[yt-users] Problem with Rockstar in yt

[Sam Skillman]

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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