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

Mon Nov 4 17:37:40 PST 2013

Sam: Yep, I am definitely sending the infiniband-disabling flags and
running it as follows

mpirun -np 48 --mca btl ^openib python halos.py --parallel

Cameron: I had originally switched to rockstar from HOP because I couldn't
get it to run on kraken due to (very clear) out of memory issues. I suppose
that since I've switched supercomputers anyway, I might as well play around
with HOP again.

On Mon, Nov 4, 2013 at 5:57 PM, Sam Skillman <samskillman at gmail.com> wrote:

> 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
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>>>>
>>>
>>>
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>>
>>
>> --
>> Cameron Hummels
>> Postdoctoral Researcher
>> Steward Observatory
>> University of Arizona
>> http://chummels.org
>>
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