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

Kacper Kowalik xarthisius.kk at gmail.com
Thu Mar 17 20:06:39 PDT 2016


On 03/17/2016 08:19 PM, Joseph Smidt 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.

Hi Joseph,
out of curiosity: did you try 'yt notebook' and it didn't work either? 
That extension was created specifically to ease up running ipython 
notebooks in "hostile" environments.
Cheers,
Kacper

> 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.
>
>
>
> 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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