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fatal error: 'Eigen/Dense' file not found

I am an Ultra Linux newbie, and I am trying to install this program and when I try to build the python wrapper I'd get this
~/Downloads/DeepMimic-master/DeepMimicCore$ make python
clang++ -c -g -std=c++11 -O3 -Wall -fPIC -I./ -I../../libraries/eigen -I../../libraries/bullet3/src -I/usr/include/python3.6m -I/usr/lib/ -lpython3.6m -o objs/Main.o Main.cpp
clang: warning: -lpython3.6m: 'linker' input unused [-Wunused-command-line-argument]
In file included from Main.cpp:3:
In file included from ./DeepMimicCore.h:3:
In file included from ./util/ArgParser.h:6:
./util/MathUtil.h:5:10: fatal error: 'Eigen/Dense' file not found
#include "Eigen/Dense"

You're missing a dependency, Eigen, which is listed under 'Dependencies' in the DeepMimic readme.
I see this problem has been encountered before:
fatal error: Eigen/Dense: No such file or directory

Looks like that program depends on Eigen. Try download Eigen and putting it in the appropriate directory.
Eigen is a template library, so you just have to download it, unzip it, and copy the folder called Eigen inside of the directory of the program.
Eigen website

How to use Boost.Python

I just recently discovered Boost.Python and I am trying to figure out how it works. I tried to go through the tutorial on the official website. However, I got
link.jam: No such file or directory
when running bjam as in the example (which appears to be just a warning),
and
Traceback (most recent call last):
File "hello.py", line 7, in <module>
import hello_ext
ImportError: libboost_python.so.1.55.0: cannot open shared object file: No such file or directory
when running python hello.py.
I also tried to compile a module as described in another tutorial with similar results. I am running Ubuntu14.04 with boost1.55 compiled myself.
I tried to compile the following:
#include <boost/python.hpp>
char const* greet()
{
return "hello, world";
}
BOOST_PYTHON_MODULE(hello_ext)
{
using namespace boost::python;
def("greet", greet);
}
with the following command from command line:
g++ -o hello_ext.so hello.cpp -I /usr/include/python2.7/ -I /home/berardo/boost_1_55_0/ -L /usr/lib/python2.7/ -L /home/berardo/boost/lib/ -lboost_python -lpython2.7 -Wl, -fPIC -expose-dynamic
which still gives me a:
/usr/bin/ld: impossibile trovare : File o directory non esistente
collect2: error: ld returned 1 exit status.

Finally, I was able to make it work. First, I fixed the linker issues, as suggested by Dan. It finally compiled but I still got:
ImportError: libboost_python.so.1.55.0: cannot open shared object file: No such file or directory
The problem was that the python module was not able to load correctly so I needed to add another linker option. Here, I report the final Makefile:
# location of the Python header file
PYTHON_VERSION = 2.7
PYTHON_INCLUDE = /usr/include/python$(PYTHON_VERSION)
# location of the Boost Python include files and library
BOOST_INC = ${HOME}/boost/include
BOOST_LIB = ${HOME}/boost/lib
# compile mesh classes
TARGET = hello_ext
$(TARGET).so: $(TARGET).o
g++ -shared -Wl,-rpath,$(BOOST_LIB) -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
Notice the -Wl,-rpath, option, which apparently makes the new created shared library available to the python script.
#Dan: Thanks for the valuable hints.

Python setuptools not including C++ standard library headers

I'm trying to compile a Python wrapper to a small C++ library I've written. I've written the following setup.py script to try to use setuptools to compile the wrapper:
from setuptools import setup, Extension
import numpy as np
import os
atmcmodule = Extension(
'atmc',
include_dirs=[np.get_include(), '/usr/local/include'],
libraries=['mcopt', 'c++'], # my C++ library is at ./build/libmcopt.a
library_dirs=[os.path.abspath('./build')],
sources=['atmcmodule.cpp'],
language='c++',
extra_compile_args=['-std=c++11', '-v'],
)
setup(name='tracking',
version='0.1',
description='Particle tracking and MC optimizer module',
ext_modules=[atmcmodule],
)
However, when I run python setup.py build on OS X El Capitan, clang complains about not finding some C++ standard library headers:
In file included from atmcmodule.cpp:7:
In file included from ./mcopt.h:11:
In file included from ./arma_include.h:4:
/usr/local/include/armadillo:54:12: fatal error: 'initializer_list' file not found
#include <initializer_list>
^
1 error generated.
error: command 'gcc' failed with exit status 1
Passing the -v flag to the compiler shows that it is searching the following include paths:
#include <...> search starts here:
/Users/[username]/miniconda3/include
/Users/[username]/miniconda3/lib/python3.4/site-packages/numpy/core/include
/usr/local/include
/Users/[username]/miniconda3/include/python3.4m
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include/c++/4.2.1
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include/c++/4.2.1/backward
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/7.0.0/include
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/System/Library/Frameworks (framework directory)
End of search list.
This apparently doesn't include the path to the C++ standard library headers. If I compile a small test C++ source with the -v option, I can see that clang++ normally also searches the path /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1, and if I include this path in the include_dirs option for Extension in my setup.py script, then the extension module compiles correctly and works. However, hard-coding this path into the script doesn't seem like a good solution since this module also needs to work on Linux.
So, my question is how do I properly make setuptools include the required headers?
Update (11/22/2015)
As setuptools tries to compile the extension, it prints the first command it's running:
gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/[username]/miniconda3/include -arch x86_64 -I/Users/[username]/miniconda3/lib/python3.4/site-packages/numpy/core/include -I/Users/[username]/Documents/Code/ar40-aug15/monte_carlo/mcopt -I/usr/local/include -I/Users/[username]/miniconda3/include/python3.4m -c /Users/[username]/Documents/Code/ar40-aug15/monte_carlo/atmc/atmcmodule.cpp -o build/temp.macosx-10.5-x86_64-3.4/Users/[username]/Documents/Code/ar40-aug15/monte_carlo/atmc/atmcmodule.o -std=c++11 -fopenmp -v
If I paste this command into a terminal and run it myself, the extension compiles successfully. So I suspect either setuptools is modifying some environment variables I'm not aware of, or it's lying a little about the commands it's actually running.

Setuptools tries to compile C/C++ extension modules with the same flags used to compile the Python interpreter. After checking the flags used to compile my Python install (from Anaconda), I found it was compiling for a minimum Mac OS X version of 10.5. This seems to make it use the GCC libstdc++ instead of clang's libc++ (which supports C++11).
This can be fixed by either setting the environment variable MACOSX_DEPLOYMENT_TARGET to 10.9 (or later), or adding '-mmacosx-version-min=10.9' to extra_compile_args.

Installing Python 3.3 on Cygwin

I'm having trouble installing Python 3.3 on Cygwin. I've tried installing from source, but make returns:
gcc -Wno-unused-result -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -IInclude -I./Include -DPy_BUILD_CORE -c ./Modules/signalmodule.c -o Modules/signalmodule.o
In file included from Include/Python.h:84:0,
from ./Modules/signalmodule.c:6:
./Modules/signalmodule.c: In function `fill_siginfo':
./Modules/signalmodule.c:745:60: error: `siginfo_t' has no member named `si_band'
PyStructSequence_SET_ITEM(result, 6, PyLong_FromLong(si->si_band));
^
Include/tupleobject.h:62:75: note: in definition of macro `PyTuple_SET_ITEM'
#define PyTuple_SET_ITEM(op, i, v) (((PyTupleObject *)(op))->ob_item[i] = v)
^
./Modules/signalmodule.c:745:5: note: in expansion of macro `PyStructSequence_SET_ITEM'
PyStructSequence_SET_ITEM(result, 6, PyLong_FromLong(si->si_band));
^
Makefile:1501: recipe for target `Modules/signalmodule.o' failed
make: *** [Modules/signalmodule.o] Error 1
Makefile:1501: recipe for target 'Modules/signalmodule.o' failed
make: ***[Modules/signalmodule.o] error 1
Any thoughts?

Building Python on Cygwin is not trivial -- I tried. However, the Python community on its bug tracker website is unusually friendly and gentle for a project its size and importance. If you find specific issues, open bugs and follow the discussion. Usually, they will accept tiny patches to fix Cygwin build issues.
This patch will solve your first problem about si->si_band. See related Python issue #21085.
This blog post (in German) is amazing. It will walk you through step-by-step how to build Python3.4 and fix all Cygwin issues.
Good luck. You will need it.

Compile file .c with embedded Python/C functions

I'm starting the study of Python/C API and I make the first code to test some functions, I write this:
file: test.c
#include "Python.h"
int main() {
PyObject* none = Py_BuildValue("");
}
I compile with command:
gcc -I/usr/include/python2.7 test.c
I've the error undefined reference to `Py_BuildValue'
After I run:
gcc -I/usr/include/python2.7 --shared -fPIC hashmem.c
this compile without errors, but when I run the compiled file I've a
Segmentation fault (core dumped)
How do I set the gcc parameters?
I've ubuntu 12.04, python 2.7.3, gcc 4.6.3 and I installed python-dev.
Thanks.

In the comments #Pablo has provided the solution
gcc -I/usr/include/python2.7 test.c -lpython2.7
I forgot to link the python library with the "-l" parameter.
-llibrary
-l library
Search the library named library when linking. (The second alternative with the library as a separate argument is only for POSIX) compliance and is not recommended.)It makes a difference where in the command you write this option; the linker searches and processes libraries and object files in the order they are specified. Thus, foo.o -lz bar.o' searches libraryz' after file foo.o but before bar.o. If bar.o refers to functions in z', those functions may not be loaded.The linker searches a standard list of directories for the library, which is actually a file named liblibrary.a. The linker then uses this file as if it had been specified precisely by name.The directories searched include several standard system directories plus any that you specify with -L.Normally the files found this way are library files—archive files whose members are object files. The linker handles an archive file by scanning through it for members which define symbols that have so far been referenced but not defined. But if the file that is found is an ordinary object file, it is linked in the usual fashion. The only difference between using an -l option and specifying a file name is that - l surrounds library withlib' and `.a' and searches several directories. 
Parameter description source