Hi Pascal and Matt, I created issue #2484 with error logs, and commands executed for installation.
> The swarming tests ($NUPIC/scripts/run_nupic_tests -w) require MySQL to be installed, so that is why you're getting that error. Can you clarify what MySQL library I have to install? mysql-server had been installed by following wiki instruction. I tried mysql-client, but which didn't make a difference. >> I think starting with a particular(stable) branch/tag/hash is easier for a newbie like me. > Yes, using the latest stable release is usually a good place to start. Currently that is https://github.com/numenta/nupic/releases/tag/0.2.11. OK, will try that. Thanks, Takenori On Fri, Aug 21, 2015 at 8:11 PM, Pascal Weinberger < [email protected]> wrote: > Ok, Thanks! > Would you mind creating an issue? So that I can fix the requirement? > :) > Thanks! > > Also, from what you wrote, it's not quite clear to me if you did run the > setup.py for nupic at all? > On Aug 21, 2015 8:45 AM, "Takenori Sato" <[email protected]> wrote: > >> Hi Pascal, >> >> I did a fresh install from scratch(reinstalling Ubuntu), and did the >> followings. >> >> $ sudo apt-get install git python-dev python-pip automake libtool >> libssl-dev g++ cmake mysql-server libpcre3-dev >> $ sudo pip install numpy >> $ sudo pip install pytest==2.5.1 >> >> Then, I can see those tests started working! Note that CUDA is not >> available here, so some tests might be skipped. >> >> $NUPIC/bin/py_region_test >> ==> ALL PASSED >> >> $NUPIC/scripts/run_nupic_tests -i --coverage >> ==> 1 failed, 55 passed, 2 skipped >> $NUPIC/scripts/run_nupic_tests -w --coverage >> ==> 1 failed, 17 skipped >> >> OperationalError: (2003, 'Can\'t connect to MySQL server on \'localhost\' >> ((1045, u"Access denied for user \'root\'@\'localhost\' (using password: >> NO)") >> * Perhaps I need to feed somewhere? >> >> $ $NUPIC/scripts/run_nupic_tests -u --coverage >> ==> 2 skipped, 1 error >> >> ==================================================== ERRORS >> ===================================================== >> ____________________ ERROR collecting >> tests/unit/nupic/research/spatial_pooler_unit_test.py _____________________ >> tests/unit/nupic/research/spatial_pooler_unit_test.py:41: in <module> >> > from nupic.bindings.proto import SpatialPoolerProto_capnp >> capnp/lib/capnp.pyx:3773: in capnp.lib.capnp._Loader.load_module >> (capnp/lib/capnp.cpp:71749) >> > ??? >> capnp/lib/capnp.pyx:3752: in capnp.lib.capnp.load >> (capnp/lib/capnp.cpp:71239) >> > ??? >> capnp/lib/capnp.pyx:3126: in capnp.lib.capnp.SchemaParser.load >> (capnp/lib/capnp.cpp:63334) >> > ??? >> E KjException: >> /home/tsato/nupic/nupic/bindings/proto/RandomProto.capnp:0: failed: >> Duplicate ID @0x88eaee6db8e1f67c. >> E stack: 0x7fdea60114c8 0x7fdea5f33369 0x7fdea5f32eaa 0x7fdea5f58eca >> 0x7fdea5f59402 0x7fdea5f5d7f6 0x7fdea5f5d8eb 0x7fdea5f5d9ac 0x7fdea5f5d9f4 >> 0x7fdea5f6bfb9 0x7fdea5f6b206 0x7fdea5f6f46c 0x7fdea5f55df5 0x7fdea5f5d77e >> 0x7fdea5f56a1e 0x7fdea5f56d27 >> >> >> I think starting with a particular(stable) branch/tag/hash is easier for >> a newbie like me. >> >> Thanks, >> Takenori >> >> On Thu, Aug 20, 2015 at 4:29 PM, Pascal Weinberger < >> [email protected]> wrote: >> >>> Try it with 2.5 and let me know, so I'll update the requirements; ) >>> On Aug 20, 2015 9:36 AM, [email protected] wrote: >>> >>> Does pip install pytest==2.5.1 do the job for you? >>> So I should Write that in the wiki as well, right? :) >>> >>> Weired, your nupic setup should have alredy taken care of all of these >>> :$ Here we specify a 2.4 version... maybe that's deprecated? >>> >>> https://github.com/numenta/nupic/blob/master/external/common/requirements.txt >>> On Aug 20, 2015 5:04 AM, "Takenori Sato" <[email protected]> wrote: >>> >>> >> Try running the examples and tests in the folders :) >>> >>> > https://github.com/numenta/nupic/wiki/Installing-and-Building-NuPIC >>> >>> Thanks. >>> >>> HTM framework API test was successful, but unit tests won't run with the >>> following error. >>> >>> > Traceback (most recent call last): >>> > File "/home/tsato/nupic/scripts/run_nupic_tests", line 265, in >>> <module> >>> > result = main(parser, sys.argv[1:]) >>> > File "/home/tsato/nupic/scripts/run_nupic_tests", line 255, in main >>> > exitStatus = call(["py.test"] + args + list(tests)) >>> > File "/usr/lib/python2.7/subprocess.py", line 522, in call >>> > return Popen(*popenargs, **kwargs).wait() >>> > File "/usr/lib/python2.7/subprocess.py", line 710, in __init__ >>> > errread, errwrite) >>> > File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child >>> > raise child_exception >>> > OSError: [Errno 2] No such file or directory >>> >>> I guessed python-pytest has to be installed, too. >>> >>> Yet, after "sudo apt-get install python-pytest", I got a version >>> conflict error as follows. >>> >>> >>> > Traceback (most recent call last): >>> > File "/usr/bin/py.test", line 5, in <module> >>> > sys.exit(load_entry_point('pytest==2.5.1', 'console_scripts', >>> 'py.test')()) >>> > File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 351, >>> in load_entry_point >>> > return get_distribution(dist).load_entry_point(group, name) >>> > File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 344, >>> in get_distribution >>> > if isinstance(dist,Requirement): dist = get_provider(dist) >>> > File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 223, >>> in get_provider >>> > return working_set.find(moduleOrReq) or >>> require(str(moduleOrReq))[0] >>> > File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 503, >>> in find >>> > raise VersionConflict(dist,req) # XXX add more info >>> > pkg_resources.VersionConflict: (pytest 2.4.2 >>> (/home/tsato/.local/lib/python2.7/site-packages/pytest-2.4.2-py2.7.egg), >>> Requirement.parse('pytest==2.5.1')) >>> >>> What's the easiest way to fix this? >>> >>> >>> > After your Numpy fix were you able to run the Unit tests for NuPIC? I >>> could only run integration and swarm. >>> >>> No, still some obstacles here. >>> >>> Thanks, >>> Takenori >>> >>> On Wed, Aug 19, 2015 at 10:27 PM, Pascal Weinberger < >>> [email protected]> wrote: >>> >>>> https://github.com/numenta/nupic/wiki/Installing-and-Building-NuPIC >>>> >>>> For the tests :) >>>> On Aug 19, 2015 3:27 PM, [email protected] wrote: >>>> >>>>> Thanks! I'll change that, where in thewiki is that? >>>>> >>>>> Try running the examples and tests in the folders :) >>>>> On Aug 19, 2015 10:04 AM, "Takenori Sato" <[email protected]> wrote: >>>>> >>>>>> Thanks, but I confirmed "git pull" showed my repository was >>>>>> up-to-date. >>>>>> >>>>>> >>>>>> I seem to fix the problem now. The problem was numpy. >>>>>> >>>>>> The command to install numpy on the wiki is: >>>>>> >>>>>> $ sudo apt-get install numpy >>>>>> >>>>>> But, there is no such a package. >>>>>> >>>>>> So I had installed a similar one. >>>>>> >>>>>> $ sudo apt-get install python-numpy >>>>>> >>>>>> Then, I got the error complaining about Python.h. >>>>>> >>>>>> After removing python-numpy, and installing with pip as follows, >>>>>> the setup command finished without an error. >>>>>> >>>>>> $ sudo pip install numpy >>>>>> >>>>>> >>>>>> Is there any command to check if the installation was successful or >>>>>> not? >>>>>> >>>>>> Thanks, >>>>>> Takenori >>>>>> >>>>>> >>>>>> On Wed, Aug 19, 2015 at 3:47 PM, Pascal Weinberger < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> Hey! >>>>>>> >>>>>>> This may be because of some recent updates that also caused travis >>>>>>> to fail, >>>>>>> You may try to update your code by pulling from github and try >>>>>>> again. It should be building now :) >>>>>>> On Aug 19, 2015 6:20 AM, "Takenori Sato" <[email protected]> wrote: >>>>>>> >>>>>>>> HI, >>>>>>>> >>>>>>>> I followed "Installing NuPIC on Ubuntu", >>>>>>>> but got stuck with some errors as follows. >>>>>>>> >>>>>>>> I would appreciate if anyone gives me some hints to fix this. >>>>>>>> >>>>>>>> ... >>>>>>>> Could not locate executable gfortran >>>>>>>> Could not locate executable f95 >>>>>>>> Could not locate executable ifort >>>>>>>> Could not locate executable ifc >>>>>>>> Could not locate executable lf95 >>>>>>>> Could not locate executable pgfortran >>>>>>>> Could not locate executable f90 >>>>>>>> Could not locate executable f77 >>>>>>>> Could not locate executable fort >>>>>>>> Could not locate executable efort >>>>>>>> Could not locate executable efc >>>>>>>> Could not locate executable g77 >>>>>>>> Could not locate executable g95 >>>>>>>> Could not locate executable pathf95 >>>>>>>> don't know how to compile Fortran code on platform 'posix' >>>>>>>> _configtest.c:1:5: warning: conflicting types for built-in function >>>>>>>> ‘exp’ [enabled by default] >>>>>>>> int exp (void); >>>>>>>> ^ >>>>>>>> _configtest.o: In function `main': >>>>>>>> /tmp/easy_install-uVwEo7/numpy-1.9.2/_configtest.c:6: undefined >>>>>>>> reference to `exp' >>>>>>>> collect2: error: ld returned 1 exit status >>>>>>>> _configtest.o: In function `main': >>>>>>>> /tmp/easy_install-uVwEo7/numpy-1.9.2/_configtest.c:6: undefined >>>>>>>> reference to `exp' >>>>>>>> collect2: error: ld returned 1 exit status >>>>>>>> _configtest.c:1:5: warning: conflicting types for built-in function >>>>>>>> ‘exp’ [enabled by default] >>>>>>>> int exp (void); >>>>>>>> ^ >>>>>>>> _configtest.c:1:20: fatal error: Python.h: No such file or directory >>>>>>>> #include <Python.h> >>>>>>>> ^ >>>>>>>> compilation terminated. >>>>>>>> _configtest.c:1:20: fatal error: Python.h: No such file or directory >>>>>>>> #include <Python.h> >>>>>>>> ^ >>>>>>>> compilation terminated. >>>>>>>> Traceback (most recent call last): >>>>>>>> File "setup.py", line 430, in <module> >>>>>>>> """) >>>>>>>> File "/usr/lib/python2.7/distutils/core.py", line 151, in setup >>>>>>>> dist.run_commands() >>>>>>>> File "/usr/lib/python2.7/distutils/dist.py", line 953, in >>>>>>>> run_commands >>>>>>>> self.run_command(cmd) >>>>>>>> File "/usr/lib/python2.7/distutils/dist.py", line 972, in >>>>>>>> run_command >>>>>>>> cmd_obj.run() >>>>>>>> File >>>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/install.py", line >>>>>>>> 73, >>>>>>>> in run >>>>>>>> self.do_egg_install() >>>>>>>> File >>>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/install.py", line >>>>>>>> 96, >>>>>>>> in do_egg_install >>>>>>>> cmd.run() >>>>>>>> File >>>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>>> line >>>>>>>> 381, in run >>>>>>>> self.easy_install(spec, not self.no_deps) >>>>>>>> File >>>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>>> line >>>>>>>> 597, in easy_install >>>>>>>> return self.install_item(None, spec, tmpdir, deps, True) >>>>>>>> File >>>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>>> line >>>>>>>> 648, in install_item >>>>>>>> self.process_distribution(spec, dist, deps) >>>>>>>> File >>>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>>> line >>>>>>>> 694, in process_distribution >>>>>>>> [requirement], self.local_index, self.easy_install >>>>>>>> File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line >>>>>>>> 620, in resolve >>>>>>>> dist = best[req.key] = env.best_match(req, ws, installer) >>>>>>>> File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line >>>>>>>> 858, in best_match >>>>>>>> return self.obtain(req, installer) # try and download/install >>>>>>>> File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line >>>>>>>> 870, in obtain >>>>>>>> return installer(requirement) >>>>>>>> File >>>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>>> line >>>>>>>> 616, in easy_install >>>>>>>> return self.install_item(spec, dist.location, tmpdir, deps) >>>>>>>> File >>>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>>> line >>>>>>>> 646, in install_item >>>>>>>> dists = self.install_eggs(spec, download, tmpdir) >>>>>>>> File >>>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>>> line >>>>>>>> 834, in install_eggs >>>>>>>> return self.build_and_install(setup_script, setup_base) >>>>>>>> File >>>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>>> line >>>>>>>> 1040, in build_and_install >>>>>>>> self.run_setup(setup_script, setup_base, args) >>>>>>>> File >>>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>>> line >>>>>>>> 1025, in run_setup >>>>>>>> run_setup(setup_script, args) >>>>>>>> File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", >>>>>>>> line 50, in run_setup >>>>>>>> lambda: execfile( >>>>>>>> File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", >>>>>>>> line 100, in run >>>>>>>> return func() >>>>>>>> File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", >>>>>>>> line 52, in <lambda> >>>>>>>> {'__file__':setup_script, '__name__':'__main__'} >>>>>>>> File "setup.py", line 251, in <module> >>>>>>>> if name is None or options is None: >>>>>>>> File "setup.py", line 243, in setup_package >>>>>>>> return ( >>>>>>>> File "/usr/lib/python2.7/dist-packages/numpy/distutils/core.py", >>>>>>>> line 169, in setup >>>>>>>> return old_setup(**new_attr) >>>>>>>> File "/usr/lib/python2.7/distutils/core.py", line 151, in setup >>>>>>>> dist.run_commands() >>>>>>>> File "/usr/lib/python2.7/distutils/dist.py", line 953, in >>>>>>>> run_commands >>>>>>>> self.run_command(cmd) >>>>>>>> File "/usr/lib/python2.7/distutils/dist.py", line 972, in >>>>>>>> run_command >>>>>>>> cmd_obj.run() >>>>>>>> File >>>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/bdist_egg.py", >>>>>>>> line >>>>>>>> 177, in run >>>>>>>> self.run_command("egg_info") >>>>>>>> File "/usr/lib/python2.7/distutils/cmd.py", line 326, in >>>>>>>> run_command >>>>>>>> self.distribution.run_command(command) >>>>>>>> File "/usr/lib/python2.7/distutils/dist.py", line 972, in >>>>>>>> run_command >>>>>>>> cmd_obj.run() >>>>>>>> File >>>>>>>> "/usr/lib/python2.7/dist-packages/numpy/distutils/command/egg_info.py", >>>>>>>> line 10, in run >>>>>>>> self.run_command("build_src") >>>>>>>> File "/usr/lib/python2.7/distutils/cmd.py", line 326, in >>>>>>>> run_command >>>>>>>> self.distribution.run_command(command) >>>>>>>> File "/usr/lib/python2.7/distutils/dist.py", line 972, in >>>>>>>> run_command >>>>>>>> cmd_obj.run() >>>>>>>> File >>>>>>>> "/usr/lib/python2.7/dist-packages/numpy/distutils/command/build_src.py", >>>>>>>> line 153, in run >>>>>>>> self.build_sources() >>>>>>>> File >>>>>>>> "/usr/lib/python2.7/dist-packages/numpy/distutils/command/build_src.py", >>>>>>>> line 170, in build_sources >>>>>>>> self.build_extension_sources(ext) >>>>>>>> File >>>>>>>> "/usr/lib/python2.7/dist-packages/numpy/distutils/command/build_src.py", >>>>>>>> line 329, in build_extension_sources >>>>>>>> sources = self.generate_sources(sources, ext) >>>>>>>> File >>>>>>>> "/usr/lib/python2.7/dist-packages/numpy/distutils/command/build_src.py", >>>>>>>> line 386, in generate_sources >>>>>>>> source = func(extension, build_dir) >>>>>>>> File "numpy/core/setup.py", line 432, in generate_config_h >>>>>>>> if haveBuild: >>>>>>>> File "numpy/core/setup.py", line 42, in check_types >>>>>>>> except urllib2.URLError: >>>>>>>> File "numpy/core/setup.py", line 293, in check_types >>>>>>>> else: >>>>>>>> SystemError: Cannot compile 'Python.h'. Perhaps you need to install >>>>>>>> python-dev|python-devel. >>>>>>>> >>>>>>>> >>>>>>>> I followed the wiki, so python-dev had been installed. >>>>>>>> >>>>>>>> $ sudo apt-get install python-dev >>>>>>>> Reading package lists... Done >>>>>>>> Building dependency tree >>>>>>>> Reading state information... Done >>>>>>>> python-dev is already the newest version. >>>>>>>> 0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded. >>>>>>>> >>>>>>>> Also, this is a freshly installed machine for NuPIC. >>>>>>>> >>>>>>>> $ lsb_release -a >>>>>>>> No LSB modules are available. >>>>>>>> Distributor ID: Ubuntu >>>>>>>> Description: Ubuntu 14.04.3 LTS >>>>>>>> Release: 14.04 >>>>>>>> Codename: trusty >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Takenori >>>>>>>> >>>>>>> >>>>>> >>> >>
