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/00527…
--
------------------------------------------------------------------------
Joseph Smidt <josephsmidt(a)gmail.com>
Theoretical Division
P.O. Box 1663, Mail Stop B283
Los Alamos, NM 87545
Office: 505-665-9752
Fax: 505-667-1931
