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 <bernhardt.phd@gmail.com> wrote:
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>:
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 <bernhardt.phd@gmail.com> 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 <bernhardt.phd@gmail.com> 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
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-- 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
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-- 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
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-- Carla Bernhardt PhD Student Universität Heidelberg ZAH Institut für Theoretische Astrophysik