[yt-users] yt and ipython notebook

Mark Krumholz mkrumhol at ucsc.edu
Wed Sep 18 14:51:25 PDT 2013


On Sep 18, 2013, at 2:42 PM, Matthew Turk wrote:

> Hi Mark,
> 
> pip install jinja2
> 
> should fix it.  I think we missed that in our dependency stack, but I
> will add it to the install script.
> 
> Thanks for the report!
> 
> -Matt


Hi Matt,

That helps, but still doesn't let me run. I tried your suggestion, and jinja2 seems to build, though it throws a bunch of warning messages:

(yt-x86_64)pfe20:hmc3_mhd_lowden mkrumhol$ pip install jinja2
Downloading/unpacking jinja2
  Downloading Jinja2-2.7.1.tar.gz (377kB): 377kB downloaded
  Running setup.py egg_info for package jinja2
    
    warning: no files found matching '*' under directory 'custom_fixers'
    warning: no previously-included files matching '*' found under directory 'docs/_build'
    warning: no previously-included files matching '*.pyc' found under directory 'jinja2'
    warning: no previously-included files matching '*.pyc' found under directory 'docs'
    warning: no previously-included files matching '*.pyo' found under directory 'jinja2'
    warning: no previously-included files matching '*.pyo' found under directory 'docs'
Downloading/unpacking markupsafe (from jinja2)
  Downloading MarkupSafe-0.18.tar.gz
  Running setup.py egg_info for package markupsafe
    
Installing collected packages: jinja2, markupsafe
  Running setup.py install for jinja2
    
    warning: no files found matching '*' under directory 'custom_fixers'
    warning: no previously-included files matching '*' found under directory 'docs/_build'
    warning: no previously-included files matching '*.pyc' found under directory 'jinja2'
    warning: no previously-included files matching '*.pyc' found under directory 'docs'
    warning: no previously-included files matching '*.pyo' found under directory 'jinja2'
    warning: no previously-included files matching '*.pyo' found under directory 'docs'
  Running setup.py install for markupsafe
    
    building 'markupsafe._speedups' extension
    gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/u/mkrumhol/yt-x86_64/include/python2.7 -c markupsafe/_speedups.c -o build/temp.linux-x86_64-2.7/markupsafe/_speedups.o
    gcc -pthread -shared -L/u/mkrumhol/yt-x86_64/lib/ -L/u/mkrumhol/yt-x86_64/lib64/ -L/u/mkrumhol/yt-x86_64/lib/ -L/u/mkrumhol/yt-x86_64/lib64/ -L/u/mkrumhol/yt-x86_64/lib/ -L/u/mkrumhol/yt-x86_64/lib64/ -L/u/mkrumhol/yt-x86_64/lib/ -L/u/mkrumhol/yt-x86_64/lib64/ build/temp.linux-x86_64-2.7/markupsafe/_speedups.o -o build/lib.linux-x86_64-2.7/markupsafe/_speedups.so
Successfully installed jinja2 markupsafe
Cleaning up...


So far so good. Then I can then start the ipython notebook and get further than I did before, but I again get a crash:

(yt-x86_64)pfe20:hmc3_mhd_lowden mkrumhol$ ipython notebook --no-browser --port=51707
2013-09-18 14:47:12.782 [NotebookApp] Using existing profile dir: u'/home3/mkrumhol/.ipython/profile_default'
2013-09-18 14:47:12.956 [NotebookApp] Using MathJax from CDN: http://cdn.mathjax.org/mathjax/latest/MathJax.js
2013-09-18 14:47:12.998 [NotebookApp] The port 51707 is already in use, trying another random port.
2013-09-18 14:47:12.998 [NotebookApp] The port 51708 is already in use, trying another random port.
2013-09-18 14:47:12.998 [NotebookApp] Serving notebooks from local directory: /nobackupp8/mkrumhol/hmc3_mhd_lowden
2013-09-18 14:47:12.998 [NotebookApp] The IPython Notebook is running at: http://127.0.0.1:51709/
2013-09-18 14:47:12.999 [NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[NotebookApp] Kernel started: 5434ad94-81be-46ad-80e1-fa9a820411f8
[NotebookApp] Connecting to: tcp://127.0.0.1:37756
[NotebookApp] Connecting to: tcp://127.0.0.1:57662
[NotebookApp] Connecting to: tcp://127.0.0.1:38185
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/u/mkrumhol/yt-x86_64/lib/python2.7/site-packages/IPython/zmq/ipkernel.py", line 55, in <module>
    from serialize import serialize_object, unpack_apply_message
  File "/u/mkrumhol/yt-x86_64/lib/python2.7/site-packages/IPython/zmq/serialize.py", line 35, in <module>
    from IPython.utils.pickleutil import can, uncan, canSequence, uncanSequence
ImportError: cannot import name canSequence

--
Mark Krumholz







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