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

Mon Nov 4 16:36:21 PST 2013

Are you tied to using rockstar?  I know yt works well with HOP, PHOP, and
FOF without many problems...

On Mon, Nov 4, 2013 at 3:50 PM, Hilary Egan <hilaryye at gmail.com> wrote:

> 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
>> _______________________________________________
>> yt-users mailing list
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>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>
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-- 
Cameron Hummels
Postdoctoral Researcher
Steward Observatory
University of Arizona
http://chummels.org
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