[yt-dev] Issue #1188: Trouble Getting Started with yt (yt_analysis/yt)

Joseph Smidt josephsmidt at gmail.com
Thu Mar 17 20:35:07 PDT 2016


> Here is a link to notebook 2 in the quickstart, in python script form:

So for whatever reason none of my students nor myself recognized that.
But now that I know this, this summer I will tell the new students
about the non-notebook links at the bottom.  So thanks.

That said, it wasn't a huge loss since I knew from experience that
basically everything they needed to learn had examples in the
cookbook/main documentation and had the advantage of "just working" in
the terminals they were doing everything else in.

> did you try 'yt notebook' and it didn't work either?

Unfortunately, LANL's firewalls seem to block the -LXXXX:...:XXXX
capability for ssh.  Maybe if I was smart I could figure a work around
but so far I have not.

But it looks like you all are going to make the documentation more
clear how to do the quickstart if you don't have access to notebooks
so that will be great come the summer.  Thanks!


On Thu, Mar 17, 2016 at 9:23 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>
>
> On Thu, Mar 17, 2016 at 8:19 PM, Joseph Smidt <josephsmidt at gmail.com> wrote:
>>
>> For what it's worth, last year I had summer students who simulated
>> large datasets (Enzo) that had to stay on the LANL machine they were
>> simulated on and ipython notebooks were not available as LANL
>> restricts web-browsers on their production machines.
>>
>> Long story short, all documentation that required a notebook to run
>> were inaccessible to these students.  If the intro documentation could
>> be rewritten so that it can also run in a terminal without a notebook
>> that would be nice.
>
>
> So this exists, but we just don't make a huge deal about it. In fact all of
> the notebooks in the documentation have a "download as python script"
> option.
>
> Here is a link to notebook 2 in the quickstart, in python script form:
>
> http://yt-project.org/docs/dev/quickstart/2)_Data_Inspection.py
>
> I think it would be possible to clean these up a bit and display them more
> prominently, or even provide alternate versions that are explicitly set up
> to be run as scripts.
>
> We should also probably make a bigger deal on the quickstart page that all
> of the code in the notebooks themselves (with the exception of the show()
> methods of yt plot objects, which I'd really like to not only work in the
> notebook but alas that's the status quo) do not require notebooks, and is
> runnable in a normal python or terminal IPython session.
>
>>
>>
>> On Thu, Mar 17, 2016 at 6:16 PM, Matthew Turk <matthewturk at gmail.com>
>> wrote:
>> > There's a lot of information in this ticket, and I wanted to highlight
>> > it for folks on the dev list that might otherwise filter these out.
>> > Sadly, the person who left it hasn't left any contact info.  But, that
>> > doesn't mean that it can't be synthesized into a plan of action,
>> > particularly for improving documentation, 2D data, and so on.  One
>> > important thing, which I personally hadn't realized is a problem, is
>> > the repeated mentions that non-notebook access should be emphasized.
>> >
>> > On Thu, Mar 17, 2016 at 6:45 PM, Anonymous <issues-reply at bitbucket.org>
>> > wrote:
>> >> New issue 1188: Trouble Getting Started with yt
>> >>
>> >> https://bitbucket.org/yt_analysis/yt/issues/1188/trouble-getting-started-with-yt
>> >>
>> >> Anonymous:
>> >>
>> >> I'm a new user to yt and I've been having a really frustrating time
>> >> getting started. I work with large simulations and have been using VisIt for
>> >> 2D data. I want to switch to yt but the frustration of just trying to get it
>> >> to run almost made me quit and go back to VisIt.
>> >>
>> >> My first problem was figuring out how to start yt at all. I went to the
>> >> quickstart guide, but all it told me to do was run a bunch of ipython
>> >> notebooks. Nowhere did it mention that yt can just be imported into python
>> >> like any other module and run from there, which would have saved me a lot of
>> >> time and trouble. I don't know how to run an ipython notebook; I've never
>> >> used them before. I eventually figured out how to create one, but then I had
>> >> to access it remotely. All my data resides on the filesystem of the
>> >> supercomputer where it was calculated. It's not feasible to fetch it to my
>> >> local machine, especially not when I'm generating new data much faster than
>> >> I could transfer it. So analysis needs to run on the viz node. Eventually I
>> >> got a notebook to connect (needed to set up an ssh tunnel apparently) but it
>> >> was really annoying to work through. I may be a programmer by profession,
>> >> but I don't often deal with web stuff, and all of this setup is
>> >> badly-explained when it's explai
>>  n
>> >  ed
>> >>   at all
>> >>  on the relevant websites. Like I said, this could have been avoided if
>> >> the quickstart guide had ever mentioned that I could just import it and work
>> >> with it like any other python module instead of diving straight into
>> >> notebooks.
>> >>
>> >> I got lost for a while in the fact that there seems to be two sets of
>> >> documentation for ipython notebooks - ipython, but then jupyter? All the
>> >> recent documentation on notebooks is written for jupyter, but that's not
>> >> installed on my viz node and yt's docs don't say anything about it. So that
>> >> also confused the heck out of me for a little while.
>> >>
>> >> The cookbook recipes are also real confusing if you're working with 2D
>> >> data. Nearly everything is written assuming you have a 3D dataset. I had to
>> >> mess around a bit before I figured out that you could do a SlicePlot with a
>> >> 2D dataset as long as you specify a slice axis that does not, technically,
>> >> exist. ProjectionPlot is really what should be used for 2D data but the name
>> >> makes it non-obvious that that's what you want.
>> >>
>> >> yt itself is great and I'd really like to use it. I understand that a
>> >> lot of the devs and members of the community work with things like bitbucket
>> >> and ipython notebooks on a daily basis, but I spend most of my time tackling
>> >> 30-year-old Fortran and I'm certainly not the only one. I have enough
>> >> trouble just getting these simulations to run in the first place; there's no
>> >> room in my workflow for me to devote large chunks of time to unraveling the
>> >> visualization software. Programs like VisIt and EnSuite might be balky and
>> >> obscenely expensive, but in general you can turn them on, click a button,
>> >> open your data, and get a simple picture in a few minutes. Please overhaul
>> >> the "quickstart" guides so that it's easier for someone like me who has
>> >> python and matplotlib experience but no notebook experience to just turn the
>> >> dang thing on and make a picture with a minimum of fuss.
>> >>
>> >>
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>>
>>
>> --
>> ------------------------------------------------------------------------
>> Joseph Smidt <josephsmidt at gmail.com>
>>
>> Theoretical Division
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-- 
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Joseph Smidt <josephsmidt at gmail.com>

Theoretical Division
P.O. Box 1663, Mail Stop B283
Los Alamos, NM 87545
Office: 505-665-9752
Fax:    505-667-1931



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