failing to run NEST + Python 3

[laurentperrinet]

I could compile NEST wrt python3 on macosx (with homebrew) using

git clone https://github.com/nest/nest-simulator.git
cd nest-simulator
cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/bin/nest -DPYTHON_EXECUTABLE=/usr/local/python3 -DPYTHON_INCLUDE_DIR=/usr/local/Cellar/python3/3.5.1/Frameworks/Python.framework/Versions/3.5/include/python3.5m/ -DPYTHON_LIBRARY=/usr/local/Cellar/python3/3.5.1/Frameworks/Python.framework/Versions/3.5/lib/libpython3.5.dylib .
make
make install

(see https://laurentperrinet.github.io/sciblog/posts/2016-06-01-compiling-and-using-pynn-%2B-nest-%2B-python3.html)
but I fail running an example:

 /usr/local/nest/share/doc/nest/examples/pynest on git:master o [0:19:37]
$ ipython balancedneuron.py
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
/usr/local/nest/share/doc/nest/examples/pynest/balancedneuron.py in <module>()
     44 from scipy.optimize import bisect
     45
---> 46 import nest
     47 import nest.voltage_trace
     48

/usr/local/nest/lib/python3.5/site-packages/nest/__init__.py in <module>()
     55     sys.setdlopenflags(ctypes.RTLD_GLOBAL)
     56
---> 57 from . import pynestkernel as _kernel      # noqa
     58 from .lib import hl_api_helper as hl_api   # noqa
     59

ImportError: dlopen(/usr/local/nest/lib/python3.5/site-packages/nest/pynestkernel.so, 8): Symbol not found: __ZNK12lockPTRDatumIN4nest12AbstractMaskEXadL_ZNS0_14TopologyModule8MaskTypeEEEE4infoERNSt3__113basic_ostreamIcNS4_11char_traitsIcEEEE
  Referenced from: /usr/local/nest/lib/python3.5/site-packages/nest/pynestkernel.so
  Expected in: flat namespace
 in /usr/local/nest/lib/python3.5/site-packages/nest/pynestkernel.so

any guidance is welcome!

[heplesser]

@Meduz We just added a formula for nest to Homebrew, so the recommended way to install NEST under OSX is now via Homebrew:

1. Add the homebrew/science tap: execute brew tap homebrew/science
2. For information on what options NEST has and what will be installed, execute brew info nest
3. To install nest with Python, execute brew install nest --with-python. This will install the most recent release.
4. To install the most recent Github version, use brew install nest --with-python --HEAD

If you want to build by hand, you must make sure that NEST does not use the clang compiler by adding -DCMAKE_C_COMPILER=gcc-5 -DCMAKE_CXX_COMPILER=g++-5 to the cmake call.

[laurentperrinet]

This seems perfectly timed!

As I wished to compile for python3, I used your second solution which worked perfectly.
(Sorry I could not test the brew recipe.)

Thanks a lot,
Laurent

PS: updated instructions on https://laurentperrinet.github.io/sciblog/posts/2016-06-01-compiling-and-using-pynn-%2B-nest-%2B-python3.html

[heplesser]

@Meduz Great, and thank you for blogging about NEST! You may want to mention that the compiler switches to cmake are only necessary on OSX; under Linux, things should work without them.

[laurentperrinet]

thanks for the feedback.

Do you plan to allow for users to mention the version of python they use? Like for numpy, the use of the brew install numpy --with-python3 option.

thanls,
Laurent

PS: @heplesser I did add a mention to that point

[heplesser]

@tammoippen What do you think?

[laurentperrinet]

Thanks for implementing the homebrew formula with python 3. However I have some problems installing it. If I run the vanilla version, I get as expected:

$ brew install homebrew/science/nest
==> Reinstalling homebrew/science/nest
==> Downloading https://homebrew.bintray.com/bottles-science/nest-2.12.0_1.sierra.bottle.tar.gz
Already downloaded: /Users/lolo/Library/Caches/Homebrew/nest-2.12.0_1.sierra.bottle.tar.gz
==> Pouring nest-2.12.0_1.sierra.bottle.tar.gz
🍺  /usr/local/Cellar/nest/2.12.0_1: 2,453 files, 19.2MB

but in the case of the py3k option, I get:

$ brew reinstall homebrew/science/nest  --with-python3

==> Reinstalling homebrew/science/nest --with-python3
==> Using Homebrew-provided fortran compiler.
This may be changed by setting the FC environment variable.
==> Downloading https://github.com/nest/nest-simulator/releases/download/v2.12.0/nest-2.12.0.tar.gz
Already downloaded: /Users/lolo/Library/Caches/Homebrew/nest-2.12.0.tar.gz
==> cmake .. -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/Cellar/nest/2.12.0_1 -Dwith-python=3
==> make
Last 15 lines from /Users/lolo/Library/Logs/Homebrew/nest/02.make:
      sli::pool::grow(unsigned long) in allocator.cpp.o
      TokenArray::~TokenArray() in arraydatum.cc.o
      lockPTRDatum<std::vector<long, std::allocator<long> >, &SLIInterpreter::IntVectortype>::clone() const in arraydatum.cc.o
      lockPTRDatum<std::vector<double, std::allocator<double> >, &SLIInterpreter::DoubleVectortype>::clone() const in arraydatum.cc.o
      lockPTR<std::vector<long, std::allocator<long> > >::~lockPTR() in arraydatum.cc.o
      lockPTR<std::vector<long, std::allocator<long> > >::~lockPTR() in arraydatum.cc.o
      ...
  "___cxa_throw_bad_array_new_length", referenced from:
      Processes::Sysexec_aFunction::execute(SLIInterpreter*) const in processes.cc.o
      RegexpModule::RegexecFunction::execute(SLIInterpreter*) const  in sliregexp.cc.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[2]: *** [sli/libsli.dylib] Error 1
make[1]: *** [sli/CMakeFiles/sli_lib.dir/all] Error 2
make: *** [all] Error 2

READ THIS: http://docs.brew.sh/Troubleshooting.html

any idea?

more info 👍

==> Formula
Tap: homebrew/science
Path: /usr/local/Homebrew/Library/Taps/homebrew/homebrew-science/nest.rb
==> Configuration
HOMEBREW_VERSION: 1.1.11
ORIGIN: https://github.com/Homebrew/brew
HEAD: 394f9fa0aaa5854aa52bc589708a079665dcf462
Last commit: 6 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: daade4cc7eb54565ad3510acd8c99b28e1c9e5d7
Core tap last commit: 10 minutes ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_REPOSITORY: /usr/local/Homebrew
HOMEBREW_CELLAR: /usr/local/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com
CPU: octa-core 64-bit ivybridge
Homebrew Ruby: 2.0.0-p648
Clang: 8.0 build 800
Git: 2.12.0 => /usr/local/bin/git
Perl: /usr/bin/perl
Python: /usr/local/bin/python => /usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/bin/python2.7
Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby
Java: 1.8.0_112, 1.8.0_40, 1.8.0_11
macOS: 10.12.3-x86_64
Xcode: 8.2.1
CLT: 8.2.0.0.1.1480973914
X11: 2.7.112 => /opt/X11
==> ENV
HOMEBREW_CC: gcc-6
HOMEBREW_CXX: g++-6
SDKROOT: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk
MAKEFLAGS: -j8
CMAKE_PREFIX_PATH: /usr/local/opt/readline:/usr/local
CMAKE_INCLUDE_PATH: /usr/include/libxml2:/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
CMAKE_FRAMEWORK_PATH: /usr/local/opt/python3/Frameworks
MACOSX_DEPLOYMENT_TARGET: 10.12
PKG_CONFIG_PATH: /usr/local/opt/gsl/lib/pkgconfig:/usr/local/opt/libpng/lib/pkgconfig:/usr/local/opt/freetype/lib/pkgconfig:/usr/local/opt/python3/lib/pkgconfig
PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/usr/local/Homebrew/Library/Homebrew/os/mac/pkgconfig/10.12
ACLOCAL_PATH: /usr/local/share/aclocal
PATH: /usr/local/Homebrew/Library/Homebrew/shims/super:/usr/local/opt/gsl/bin:/usr/local/opt/numpy/bin:/usr/local/opt/libpng/bin:/usr/local/opt/freetype/bin:/usr/local/opt/libtool/bin:/usr/local/opt/cmake/bin:/usr/local/opt/python3/bin:/usr/local/opt/gcc/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/opt/python3/Frameworks/Python.framework/Versions/3.6/bin:/usr/local/Cellar/gcc/6.3.0_1/bin

Error: homebrew/science/nest 2.12.0 did not build

[heplesser]

@tammoippen Could you take a look at this?

[tammoippen]

Hi @laurentperrinet and @heplesser ,

I am looking into it.

[tammoippen]

@laurentperrinet
I cannot reproduce your error. However, I created a PR on homebrew (https://github.com/Homebrew/homebrew-science/pull/5293) to get the right python3 dependancies. Maybe you can locally change these dependancies and try again:

brew edit homebrew/science/nest  # and add the   ' => "with-python3"' to numpy, scipy, matplotlib in python3 sction

If it still fails, please give the relevant output of brew install --verbose homebrew/science/nest --with-python3.

[tammoippen]

Both of the nest related homebrew PR's are merged by now. @laurentperrinet , can you please state, whether there are still issues with installing nest via homebrew?

[heplesser]

@laurentperrinet Do you still have problems with homebrew?� If not, would you close this issue?

[heplesser]

Closing due to inactivity.