[yt-users] Problem with Rockstar in yt

Brian O'Shea bwoshea at gmail.com
Mon Aug 5 09:57:17 PDT 2013 

Hi Sam, all,

This fixed the problem - thank you!

--Brian



On Mon, Aug 5, 2013 at 9:54 AM, Sam Skillman <samskillman at gmail.com> wrote:

> Err, just to be clear, keep the pf = load(...) line in there before the ts
> = TimeSeriesData([pf]) line.
>
>
> On Mon, Aug 5, 2013 at 8:52 AM, Sam Skillman <samskillman at gmail.com>wrote:
>
>> Hi Brian,
>>
>> I think what is going on here is that the Rockstar HF expects a
>> TimeSeries object.  If you change
>>
>> pf = load("DD0057/data0057")
>> rh = RockstarHaloFinder(pf)
>>
>> to
>>
>> ts = TimeSeriesData([pf])
>> rh = RockstarHaloFinder(ts)
>> rh.run()
>>
>> I think it should work.  Also just for reference, I think Daegene is
>> correct that Rockstar requires at least 3 processors.
>>
>> Best,
>> Sam
>>
>>
>> On Sun, Aug 4, 2013 at 8:20 PM, Brian O'Shea <bwoshea at gmail.com> wrote:
>>
>>> Hi Daegone,
>>>
>>> Sorry, I think my last email was imprecise: after that first email, I am
>>> now running in parallel on 4 processors, using the command line:
>>>
>>> mpirun -np 4 python ./test_rockstar.py --parallel
>>>
>>> Rockstar gives a similar error both running on a single core (with
>>> mpirun) and in parallel.  :-(
>>>
>>> --Brian
>>>
>>>
>>>
>>> On Sun, Aug 4, 2013 at 8:57 PM, Daegene Koh <dkoh30 at gatech.edu> wrote:
>>>
>>>> Hi Brian,
>>>>
>>>> If I recall correctly, I believe you need at least 3 processors to get
>>>> Rockstar running properly. And it must always be run in parallel.
>>>> I'm afraid I don't know much much more beyond that.
>>>>
>>>> Cheers,
>>>> DK
>>>>
>>>> On Aug 4, 2013, at 7:54 PM, "Brian O'Shea" <bwoshea at gmail.com> wrote:
>>>>
>>>> Hi folks,
>>>>
>>>> Just a quick followup: I've now run this on a different machine and
>>>> verified that the reason I couldn't use Rockstar in parallel was due to a
>>>> MPI problem.  *HOWEVER*, I still have the same Rockstar error that I was
>>>> reporting before when I was using one core (all using the same script as in
>>>> my previous email):
>>>>
>>>> http://paste.yt-project.org/show/3747/
>>>>
>>>> So, it does seem like there is a bug, or I am simply using Rockstar
>>>> incorrectly...
>>>>
>>>> --Brian
>>>>
>>>>
>>>>
>>>> On Sun, Aug 4, 2013 at 6:26 PM, Brian O'Shea <bwoshea at gmail.com> wrote:
>>>>
>>>>> Dear yt-users,
>>>>>
>>>>> I'm trying to use the Rockstar halo finder within yt, and am
>>>>> encountering some odd problems.  I'm using the main development tree (
>>>>> https://bitbucket.org/yt_analysis/yt) with changeset f936432ed45d,
>>>>> and attempting to use Rockstar to find halos on a small server running
>>>>> Ubuntu 12.04.  When I call this script:
>>>>>
>>>>> ---- file test_rockstar.py ----
>>>>>
>>>>> from yt.mods import *
>>>>> from yt.analysis_modules.halo_finding.rockstar.api import
>>>>> RockstarHaloFinder
>>>>>
>>>>> pf = load("DD0057/data0057")
>>>>> rh = RockstarHaloFinder(pf)
>>>>>
>>>>> ---
>>>>>
>>>>> using the command line sequence "mpirun -np 2 python
>>>>> ./test_rockstar.py --parallel", I seem to be getting a seg fault (as can be
>>>>> seen at http://paste.yt-project.org/show/3745/).  However, if I use a
>>>>> single processor (with "mpirun -np 1 python ./test_rockstar.py
>>>>> --parallel"), I get a very different error:
>>>>>
>>>>> Traceback (most recent call last):
>>>>>   File "./test_rockstar.py", line 6, in <module>
>>>>>     rh = RockstarHaloFinder(pf)
>>>>>   File
>>>>> "/data/bwoshea/galparttest/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py",
>>>>> line 230, in __init__
>>>>>     self.pool, self.workgroup = self.runner.setup_pool()
>>>>>   File
>>>>> "/data/bwoshea/galparttest/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py",
>>>>> line 112, in setup_pool
>>>>>     (self.num_writers, "writers") ]
>>>>>   File
>>>>> "/data/bwoshea/galparttest/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
>>>>> line 335, in from_sizes
>>>>>     pool.add_workgroup(size, name = name)
>>>>>   File
>>>>> "/data/bwoshea/galparttest/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
>>>>> line 303, in add_workgroup
>>>>>     group = self.comm.comm.Get_group().Incl(ranks)
>>>>> AttributeError: 'NoneType' object has no attribute 'Get_group'
>>>>>
>>>>> I'm puzzled about the error, since I can use other parallel yt scripts
>>>>> without any problems (a 4-processor script making projections works just
>>>>> fine).  This machine doesn't have infiniband (as warned about at
>>>>> http://yt-project.org/doc/analysis_modules/running_halofinder.html#rockstar-halo-finding),
>>>>> and both FOF and Hop find several hundred halos with my dataset.  I'd just
>>>>> use another halo finder, but I'm trying to do something that requires
>>>>> Rockstar to be run inline with Enzo, so I'm stuck with it...
>>>>>
>>>>> Does anybody have any idea what might be going on?
>>>>>
>>>>> Thanks!
>>>>>
>>>>> Brian
>>>>>
>>>>>
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