You need the server. You must figure out how to start it up. Google search for your operating system + mysql. It can vary a lot between operating systems.
Thank you for creating the issue. --------- Matt Taylor OS Community Flag-Bearer Numenta On Mon, Aug 24, 2015 at 8:32 PM, Takenori Sato <[email protected]> wrote: > 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 >>>>>>>>> >>>>>>>> >>>>>>> >>>> >>> >
