[yt-users] Problem with Rockstar in yt

[Sam Skillman]

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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