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

[Hilary Egan]

Hi all,

I'm still having trouble getting rockstar to run on my dataset. I've moved
my data to a different super computer that uses the mpirun command rather
than kraken's aprun so that I could make sure there aren't any infiniband
issues, but Im still seeing similar issues. I've also determined I can run
the halo finder just fine on a smaller test dataset, which is leading me to
believe that its some sort of memory issue, but I can't quite figure out
how I would go about fixing it. I've tried playing with the number of
readers and the number of nodes I'm running on, to no avail. For reference,
the dataset is a 1024^3 unigrid enzo run. If anyone has any suggestions,
I'd love to hear them!

Thanks!
Hilary

Script: http://paste.yt-project.org/show/4025/

Error message: http://paste.yt-project.org/show/4024/


On Wed, Oct 30, 2013 at 8:50 AM, John Wise <jwise at physics.gatech.edu> wrote:

> 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
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