[yt-users] reading Gadget-HDF5 format in yt-3.0

[Matthew Turk]

Hi Brendan,

Thanks for writing.

On Thu, Sep 26, 2013 at 9:41 PM, Brendan Griffen
<brendan.f.griffen at gmail.com> wrote:
> Hi,
>
> I noticed in the update log of yt-3.0 you can now read Gadget HDF5 format
> (for OWLS project), but it is possible for Rockstar to read the exact same
> formats? I have some HDF5 data and I'd like to run Rockstar on it through yt
> if it has this capability in 3.0.

Good question!  So there are a couple of things to address in this.

The first is that of the HDF5 formats for reading data.  I have issued
a pull request, with Desika Narayanan's help, to add support for
Gadget HDF5 data files, which are subtly different than the OWLS data
files.  I would *very* much appreciate it if you could help by testing
this out.  You can do so by doing:

cd $YT_DEST/src/yt-hg   # or wherever "yt instinfo" tells you, if you
have run the install script
hg pull -r d996eff https://bitbucket.org/MatthewTurk/yt-3.0
hg up -r d996eff
python2.7 setup.py build_ext -i -f

This will update you to that version of the code, and you should now
be able to execute this command:

from yt.mods import *
ds = load("gadget_filename.hdf5")

Things like projecting and analyzing particles and so on should now
work.  *Please* let us know if this works for your data, and if so,
click on the "approve" button or leave a comment on the pull request:

https://bitbucket.org/yt_analysis/yt-3.0/pull-request/99/implement-gadget-hdf5-and-some-helpful/diff

I think we really only need one more external tester (Desika has
tested it) and we can bring it in.

The second thing is about Rockstar.  I've been working on a pull
request against my fork of Rockstar (
http://bitbucket.org/MatthewTurk/rockstar ) that enables deeper and
better yt integration; these changes have been submitted upstream so
hopefully I won't need a fork for much longer and we can all go back
to tarballs of R*.

I've been testing this in my bookmark "rockstar_work" (which I haven't
merged with HDF5-gadget work, sorry!) and I am getting weird results.
The process is working, but the halo masses are scaled incorrectly and
I am going to be investigating units to figure out the problem.  This
is actually a regression, as it had previously well, and I will be
investigating it in more detail.  I hope to have some results shortly.

Let me know if you get a chance to check the Gadget-HDF5, and
hopefully by then I'll have the Rockstar stuff up and running!

-Matt

>
> Are there any examples of carrying out such a process? Thanks.
>
> Thanks.
>
> Brendan
>
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