[yt-users] Re: refining rockstar-galaxies halo minimum mass

Hi Carla, The version of rockstar that yt uses is now the latest rockstar-galaxies, which supports multi-mass simulations. You should no longer need to create particle filters to select only the high-resolution particles. The other error you're getting is from a recent change in yt's configuration system. If you update your source yt installation, that should take care of it. If you're not currently using a source installation, there is more information here on that: https://yt-project.org/docs/dev/installing.html#installing-yt-from-source Britton On Mon, Mar 29, 2021 at 1:42 PM C Bernhardt wrote:

Hi Britton,

Thank you for helping me along with this. I don't see much in the documentation on any different approach for using rockstar through the HaloCatalog with nested grids, is there any extra treatment needed (similar to the necessary particle filters [i.e. "enzo_2_dark_matter_nested"] added to RockstarHaloFinder)?

I tried with

es = yt.simulation(sys.argv[1], "Enzo", find_outputs=True)

hc = HaloCatalog(data_ds=es, finder_method='rockstar', finder_kwargs={ "num_readers": 2, "num_writers": 4})

hc.create()

and get this error:

File "/users/carla/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py", line 224, in _run

self.finder_method(self)

File "/users/carla/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_finding_methods.py", line 39, in __call__

return self.function(hc, *self.args, **self.kwargs)

File "/users/carla/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_finding_methods.py", line 87, in _rockstar_method

rh = RockstarHaloFinder(ds, **finder_kwargs)

File "/users/carla/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py", line 214, in __init__

self.runner = InlineRunner()

File "/users/carla/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py", line 44, in __init__

psize = ytcfg.get("yt", "internals", "global_parallel_size")

File "/users/carla/yt/lib/python3.8/site-packages/yt/config.py", line 137, in get

val = super(YTConfigParser, self).get(section, option, *args, **kwargs)

TypeError: get() takes 3 positional arguments but 4 were given

Thanks, Carla

Am Mi., 24. März 2021 um 12:33 Uhr schrieb Britton Smith < brittonsmith@gmail.com>:

...

Hi Carla,

Sorry, the halo finding call and import have changed. You now use the HaloCatalog for all halo finding, including rockstar. It should now look like this: import yt from yt.extensions.astro_analysis.halo_analysis import HaloCatalog

my_sim = yt.load_simulation('enzo_tiny_cosmology/32Mpc_32.enzo', 'Enzo') hc = HaloCatalog(data_ds=my_sim, finder_method='rockstar', finder_kwargs={"num_readers": 1, "num_writers": 1}) hc.create()

See the link below for more info https://yt-astro-analysis.readthedocs.io/en/latest/halo_finding.html

Britton

On Wed, Mar 24, 2021 at 9:57 AM C Bernhardt wrote:

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Hi Britton,

I updated my yt_astro_analysis package, but now I get this error: When trying to run

from yt.extensions.astro_analysis.halo_finding.rockstar.api import RockstarHaloFinder

Traceback (most recent call last):

File "<stdin>", line 1, in <module>

File "/users/carla/yt/lib/python3.8/site-packages/yt/exthook.py", line 88, in load_module

raise ImportError('No module named %s' % fullname)

ImportError: No module named yt.extensions.astro_analysis.halo_finding

My first thought was that yt_astro_analysis wasn't finding my installation of rockstar-galaxies, but I still have the file rockstar.cfg with the correct path to rockstar in my cloned repository of yt_astro_analysis. I am using the rockstar-galaxies repository from John Wise, which did not throw this error before I updated my yt_astro_analysis. Do you use the same repository or the one from Peter Behroozi?

Thanks, Carla

Am Mo., 22. März 2021 um 17:15 Uhr schrieb Britton Smith < brittonsmith@gmail.com>:

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Hi Carla,

Ok, this new version was only merged on Friday, so if you installed before then, you won't have it.

Britton

On Mon, Mar 22, 2021 at 4:09 PM C Bernhardt wrote:

...

Hi Britton,

Thanks for clarifying. I installed yt_astro_analysis as part of the process of installing rockstar-galaxies, so I think this shouldn't be the issue. I did not have this installed in my previous version, so I did not need to worry about older versions getting in the way.

Cheers, Carla

Am Mo., 22. März 2021 um 15:29 Uhr schrieb Britton Smith < brittonsmith@gmail.com>:

...

Hi Carla,

Ok, great. Just to be clear, though, it's not rockstar you need to update, but the yt_astro_analysis package. If you have cloned the repository, you would need to go into it and do:

git pull origin master ./clean.sh pip install -e .

On Mon, Mar 22, 2021 at 2:12 PM C Bernhardt wrote:

> Hi Britton, > > Thanks for the feedback. I updated rockstar-galaxies about a month > ago, but I can try running with fof or hop and see if I get better results. > Thanks. > > Best, > Carla > > Am Mo., 22. März 2021 um 14:00 Uhr schrieb Britton Smith < > brittonsmith@gmail.com>: > >> Hi Carla, >> >> I would have expected some smaller halos, too, but I have no reason >> to believe the halo finder is not doing what it should be. You might try >> using fof or hop instead to see if things change. By the way, the halo >> finders were very recently updated. I would suggest pulling in the latest >> changes. The documentation has also been substantially improved. >> https://yt-astro-analysis.readthedocs.io/en/latest/halo_finding.html >> >> Britton >> >> On Mon, Mar 22, 2021 at 9:36 AM C Bernhardt < >> bernhardt.phd@gmail.com> wrote: >> >>> Hi Britton, >>> >>> Thank you for your reply. Adding the keyword "min_halo_size" >>> changed the parameter in my rockstar config file, but when I redid the >>> analysis, the halo sizes were still larger than expected. With a Particle >>> mass of 1.31418e+05 Msun/h and MIN_HALO_OUTPUT_SIZE = 10, I was >>> expecting to get halos on the order of 1e7 Msun/h. The smallest halos I get >>> now are 1.2e8 Msun/h. Is that reasonable to expect and if so, what do I >>> need to change to see those smaller halos? >>> >>> Thanks, >>> Carla >>> >>> Am Di., 9. März 2021 um 17:08 Uhr schrieb Britton Smith < >>> brittonsmith@gmail.com>: >>> >>>> Hi Carla, >>>> >>>> It looks like RockstarHaloFinder accepts a keyword called >>>> "min_halo_size" which sets the minimum particle number for halos. The >>>> RockstarHaloFinder code writes its own config file, which is then passed to >>>> rockstar itself, so that's why modifying that file by hand doesn't do >>>> anything. >>>> >>>> Britton >>>> >>>> On Mon, Mar 8, 2021 at 9:29 AM C Bernhardt < >>>> bernhardt.phd@gmail.com> wrote: >>>> >>>>> Dear yt and rockstar users, >>>>> >>>>> I recently installed the newest version of rockstar-galaxies as >>>>> I had been using a much older version. Although the output reports a >>>>> particle mass of 1.31418e+05 Msun/h, I don't see any halos smaller than >>>>> 1e+08 Msun/h. I was expecting to get the minimum masses an order of >>>>> magnitude lower. >>>>> >>>>> I see in the config includes MIN_HALO_OUTPUT_SIZE = 25, set as >>>>> a default. I tried to change this parameter to 10 and restart from the >>>>> beginning, but I run rockstar within yt with RockstarHaloFinder ( >>>>> yt.extensions.astro_analysis.halo_finding.rockstar.api), but my >>>>> config file was overwritten by the defaults. Is this even the right >>>>> approach? If so, how do I restart rockstar (more detailed than just >>>>> rh.run(restart=True), please) with customized parameters within >>>>> yt's RockstarHaloFinder? >>>>> >>>>> Thanks in advance, >>>>> -- >>>>> Carla Bernhardt >>>>> PhD Student >>>>> Universität Heidelberg >>>>> ZAH Institut für Theoretische Astrophysik >>>>> _______________________________________________ >>>>> yt-users mailing list -- yt-users@python.org >>>>> To unsubscribe send an email to yt-users-leave@python.org >>>>> https://mail.python.org/mailman3/lists/yt-users.python.org/ >>>>> Member address: brittonsmith@gmail.com >>>>> >>>> _______________________________________________ >>>> yt-users mailing list -- yt-users@python.org >>>> To unsubscribe send an email to yt-users-leave@python.org >>>> https://mail.python.org/mailman3/lists/yt-users.python.org/ >>>> Member address: bernhardt.phd@gmail.com >>>> >>> >>> >>> -- >>> Carla Bernhardt >>> PhD Student >>> Universität Heidelberg >>> ZAH Institut für Theoretische Astrophysik >>> >> _______________________________________________ >> yt-users mailing list -- yt-users@python.org >> To unsubscribe send an email to yt-users-leave@python.org >> https://mail.python.org/mailman3/lists/yt-users.python.org/ >> Member address: bernhardt.phd@gmail.com >> > > > -- > Carla Bernhardt > PhD Student > Universität Heidelberg > ZAH Institut für Theoretische Astrophysik > _______________________________________________ > yt-users mailing list -- yt-users@python.org > To unsubscribe send an email to yt-users-leave@python.org > https://mail.python.org/mailman3/lists/yt-users.python.org/ > Member address: brittonsmith@gmail.com > _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org https://mail.python.org/mailman3/lists/yt-users.python.org/ Member address: bernhardt.phd@gmail.com

-- Carla Bernhardt PhD Student Universität Heidelberg ZAH Institut für Theoretische Astrophysik _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org https://mail.python.org/mailman3/lists/yt-users.python.org/ Member address: brittonsmith@gmail.com

_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org https://mail.python.org/mailman3/lists/yt-users.python.org/ Member address: bernhardt.phd@gmail.com

-- Carla Bernhardt PhD Student Universität Heidelberg ZAH Institut für Theoretische Astrophysik _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org https://mail.python.org/mailman3/lists/yt-users.python.org/ Member address: brittonsmith@gmail.com

_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org https://mail.python.org/mailman3/lists/yt-users.python.org/ Member address: bernhardt.phd@gmail.com

-- Carla Bernhardt PhD Student Universität Heidelberg ZAH Institut für Theoretische Astrophysik _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org https://mail.python.org/mailman3/lists/yt-users.python.org/ Member address: brittonsmith@gmail.com