Very nice error report, thank you. --------- Matt Taylor OS Community Flag-Bearer Numenta
On Wed, Jan 28, 2015 at 3:45 PM, Ruaridh O'Donnell <[email protected]> wrote: > Issue created: > https://github.com/numenta/nupic/issues/1791 > Let me know if there’s any details I’ve left out. > > Cheers, > Ruaridh > > On 28 Jan 2015, at 15:44, Matthew Taylor <[email protected]> wrote: > > Ruaridh, I would really appreciate it if you filed a bug report, > including the details of your OS, compilers, python version, etc: > > https://github.com/numenta/nupic/issues/new?body=%3E%20What%20did%20you%20do%3F%20(steps%20to%20reproduce)%0A%0A%3E%20What%20happened%3F%20(actual%20results)%0A%0A%3E%20What%20should%20have%20happened%3F%20(expected%20results)%0A%0A%3E%20Additional%20Information%20(operating%20system%2C%20python%20version%2C%20NuPIC%20commit%20SHA%2C%20etc.) > > Thanks, > --------- > Matt Taylor > OS Community Flag-Bearer > Numenta > > > On Tue, Jan 27, 2015 at 7:26 PM, Matthew Taylor <[email protected]> wrote: > > I'm out of ideas. Anyone else want to try? > --------- > Matt Taylor > OS Community Flag-Bearer > Numenta > > > On Tue, Jan 27, 2015 at 6:33 PM, Ruaridh O'Donnell > <[email protected]> wrote: > > 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 > > > > > >
