Bad news I’m afraid. Still got the same problem. I cloned and build nupic.core following your instructions. It all went ok by the looks of it.
I then installed nupic again in a new virtualenv. python setup.py install —nupic-core-dir=$NUPIC_CORE/build/release It said that it was using binaries from $NUPIC_CORE/build/release. Then I ran the tests but still got the same problem. I used otool to check the _math.so file that is imported when you run “import nupic.bindings.math”: > otool -L $NUPIC/nupic/bindings/_math.so > /Users/ruaridh/dev/nupic/nupic/bindings/_math.so: > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current > version 1213.0.0) > /System/Library/Frameworks/Python.framework/Versions/2.7/Python > (compatibility version 2.7.0, current version 2.7.6) > /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version > 120.0.0) It seems to be linked to the System python rather than home-brew’s python. I’m not sure why it’s doing this. Running “python” gives the home-brew version (/usr/local/bin/python). However /usr/bin/python is still the system version. My $PATH starts with “/usr/local/bin”. If this proves complicated to fix I could uninstall Homebrew python and just use the system version. It might be easier. Cheers, Ruaridh > On 28 Jan 2015, at 01:13, Matthew Taylor <[email protected]> wrote: > > Ugh, ok. Well then, the next step is to try to install nupic.core. > > Checkout or download and expand the nupic.core zip from > https://github.com/numenta/nupic.core. You should have clang already > on your Mac if you've installed XCode Developer Tools, but you might > not have cmake (you can brew install it). Then follow the readme > instructions: > >> mkdir -p $NUPIC_CORE/build/scripts >> cd $NUPIC_CORE/build/scripts >> cmake $NUPIC_CORE/src -DCMAKE_INSTALL_PREFIX=../release >> make install > > The -DCMAKE_INSTALL_PREFIX option will build out the binary release > into $NUPIC_CORE/build/release, and you'll use this path now when you > build NuPIC. > > Now you go back to NUPIC and build with the option to specify the > location of nupic.core: > >> cd $NUPIC >> python setup.py install --user --nupic-core-dir=$NUPIC_CORE/build/release > > For extreme detail, see > https://github.com/numenta/nupic/wiki/NuPIC's-Dependency-on-nupic.core > > Fingers crossed! > > --------- > Matt Taylor > OS Community Flag-Bearer > Numenta > > > On Tue, Jan 27, 2015 at 5:05 PM, Ruaridh O'Donnell > <[email protected]> wrote: >> Thanks again for the help, >> >> Still got the same error I’m afraid. >> But I found some more information online. >> >> Here’s what I did: >> I had a virtualenv that I pip installed nupic into before. (which was >> currently activated) >> I ran “pip uninstall nupic” until there was no more nupic. ("pip list" just >> shows the installed dependencies) >> I had deleted the nupic repo before so I cloned it again, and set $NUPIC. >> "cd $NUPIC" >> “python setup.py install” (I checked to make sure this python referred to >> Homebrew’s python) >> It all seemed to build fine. I saw the file being downloaded from AWS S3 >> ending in “-darwin64.tar.gz" >> I ran the tests “./scripts/run_nupic_tests -u” and it crashed almost >> immediately >> Running "python” then “import nupic.bindings.math” gives the same error as >> before: >> >> Fatal Python error: PyThreadState_Get: no current thread >> Abort trap: 6 >> >> >> I found a stack overflow question with the same error: >> >> this error shows up when a module tries to use a python library that is >> different than the one the interpreter uses >> >> http://stackoverflow.com/questions/15678153/homebrew-python-on-mac-os-x-10-8-fatal-python-error-pythreadstate-get-no-cu?lq=1 >> >> I had a look at my console output and there’s line referring to >> “/System/Library/Frameworks/Python.framework/Versions/2.7/Python” and >> another referring to >> “/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/Python”. >> I’m guessing I need to build nupic.core myself to get it to use homebrew’s >> version of python rather than Apple’s. >> >> Cheers, >> Ruaridh >> >> On 27 Jan 2015, at 23:58, Matthew Taylor <[email protected]> wrote: >> >> Well crap. I'd like to step back and try to get you building from the >> source code first. You said you cloned the repo, so be sure to "git >> pull" first, then... >> >> First make sure no old or half-installed versions of nupic are laying >> around: >> >> pip uninstall nupic >> >> >> Run this command several times, until you get an error that "nupic" >> cannot be found. Sometimes you have several versions installed, >> especially if you're been trying to install over time. Then... >> >> cd $NUPIC >> python setup.py install --user >> >> >> No virtualenv required, but feel free to use one and omit the --user >> option. You should notice that the first thing happening is a download >> of the nupic.core binary file for your platform from AWS S3. The >> platform and SHA will be in the filename downloaded. If this command >> runs without an error, try running unit tests: >> >> ./scripts/run_nupic_tests -u >> >> >> If you have that _math.so problem, it should pop up here right away. >> If not, and all the tests pass, the next test is to run the simple >> hotgym example: >> >> python examples/opf/clients/hotgym/simple/hotgym.py >> >> >> This will output some junk to your console, but should no throw any >> exceptions. >> >> Please tell me how that goes and at what stage you received your first >> error and I'll give you instructions on building nupic.core yourself >> manually (it's not that hard if you have the right compiler). >> >> Thanks for your time, >> --------- >> Matt Taylor >> OS Community Flag-Bearer >> Numenta >> >> >> On Tue, Jan 27, 2015 at 3:39 PM, Ruaridh O'Donnell >> <[email protected]> wrote: >> >> Thanks for the reply, >> I’ve tried a few things, unfortunately none of them have worked. >> >> 1) I noticed when pip was downloading nupic from PYPI it was downloading >> "nupic-0.1.0-cp27-none-macosx_10_9_intel.whl”. I assumed this was meant for >> mavericks not yosemite, so I tried downloading the 10_10 version and got >> pip to install it. But I ended with exactly the same error as before. >> >> 2) I also tried building nupic from source. I cloned the repo, set up >> $NUPIC, and build it (inside a virtualenv) using “pip install -e >> path/to/nupic/repo/“. The -e option in pip apparently just uses "setup.py >> develop”. It seemed to build OK. >> But I still ended up with the same error as before. >> >> 3) I got your email so I uninstalled home-brew’s python and tried “brew >> install python-devel”. But brew couldn’t find any formulas with that name. >> I couldn’t find any reference on development headers for home-brew python >> through google. >> So I tried just installing python as I had it before (with "brew install >> python”) and installing nupic 0.1.2 but again I’m coming up against the same >> error. >> >> Out of curiosity I looked at what point python crashes when running “import >> nupic.bindings.math”. >> It looks like it finds a file named _math.so and then crashes when trying to >> import it. >> >> I’m not sure if any of that was helpful, I’m not too knowledgable in this >> area. >> >> Thanks, >> Ruaridh >> >> On 26 Jan 2015, at 17:50, Matthew Taylor <[email protected]> wrote: >> >> Ruaridh, >> >> You may not have python development headers installed. Try "brew >> install python-devel", then re-install NuPIC. Let me know if that >> helps. >> --------- >> Matt Taylor >> OS Community Flag-Bearer >> Numenta >> >> >> On Fri, Jan 23, 2015 at 12:13 PM, Ruaridh O'Donnell >> <[email protected]> wrote: >> >> Hello, >> I’m having trouble installing NuPIC with pip on a new mac with OS X >> Yosemite. >> In python, NuPIC imports OK ("import nupic"), but importing >> nupic.bindings.math and many other modules crashes python. >> >> For example >> >> import nupic.bindings.math >> >> Fatal Python error: PyThreadState_Get: no current thread >> Abort trap: 6 >> >> or >> >> from nupic.frameworks.opf.modelfactory import ModelFactory >> >> Fatal Python error: PyThreadState_Get: no current thread >> Abort trap: 6 >> >> Here’s how I installed everything (on a new mac): >> - I installed home-brew in the standard way (“ruby -e "$(curl -fsSL >> https://raw.githubusercontent.com/Homebrew/install/master/install)"”) >> - installed python 2.7.9 ("homebrew install python”) >> - installed virtualenv ("pip install virtualenv”) (this used the pip >> corresponding to homebrew’s python) >> - set up a virtual env in called ‘all’ in ~/ (“virtualenv all”) >> - installed nupi dependencies ("brew install automake libtool cmake”) >> - activated my virtualenv >> - installed NuPIC ("pip install nupic”) >> Everything seemed to run fine but I now get the errors mentioned above. >> >> I’m trying to use home-brew’s versions of python (2.7.9) rather the system >> one that came pre installed (2.7.6). >> Entering “python” in terminal points to homebrew’s python, not the system >> python. >> I tested out installing other modules with pip (in my virtualenv) and they >> all seem to work fine. (matplotlib) >> Creating a virtualenv uses homebrew's python >> >> Also when pip was installing nupic I noticed the wheel it was downloading >> was the 10_9 file not the 10_10 that is listed on PYPI: >> >> Collecting nupic >> Downloading nupic-0.1.0-cp27-none-macosx_10_9_intel.whl (6.6MB) >> 100% |################################| 6.6MB 848kB/s >> >> Not sure if that’s relevant >> >> Any help/insight into this would be appreciated, >> >> Ruaridh >> >> >> >>
