[yt-users] Running Rockstar Halo Finder to create a merger tree

[John Wise]

Hi Hilary,

On 10/29/2013 12:30 PM, Hilary Egan wrote:

> I'm quite confused on a number of points related to running the rockstar
> halo finder, so I hope its alright that I put all these questions into
> this one email!

It's no problem at all to include all of your questions in a single 
email.  It's probably better this way!

> 1. I can't seem to run the rockstar halo finder at all without getting
> this error followed by a segmentation fault and crash.
>
> [Warning] Network IO Failure (PID XXXXXX): Connection reset by peer
> [Network] Packet receive retry count at: 1
>
> It sort of seems like this issue
> (http://lists.spacepope.org/htdig.cgi/yt-dev-spacepope.org/2012-November/002681.html)
> but I couldn't really figure out what the resolution was from the
> thread. Im attempting to run this on kraken and it doesn't matter if I
> use a single compute node or multiple, I get the same error. (I hope
> this isn't the infiniband issue the docs warned about, I couldn't figure
> out if that is how kraken is connected and I got an error that the
> suggested flag doesn't exist so I didn't press the issue.)

I haven't seen that error before, but I still have to specific to *not* 
run on infiniband when running Rockstar on a single node.  With OpenMPI, 
you would use "mpirun -n 32 --mca btl ^openib ...", but I haven't done 
this on kraken with their aprun but hopefully it's easily accompolished!

> 2. Whenever I finally do get the halo finder to work, I need the results
> to be in a form that the merger tree can use. It seems as though the
> MergerTree needs the results in the same form as the other halo finders
> give, so would getting the halo list and then dumping it as usual be the
> appropriate strategy? Ie:
>
>          rh.run()
>          halo_list = rh.halo_list()
> halo_list.dump('MergerHalos')
>
> 2.5. The docs sort of give mixed messages on whether or not I could just
> be calling MergerTree with the argument halo_finder_function =
> RockstarHaloFinder. At this point I've pretty thoroughly convinced
> myself that I can't, but it would be nice if that was clarified. (Just a
> thoroughly overwhelmed new user's perspective!)

I'm not sure whether you can use yt's merger tree code with the Rockstar 
halos.  I haven't tried.

However, I've used Consistent Trees

https://code.google.com/p/consistent-trees/

with Rockstar's halo lists, which is also written by Peter Behroozi. 
I've chosen this route because the algorithm seems to be more physically 
robust in constructing parent/child relationships and boundness.  All of 
the instructions are in the README of the code, and it's pretty 
straightforward and fast (probably 5-10 minutes for a 512^3 simulation 
with 60 outputs) to run.

I also have a visualizing script for consistent tree's output.

https://bitbucket.org/jwise77/rockstar-dot

 From consistent tree's output, you can use the provided script, 
halo_trees_to_catalog.pl, (instructions also in the README) to convert 
the tree output into halo lists.

> 3. I'm a little confused as to whether or not I have to use a
> TimeSeriesData object rather than the usual single time output when
> instantiating the halo finder. Under "Rockstar Halo Finding" it uses
> TimeSeriesData, unlike the rest of the examples, but under the
> subheading "Output Analysis" it just uses pf. The "Output Analysis"
> example also doesn't call the run() method, which leads me to believe
> something else entirely is going on, but its not quite clear.

This actually came up recently.  It's best to supply a TimeSeriesData 
object.  Here's the link to the email for more details.

http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-August/003845.html

Cheers,
John

-- 
John Wise
Assistant Professor of Physics
Center for Relativistic Astrophysics, Georgia Tech
http://cosmo.gatech.edu