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

Mon Nov 4 16:57:21 PST 2013

Cameron -- My experience has been that HOP/FOF are slow on datasets this
large, and PHOP uses a large amount of memory.  Anyways, regardless of that
we should figure out what is going on with rockstar given its use in the
community.

Hilary -- Just to be clear, you are sending the infiniband-disabling flags
to this last run, correct?

On Mon, Nov 4, 2013 at 4:36 PM, Cameron Hummels <chummels at gmail.com> wrote:

> 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
>>> yt-users at lists.spacepope.org
>>> 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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