Closed jzuhone closed 6 years ago
Sure, it says: pip 1.5.4 from /home/allblues1001/tensorflow/local/python2.7/site-packages (python 2.7)
@allblues1001 and forgive me if this is obvious, but the kernel you're starting in ipython is the same version as the one in bash? try this on both the python REPL and the ipython notebook:
import sys
print sys.version_info
and compare.
@rdodev For python REPL and jupyter notebook it is the same: sys.version_info (major=2, minor=7, micro=6, releaselevel='final', serial=0)
@allblues1001 try this on both
import sys
sys.path
and see if they are the same.
For python: ['', '/home/allblues/tensorflow/lib/python2.7', '/home/saad-omar/tensorflow/lib/python2.7/plat-x86_64-linux-gnu', '/home/allblues/tensorflow/lib/python2.7/lib-tk', '/home/saad-omar/tensorflow/lib/python2.7/lib-old', '/home/allblues/tensorflow/lib/python2.7/lib-dynload', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-x86_64-linux-gnu', '/usr/lib/python2.7/lib-tk', '/home/allblues/tensorflow/local/lib/python2.7/site-packages', '/home/allblues/tensorflow/lib/python2.7/site-packages', '/usr/local/lib/python2.7/site-packages', '/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages/PILcompat', '/usr/lib/python2.7/dist-packages/gtk-2.0', '/usr/lib/pymodules/python2.7'] For jupyter notebook: ['', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-x86_64-linux-gnu', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages/PILcompat', '/usr/lib/python2.7/dist-packages/gtk-2.0', '/usr/lib/pymodules/python2.7', '/usr/local/lib/python2.7/dist-packages/IPython/extensions', '/home/allblues/.ipython']
@allblues1001 you left a few 'saad-omar' there :p That said, you have an issue. Both paths should look more or less the same. It would seem tensorflow installed its own version of python? Either way, your issue is not related to Bash on Windows or ipython. I would suggest seeking help from the folks at tensorflow.
thank you!
@RitwikGupta ipython notebook --no-browser says 0 active kernel. I opened http://localhost:8888/tree# in my browser and then when I open a new notebook (python[root]) it says connecting to kernel and closes automatically. Can you please let me know what is the possible solution for this? Thanks! Anand Bhattad
this is what I get
Check your console and ensure there are no errors first. If getting the socket error, follow the steps above.
On Wed, Aug 31, 2016 at 11:37 PM -0400, "bhattad2" notifications@github.com<mailto:notifications@github.com> wrote:
@RitwikGuptahttps://github.com/RitwikGupta ipython notebook --no-browser says 0 active kernel. I opened http://localhost:8888/tree# in my browser and then when I open a new notebook (python[root]) it says connecting to kernel and closes automatically. Can you please let me know what is the possible solution for this? Thanks! Anand Bhattad
this is what I get [image]https://cloud.githubusercontent.com/assets/16907734/18154563/5a082604-6fcb-11e6-8ab8-1a488becb7cf.png
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There are no console errors. And I'm able to use ipython from the terminal and I am able to import tensorflow, numpy without any error
This seems like an iPython issue rather than BashOnWindows, so I would suggest taking this issue to that repo, but I think the error is in your kernel config. Is python[root] your kernel? It should be called “Python 2” or “Python 3” for a fresh install.
@aseering Please clarify few things about the solution:
Thank you
Also, shouldn't Microsoft be moving towards an actual solution to this rather than just @aseering's workaround?
On Thu, Sep 1, 2016 at 5:11 PM, bobev18 notifications@github.com wrote:
@aseering https://github.com/aseering Please clarify few things about the solution:
- does it work only for Python 2.7 or does it cover Python 3.x?
- you keep referring to IPython rather than Jupyter - does this mean Jupyter is not covered?
- how should we integrate the solution in case of virtualenv or anaconda environments?
Thank you
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@bobev18 , maybe this helps to understand the issue: This bug is not a bug in Python. IPython (and Jupyter) Notebook are not pure Python; they contain some native code as well, and that native code links against some third-party native systemwide C libraries. The problem is a bug in one of those libraries, "libzmq". All versions of Notebook link libzmq. Because it's an independent system library, it doesn't matter what version of iPython/Jupyter you're using, nor what version of Python.
But which libzmq do they link? The iPython that comes with Ubuntu uses the libzmq that comes with Ubuntu. I believe pip will try to use the system libzmq as well. My updated patch fixes Ubuntu's version of the library. Anaconda bundles their own copy of libzmq, so you have to use @jzuhone 's solution to get their fix.
@yasirs -- for what it's worth, this is actually a bug in Ubuntu's package. The bug has been acknowledged and fixed upstream. It happens to be much more disruptive on WSL, but it's a bug either way. My "workaround" is simply to backport the fix to Ubuntu 14.04.
Sure, Microsoft should make their code more robust to buggy code. I hope they've gotten that memo :-) But this is a known bug whose fix has been submitted to Ubuntu. They could accept the patch today and ... well, sure, some important edge cases, but it would help a lot of people. So, could some of the enthusiastic folks here go upvote / encourage them to do that?:
https://bugs.launchpad.net/ubuntu/+source/zeromq3/+bug/1602900
@aseering Do you mind sharing latest instructions for clean install please? The thread is quite long, and it's not clear if things are changed since your last instructions post
This worked for me a few weeks ago from a fresh install:
Sudo apt-get update Sudo apt-get install python-pip ipython ipython-notebook ipython3 ipython3-notebook sudo add-apt-repository ppa:aseering/wsl sudo apt-get update sudo apt-get install libzmq3 sudo apt-get install python3-pip sudo pip3 install jupyter sudo pip install jupyter jupyter notebook --no-browser
No reason to believe it wouldn't work now. But it would be great with confirmation if you decide to try this out.
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@aseering https://github.com/aseering Do you mind sharing latest instructions for clean install please? The thread is quite long, and it's not clear if things are changed since your last instructions post
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(Email client on phone capitalized s couple of sudo there, sorry. Just lowercase the S.)
On Tue, Sep 20, 2016, 5:50 PM Arthur Hjorth arthur.hjorth@stx.oxon.org wrote:
This worked for me a few weeks ago from a fresh install:
Sudo apt-get update Sudo apt-get install python-pip ipython ipython-notebook ipython3 ipython3-notebook
sudo add-apt-repository ppa:aseering/wsl sudo apt-get update sudo apt-get install libzmq3
sudo apt-get install python3-pip sudo pip3 install jupyter sudo pip install jupyter jupyter notebook --no-browser
No reason to believe it wouldn't work now. But it would be great with confirmation if you decide to try this out.
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@aseering https://github.com/aseering Do you mind sharing latest instructions for clean install please? The thread is quite long, and it's not clear if things are changed since your last instructions post
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@arthurhjorth Thanks! I am actually trying to install with python 2, as I want to use tensorflow and gym, and they don't support 3 as well as 2 yet. I have tried
apt-get install python-pip ipython ipython-notebook add-apt-repository ppa:aseering/wsl apt-get update apt-get install libzmq3 pip install jupyter jupyter notebook --no-browser
(no sudos didn't give any errors during installation, and I wanted to do anything as myself to avoid permission problems in the future) but that didn't work (as in still the same error "Invalid argument (bundled/zeromq/src/tcp_address.cpp:190")
Using @rdodev 's advice exactly (without sudo as I logged in as root) https://github.com/Microsoft/BashOnWindows/issues/185#issuecomment-241515056, with full reinstall of Ubuntu, ipython notebook worked!
Further pip install jupyter
worked for running jupyter instead.
After upgrading to 14936, jupyter notebook no longer works on my machine. If you're in this thread, you probably care about that, so don't upgrade unless you have to.
Reverting back fixed it.
On the new build, I got an error about unsupported operation at tcp_address.cpp:169 and the kernel kept restarting until it had tried five times, and then it gave up.
I am using my computer to do a presentation including some coding, so I can't help with debugging atm or offer any other information.
FWIW, I'm seeing the exact same thing as @arthurhjorth with python and jupyter installed from conda
@arthurhjorth +1 In 14936,
[I 23:55:53.388 NotebookApp] Kernel started: 99311cb2-a24a-4f51-983b-7187e3fe940d
Operation not supported (tcp_address.cpp:169)
[I 23:55:56.383 NotebookApp] KernelRestarter: restarting kernel (1/5)
Operation not supported (tcp_address.cpp:169)
[I 23:55:59.465 NotebookApp] KernelRestarter: restarting kernel (2/5)
Operation not supported (tcp_address.cpp:169)
[I 23:56:02.523 NotebookApp] KernelRestarter: restarting kernel (3/5)
^C[I 23:56:03.049 NotebookApp] interrupted
Serving notebooks from local directory: /root
1 active kernels
The Jupyter Notebook is running at: http://localhost:8192/
Shutdown this notebook server (y/[n])? ^C[C 23:56:03.195 NotebookApp] recei
Fix:
In 14936, kernel use EOPNOTSUPP
instead of EINVAL
.
So, after using https://launchpadlibrarian.net/261891465/zeromq3_4.0.4+dfsg-2_4.0.4+dfsg-2wsl1.diff.gz
this patch, EOPNOTSUPP
is not ignored.
Line 161 should be if (rc != 0 && (errno == EINVAL || errno == EOPNOTSUPP))
and it should works.
@phobson @arthurhjorth
PS: you may use this libzmq3 (if you trust me), or you can modify that line and build the package
Hint: If you are building & packing this library under WSL, you should skip all tests (some tests may not pass under WSL)
@Yangff Thanks for the information! Very insightful.
I'm less interested in getting this running now than I am in poking the right people (e.g., jupyter, zeromq) so that they are aware of the issue and can support WSL
Ideally people shouldn't have to make changes to support WSL. It's more a matter of us making sure to return the right error code in this condition. I'll take a look at this tomorrow and see what the problem is.
@benhillis Thanks for making sure this issue is taken care of :smile:
Thanks! Can @aseering update his branch with this patch, so people can use the the same instructions to use the patched package?
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@benhillis https://github.com/benhillis Thanks for making sure this issue is taken care of 😄
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@Yangff thanks so much! I have too much work this week to dare do anything other than just stick with the old build for now. Unless there's a WSL fix in sight by some time after next week, I'll use your libzmq. Thank you!!
I'm having trouble reproducing this issue. Could somebody give me a list of steps / instructions? Here's what I did:
apt-get update
apt-get install python-pip ipython ipython-notebook libzmq3
pip install jupyter
jupyter notebook --no-browser
I then launched a browser and navigated to the URL that was spit out by the jupyter command.
@benhillis can you then start a notebook and execute python?
IME, launching the server seems to work fine. The problems arise when you create a new notebook and try to execute even the most basic code. For example:
import os
print(os.getcwd())
Should trigger a restart to the kernel (if it let's you get that far).
On the site New, then Terminal and ran python inside of that. Is that what you mean?
Hm, it may be that the Ubuntu trunk libzmq may be working properly now with WSL. @benhillis, can you try the steps listed on https://github.com/Microsoft/BashOnWindows/issues/185#issuecomment-225449188 and see if that breaks it? If so, the libzmq on @aseering's PPA might be borked.
EDIT: Disregard, I misidentified the issue. See @phobson's comment below for repro.
@benhillis
You need to make a new notebook, not a terminal:
Then you get stuck in a loop of dead/restarting kernels:
Console output looks like this:
(jup) paul@POR-PHOBSON10:/mnt/c/Users/phobson$ jupyter notebook --no-browser
[W 11:13:39.836 NotebookApp] Widgets are unavailable. Please install widgetsnbextension or ipywidgets 4.0
[I 11:13:39.851 NotebookApp] Serving notebooks from local directory: /mnt/c/Users/phobson
[I 11:13:39.852 NotebookApp] 0 active kernels
[I 11:13:39.852 NotebookApp] The Jupyter Notebook is running at: http://localhost:8888/
[I 11:13:39.852 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[I 11:14:20.160 NotebookApp] 302 GET / (127.0.0.1) 4.28ms
[I 11:15:47.918 NotebookApp] Creating new notebook in
[W 11:15:48.907 NotebookApp] 404 GET /nbextensions/widgets/notebook/js/extension.js?v=20161003111339 (127.0.0.1) 14.75ms referer=http://127.0.0.1:8888/notebooks/Untitled.ipynb?kernel_name=python3
[I 11:15:49.166 NotebookApp] Kernel started: 03a01c40-5d09-444d-a173-bf97447956bd
Invalid argument (src/tcp_address.cpp:172)
[I 11:15:52.165 NotebookApp] KernelRestarter: restarting kernel (1/5)
Invalid argument (src/tcp_address.cpp:172)
[I 11:15:55.232 NotebookApp] KernelRestarter: restarting kernel (2/5)
Invalid argument (src/tcp_address.cpp:172)
[I 11:15:58.295 NotebookApp] KernelRestarter: restarting kernel (3/5)
[W 11:15:59.202 NotebookApp] Timeout waiting for kernel_info reply from 03a01c40-5d09-444d-a173-bf97447956bd
Invalid argument (src/tcp_address.cpp:172)
[I 11:16:01.380 NotebookApp] KernelRestarter: restarting kernel (4/5)
WARNING:root:kernel 03a01c40-5d09-444d-a173-bf97447956bd restarted
Invalid argument (src/tcp_address.cpp:172)
[W 11:16:04.456 NotebookApp] KernelRestarter: restart failed
[W 11:16:04.458 NotebookApp] Kernel 03a01c40-5d09-444d-a173-bf97447956bd died, removing from map.
ERROR:root:kernel 03a01c40-5d09-444d-a173-bf97447956bd restarted failed!
[W 11:16:04.504 NotebookApp] Kernel deleted before session
[W 11:16:04.509 NotebookApp] 410 DELETE /api/sessions/84ce5660-b868-4824-805b-200a40c62596 (127.0.0.1) 12.75ms referer=http://127.0.0.1:8888/notebooks/Untitled.ipynb?kernel_name=python3
[W 11:16:22.342 NotebookApp] Session not found: session_id='84ce5660-b868-4824-805b-200a40c62596'
[W 11:16:22.342 NotebookApp] 404 DELETE /api/sessions/84ce5660-b868-4824-805b-200a40c62596 (127.0.0.1) 2.19ms referer=http://127.0.0.1:8888/notebooks/Untitled.ipynb?kernel_name=python3
[I 11:16:22.398 NotebookApp] Kernel started: 1da56c55-9360-4f85-89b1-76da21623cd6
Invalid argument (src/tcp_address.cpp:172)
[I 11:16:25.397 NotebookApp] KernelRestarter: restarting kernel (1/5)
Invalid argument (src/tcp_address.cpp:172)
[I 11:16:28.432 NotebookApp] KernelRestarter: restarting kernel (2/5)
Invalid argument (src/tcp_address.cpp:172)
[I 11:16:31.489 NotebookApp] KernelRestarter: restarting kernel (3/5)
Invalid argument (src/tcp_address.cpp:172)
[W 11:16:32.421 NotebookApp] Timeout waiting for kernel_info reply from 1da56c55-9360-4f85-89b1-76da21623cd6
[I 11:16:34.568 NotebookApp] KernelRestarter: restarting kernel (4/5)
WARNING:root:kernel 1da56c55-9360-4f85-89b1-76da21623cd6 restarted
Invalid argument (src/tcp_address.cpp:172)
[W 11:16:37.647 NotebookApp] KernelRestarter: restart failed
[W 11:16:37.649 NotebookApp] Kernel 1da56c55-9360-4f85-89b1-76da21623cd6 died, removing from map.
ERROR:root:kernel 1da56c55-9360-4f85-89b1-76da21623cd6 restarted failed!
[W 11:16:37.691 NotebookApp] Kernel deleted before session
[W 11:16:37.694 NotebookApp] 410 DELETE /api/sessions/93443e32-9137-48b4-ba40-2ee6c963ca34 (127.0.0.1) 7.89ms referer=http://127.0.0.1:8888/notebooks/Untitled.ipynb?kernel_name=python3
@rdodev you mean /uninstall /full
?
By the way, if you are mostly using bash to run TensorFlow there is now an alpha Windows support to run it natively on CPU only here.
Currently, only CPU builds are supported, but we are working on providing a GPU build as well.
I follow this step, yet the kernel keeps dying
sudo add-apt-repository ppa:aseering/wsl sudo apt-get update sudo apt-get install libzmq3 libzmq3-dev export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu pip install --no-use-wheel -v pyzmq pip install jupyter
Kernel started: c81deaed-dfc4-4733-8ba7-173dc82d646c Invalid argument (src/tcp_address.cpp:190) KernelRestarter: restarting kernel (1/5) Invalid argument (src/tcp_address.cpp:190) KernelRestarter: restarting kernel (2/5) Invalid argument (src/tcp_address.cpp:190) KernelRestarter: restarting kernel (3/5) Invalid argument (src/tcp_address.cpp:190) Timeout waiting for kernel_info reply from c81deaed-dfc4-4733-8ba7-173dc82d646c KernelRestarter: restarting kernel (4/5) WARNING:root:kernel c81deaed-dfc4-4733-8ba7-173dc82d646c restarted Invalid argument (src/tcp_address.cpp:190) ![applicationframehost_2016-10-18_18-37-29] KernelRestarter: restart failed Kernel c81deaed-dfc4-4733-8ba7-173dc82d646c died, removing from map. ERROR:root:kernel c81deaed-dfc4-4733-8ba7-173dc82d646c restarted failed! Kernel deleted before session 410 DELETE /api/sessions/21a9b67b-1a2c-45cd-8df7-41885ae62f2e (127.0.0.1) 4.49ms referer=http://localhost:8888/notebooks/a.ipynb
@Carmezim
By the way, if you are mostly using bash to run TensorFlow there is now an alpha Windows support to run it natively on CPU only now Most people still have problem getting the CPU only version to work :-(
@JimSEOW The native TensorFlow windows support is an alpha as you've read I mentioned, so you are expected to face some instability although it's made progress since then and seems to be working fine. For more information about it check their thread here. There is also a build now running with bazel. I have it running perfectly natively.
Now regarding bash and ipython, did you try to install on a clean bash installation?
In @benhillis case: Invalid argument (src/tcp_address.cpp:172) In my case: Invalid argument (src/tcp_address.cpp:190)
Is this related to Bash on Windows? Any suggestion?
@Carmezim Yes, it is a clean bash installation. Do you have stable Juypter running on bash on Window? If so, I would try again, before moving to Hyper-V Ubuntu.
@JimSEOW Yes, I had problems to get it working at first but after a fresh installation and following some instructions above it worked normally.
@Yangff (or others that can help): I don't know what to do with the modified libzmq3 files you uploaded. I tried installing them using sudo dpkg -i filename
and then sudo apt-get install -f
afterwards, but it didn't seem to work.
How should this library get installed?
@thwump dpkg -i
should work.
Have you reinstalled pyzmq after change libzmq?
For what it's worth, the latest WSL Insider build contains a change that might work around this issue. I'm not at a Windows machine right now but I would be interested to know if the stock libzmq does indeed work now.
@aseering forgive my ignorance. how does one update to the latest build? (I presume it takes more than just sudo apt-get update && sudo apt-get upgrade --yes
)
@phobson -- I'm guessing based on your question that you're running the standard stable version of Windows, and are not part of the Insider program? You can learn more about the program here:
It's easy (and free) to join. Once you join, updates will automatically appear through Windows Update. But you can't selectively update (you can't just upgrade WSL, for example); you're opting in to receive a pre-release version of all of Windows. This new version contains new features; also new bugs :-)
Features added to the Insider releases eventually make it into the next major Windows release. So, if you don't choose to join the Insider program, you'll get the new features when the next major Windows version ships, probably some number of months from now.
It works for me, but I need to run all pip install
or pip3 install
with sudo -H
flag so that everything installs in the home directory. I do not use the -H
flag when installing things with apt-get
. I don't know enough about all this stuff to make sense of why, but doing that makes everything run "out of the box" for me!
(If anyone understands why this would work and can spare the time to explain it or point to a good resource on it, I would love to learn. I've googled around and read stuff online but still can't put together a coherent explanation in my head.)
Hi @arthurhjorth -- what arguments are you running pip
with?
sudo -H
will not, by itself, cause things to be installed to your home directory. sudo
(by default) runs commands as the root
user rather than as your normal user account; root
has elevated privileges to install things systemwide. sudo -H
says, even though you're running as the root
user, set the $HOME
environment variable to point at your regular user's home directory. This affects programs that try to write to "the current user's home directory".
apt-get
always installs software systemwide. (It's the Ubuntu package manager; it installs packages for your Ubuntu system.) Therefore, by default it must be run as root
, and the value of the $HOME
environment variable (and therefore the -H
flag to sudo
) doesn't affect it.
pip
(and pip3
) can install either systemwide or just for your current user account. By default, it decides where to install based on whether you run pip
with the --user
flag: With that flag, it will install to your home directory; without that flag, it will install systemwide. If you install systemwide, by default it will need to run as root
. If you install to your home directory, you should not need to install as root
-- this is very useful for users on shared machines who don't have sudo
access.
There are a few weird edge cases to consider:
sudo pip install --user <some package>
: sudo
means "run the following command as root
". pip install --user
means "install to the current user's home directory. But the current user is root
. So this will install the package to root
's home directory, and it will only be available if you run as root
. Which is probably not useful, unless you really know what you are doing.sudo -H pip install --user <some package>
: This is the same as above, except, you're telling pip
that root
's home directory is your current directory. That's actually bad: It means that pip
will install the package to your home directory, but your user's package repository will be corrupted / updated to be owned by root
. By default, this means that you can run packages, but the next time you try to install using pip
without sudo
, you won't be allowed to do so. You can fix this by running sudo chown -R $USER ~/.local
.apt-get
and pip
? Some packages will conflict. In this case, apt-get
, which is a general-purpose package manager and has only a minimal understanding of Python in particular, will simply error out and say (I'm paraphrasing here) "go fix your package!" pip
is a little more clever; it will try to resolve the dependency in favor of whatever version it is installing. However, most packages won't conflict. This is because Python has a "search path": When you go to import
a package in a Python script, first, Python checks for packages installed to your user account's home directory (where pip install --user
puts them): $HOME/.local/lib/python2.7
. If it doesn't find a package there, next it looks in /usr/local/lib/python2.7
(or similar for Python 3), which is where sudo pip install
puts them. If it still doesn't find the package, then it looks in /usr/lib/python2.7
, which is where apt-get
installs its packages. If it still doesn't find the package, only then does it error out. So if you install a package multiple times using different tools or commands, Python will pick whichever it sees first. This can cause a lot of confusion -- for example, if you install using pip
, then you decide you want the official Ubuntu version so you install using apt-get
, you'll keep getting the pip
version because it's first in the search path. Also, if you have a broken version of a package early in the search path that won't uninstall for whatever reason, installing a correct package may not fix it if the correct one is installed later in the search path.All of the above assumes that you're using the standard version of Python packaged for Ubuntu Linux (which is what WSL uses). If you're running on CentOS, or Mac, or on Ubuntu using an alternative version of Python such as Anaconda or Linuxbrew, or if you compile and install Python yourself from source, then at minimum the number and location of paths in Python's search path will change; also, some of those installations will reconfigure your system to not require root
access to install Python packages systemwide.
@jzuhone Hey man thks for the fix. I tried to fix this for days now and your package made it work like a charm! I appreciate it!
Sorry, found some issues with the above. Try: conda install -c jzuhone zeromq=4.1.dev0 instead
Aye, also just saved by @jzuhone. For anyone working from an anaconda install, his package totally works. Thanks!
When attempting to run a jupyter notebook or qtconsole, I get error messages like this:
Invalid argument (bundled/zeromq/src/tcp_address.cpp:171)
The normal ipython prompt works fine.