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

[Hilary Egan]

Hi all,

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!

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.)

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!)

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.

Thanks!
-Hilary
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20131029/306d3c45/attachment.htm>