Hi Joseph,
Thanks for writing. Having been on SC viz papers, and also seeing
both the stage-front and back-stage of doing press releases, etc, I
can definitely see how this could happen!
When I initially saw the paper, my feelings were a bit hurt -- it felt
like yt was being "punched down" at. After time and reflection my
personal feelings on it mellowed, but I still feel like there was a
missed opportunity for a deeper collaboration. Figuring out how to
bring the different types of communities together (particularly since
the means of production of software in the two relevant communities
are so vastly different) would be an interesting opportunity, but it
felt like that was sidestepped here.
I'm not going to respond *here* to the point-by-point items you note
above, but I will end by saying that I do think that there's a bigger
conversation we should have, and that until folks in the yt community
can have a discussion about the flaws *without* getting defensive when
those flaws are held up to other software packages (and I'm talking
about myself here -- I am *not* referring to anyone else) we will be
limited in our growth opportunities.
I want to end by noting something else. You mention that some of us
work with Alex -- that's true! And in fact, it was during group
meeting that I discovered this paper, and mentioned it, sharing my
annoyance with how it discussed yt. I privately apologized to Alex
afterward and intended to do so in our subsequent group meeting. I
will replicate my apology here:
"Hey Alex, I realized that maybe I was a bit too harsh yesterday about
that paper. I actually didn't really feel like it was that bad.
People write papers -- they don't always say the stuff the people
they're talking about would want them to. It's how it goes. I didn't
need to be such a jerkwad about it. It was pretty inappropriate, and
facetious or not, it was rude and uncalled for on my part. I think I
reacted because I felt like they were "punching down" but on
reflection, that turned into *me* "punching down" in a way that caught
you up in the middle."
-Matt
On Mon, Apr 8, 2019 at 10:40 AM Joseph Smidt <josephsmidt@gmail.com> wrote:
>
> Hey everyone,
>
> This tweet [1] was brought to my attention. There is good criticism in that thread so let me respond:
>
> 1. It is ridiculous the YT paper is not cited. It defiantly was last I checked. How that was dropped is beyond me. I will make sure that is somehow fixed.
>
> 2. The "single slice plot of a single time step took 13 minutes" is also misleading and is a mistake that I will make sure is somehow corrected. I ran the simulations and wrote those sections and someone else ran the plotting routines - who is admittedly a Paraview developer - and I should have checked this text more closely. They were running both YT and Paraview from their Apple Macbook. The 13 minutes was how long it took that Macbook to volume render the dump versus Paraview, also running on a Macbook but using an HPC set of nodes in the backend. It's a feature of Paraview that you can do this.
>
> Thus it is very misleading, I am embarrassed I missed it, and will make sure it is corrected.
>
> 3. That said, there are some real deficiencies in YT for HPC-class datasets
>
> - The ability to overlay several variables using different color schemes on the same plot. There are times when having a temperature field and metallically field - for example - overlaying a density field is helpful. This was mentioned in the paper.
>
> - The ability to volume render interactively until you get a plot exactly how you want it. With YT you have to keep running a script over and over again until it looks right. With paraview - even with a 26 Tb dump on our classified systems - files can be open and rotated and modified in real time to be exactly how you want in like 5 minutes. This was the cumbersome comment.
>
> - Paraview's ability to open up a huge file - again, we have a 26 terabyte file on our classified side we used Paraview - and let the clusters do all the work in minutes from the comfort of your personal Macbook. A file that YT was unable to ever fit in memory for volume rendering no matter how many nodes we tried. This failure was not mentioned in the paper, even though some working with such huge datsets may be interested.
>
> - Another omission from the paper is we did the same thing with gadget data, that is arguably used more than Enzo. Long story short, YT could never volume render the data, a known issue for at least 5 years [2], whereas paraview both reads and volume renders gadget data natively. Again, there is no reason to point this out in print even though some would be interested.
>
> - The issue with Paraview not reading Enzo natively was true at the time of the analysis but is no longer true. There is a development version by the above developer that reads Enzo.
>
> - Some of you work with Alex Gagliano. Though he has been working on this water network, he has nothing to do with how any of this paper is worded. Please do not give him grief for what is in it. He has a future paper on the subject and I guarantee these problems will not be repeated.
>
> Anyway, I think YT is a fine product. I use it almost every day and encourage all students to use it. I am embarrassed this was lost from the paper and will work to restore it. But at the same time, to deny that Paraview comes with many advantages - especially as the world becomes more huge 3D TB sized datasets - is a little naive.
>
>
> [1] https://twitter.com/njgoldbaum/status/1113163672120119298
>
> [2] http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2014-June/005272.html
>
> --
> ------------------------------------------------------------------------
> Joseph Smidt <josephsmidt@gmail.com>
>
> Theoretical Division
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