-i686-2.7/gevent/core.dll
/usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld: cannot find -levent
/usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld: cannot find -lpython2.7
... so...
I think I need to tell libevent to build .dll instead of .a, but libevent's Makefile does not actually have a .a target, and it's not clear to me how the abstractions being used would have to change to accomplish this.
So, taking a step back: how do I install gevent under python 2.7 under cygwin?
Can you try a beta release from http://code.google.com/p/gevent/downloads/list ?
It does not require any external dependencies.
I have the newest XCode (4D199) installed and in terminal when I type
new-host-2: me$ gcc -version
i686-apple-darwin11-llvm-gcc-4.2: no input files
Is that the default xcode/mac gcc compiler version? Because when I try to do a
sudo easy_install cython
I get:
Running Cython-0.15.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-qS3Kqb/Cython-0.15.1/egg-dist-tmp-Zh0Vnv
cc1: error: unrecognized command line option "-arch"
cc1: error: unrecognized command line option "-arch"
I've read that -arch is a Apple GCC compiler only function. I think when I installed a port from macports I remember it installing something called "llvm" and now I suspect that that is being used instead of the one that comes with XCODE.
Any way to switch it back?
Oh, and when I type "sudo port select gcc" I get (this might be relevent to knowing which gcc version I have):
Available versions for gcc:
apple-gcc42
gcc42
llvm-gcc42
mp-gcc44
mp-llvm-gcc42
none
Does sound like you're getting a non-apple version. If you don't need any non-standard compilers, I'd remove any that macports has installed. The apple infrastructure is different enough that using compilers from macports causes grief fairly easily.
This is not extremely related to your problem but you will find a solution here: Can't install Ruby under Lion with RVM – GCC issues
This answer was edited multiple times and now contains three alternative solutions. Skip to the end and try the simple “edit 3” solution first, it seems to work for most people.
You need a non-LLVM version of GCC, which is no longer included with XCode 4.2. Install it yourself (or downgrade to XCode 4.1 temporarily), then do CC=/usr/local/bin/gcc-4.2 rvm install 1.9.3 (substituting the path to your non-LLVM gcc).
Edit: https://github.com/kennethreitz/osx-gcc-installer/downloads may help for installing GCC.
Edit 2 (apparently the easiest solution): Alternatively you can try to add --with-gcc=clang to the arguments to configure for Ruby to use clang.
Edit 3: rvm install 1.9.3 --with-gcc=clang does that for you.