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 >>>>>> >>>>> >>>> >
