[yt-users] Problems using Rockstar in yt

Nathan Goldbaum nathan12343 at gmail.com
Thu Aug 14 10:00:16 PDT 2014


This also works:

timeseries = yt.load(glob_pattern, setup_function=setup_ds)


On Thu, Aug 14, 2014 at 6:29 AM, Britton Smith <brittonsmith at gmail.com>
wrote:

> Hi David,
>
> I am not familiar with how particles are distinguished in RAMSES, so I
> couldn't tell you exactly the criteria you could use for filtering.
>  However, if you are asking specifically about how you add a filter to a
> DatasetSeries object, then the key is the setup_function in the above
> example.  You can create a function that accepts a Dataset object, and then
> does whatever you want with it.  Above, this is the "setup_ds" function,
> which is applying the dark matter filter.  You can pass this function
> during the creation of a DatasetSeries object through the "setup_function"
> keyword.  The above example uses a slight variant on the DatasetSeries
> object that currently doesn't work for RAMSES, but you can use the regular
> one:
>
> timeseries = DatasetSeries(..., setup_function=setup_ds)
>
> Britton
>
>
> On Tue, Aug 12, 2014 at 10:53 PM, David Sullivan <D.Sullivan at sussex.ac.uk>
> wrote:
>
>> Hi Britton, all,
>>
>> That took care of my issues, now it’s run successfully. Just one more
>> question: as I’m using RAMSES I create a DatasetSeries using:
>>
>> es = yt.load('../output_*/info_*.txt’)
>> rh = RockstarHaloFinder(es, num_readers=1, num_writers=2)
>>
>> Is there a way for me to add a dark matter only filter as done here for
>> an enzo dataset:
>>
>> # create a particle filter to remove star particles
>> @yt.particle_filter("dark_matter", requires=["creation_time"])
>> def _dm_filter(pfilter, data):
>>         return data["creation_time"] < 0.0
>>
>> def setup_ds(ds):
>>         ds.add_particle_filter("dark_matter”)
>>
>> es = yt.simulation("enzo_tiny_cosmology/32Mpc_32.enzo", "Enzo")
>> es.get_time_series(setup_function=setup_ds, redshift_data=False)
>>
>> rh = RockstarHaloFinder(es, num_readers=1, num_writers=2,
>>                         particle_type="dark_matter")
>>
>> I’ve looked at the docs on particle filtering but I can’t add filters to
>> the DatasetSeries object I have.
>>
>> Many thanks for the help so far!
>> David
>>
>>  On 12 Aug 2014, at 12:44, yt-users-request at lists.spacepope.org wrote:
>>
>> Hi Cameron, David,
>>
>> Cameron, you are correct, on Mac systems you need to set DYLD_LIBRARY_PATH
>> instead of LD_LIBRARY_PATH.  The fact that this causes vi and other things
>> to fail is apparently an OS X bug (I found some discussions of it on the
>> internet) and has nothing to do with yt.  I went through a similar thing
>> and had to resort to having a separate terminal for running rockstar that
>> I
>> didn't try to do anything else in.  For what it's worth, this behavior
>> seems to have been fixed.  I am on OS X 10.8.5 and no longer have the
>> issue
>> of things crashing in a terminal where I have edited DYLD_LIBRARY_PATH.
>>
>> On the second issue that you both reported, the problem is the way in
>> which
>> one tells yt to run in parallel depends on how you import yt.
>>
>> If you do "from yt.mods import *", the parallelism is enabled by adding
>> the
>> --parallel flag on the command line.  However, if you do "import yt", then
>> parallelism is enabled by doing "yt.enable_parallelism()" directly below
>> the import statement within your script.
>>
>> I looked at the latest documentation on parallelism (
>> http://yt-project.org/doc/analyzing/parallel_computation.html) and is
>> discusses the use of yt.enable_parallelism(), but not the old way that
>> works with "from yt.mods import *".  There should probably be a short
>> discussion added of how this has changed.  Additionally, let's make sure
>> that the yt-rockstar docs get any needed additions there as well.
>>
>> Britton
>>
>>
>>
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>>
>
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