> 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.
I confirmed mysql server is up and running. I can login with "root" user and its password as follows. ~$ mysql -u root -p Enter password: Welcome to the MySQL monitor. Commands end with ; or \g. Your MySQL connection id is 37 Server version: 5.5.44-0ubuntu0.14.04.1 (Ubuntu) Copyright (c) 2000, 2015, Oracle and/or its affiliates. All rights reserved. Oracle is a registered trademark of Oracle Corporation and/or its affiliates. Other names may be trademarks of their respective owners. Type 'help;' or '\h' for help. Type '\c' to clear the current input statement. mysql> status -------------- mysql Ver 14.14 Distrib 5.5.44, for debian-linux-gnu (x86_64) using readline 6.3 Connection id: 38 Current database: Current user: root@localhost SSL: Not in use Current pager: stdout Using outfile: '' Using delimiter: ; Server version: 5.5.44-0ubuntu0.14.04.1 (Ubuntu) Protocol version: 10 Connection: Localhost via UNIX socket Server characterset: latin1 Db characterset: latin1 Client characterset: utf8 Conn. characterset: utf8 UNIX socket: /var/run/mysqld/mysqld.sock Uptime: 2 min 43 sec Threads: 1 Questions: 113 Slow queries: 0 Opens: 48 Flush tables: 1 Open tables: 41 Queries per second avg: 0.693 -------------- But I get the same error when running swarming test. OperationalError: (2003, 'Can\'t connect to MySQL server on \'localhost\' ((1045, u"Access denied for user \'root\'@\'localhost\' (using password: NO)"))') This message says, it tried to connect without password. That's why rejected. How does the test program pick up root password? If it connects without password, such an account should exist. Oh, I noticed I had to update a config file with my own root password. https://github.com/numenta/nupic/wiki/MySQL-Settings But there is no such a file on the current repository. I quickly searched for the file(nupic-default.xml) on github, but didn't find the one. Where is the file? Thanks, Takenori On Tue, Aug 25, 2015 at 1:21 PM, Matthew Taylor <[email protected]> wrote: > 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 >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>> >>>> >> >
