Hi Carla, I apologize for this, there is a necessary line missing from the documentation. After this line: es = yt.load_simulation(sys.argv[1], "Enzo", find_outputs=True) you need to add the following: es.get_time_series() I will correct the documentation as soon as possible. Sorry for the delay and the inconvenience. Britton On Thu, Apr 22, 2021 at 6:01 PM C Bernhardt <bernhardt.phd@gmail.com> wrote:
Hi Britton,
I apologize for the slow response. Another tech guy on my server managed to get yt installed from source and linked it with the yt_astro_analysis from source. When I try to run a simple rockstar analysis:
import sys,yt
from yt.extensions.astro_analysis.halo_analysis import HaloCatalog
yt.enable_parallelism()
es = yt.load_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()
When the script gets to "hc.create()", this error arises: "AttributeError: 'EnzoSimulation' object has no attribute 'kwargs'". This is coming from yt/data_objects/time_series.py. I looked at the code with our tech guy and I agree with him that kwargs may not be properly defined. Here is the full series of calls <https://pastebin.com/kDeUDpRX>.
Has anyone here run rockstar with yt and yt_astro_analysis from source? Does it work for you??
Best, Carla
Am Mo., 12. Apr. 2021 um 12:19 Uhr schrieb Britton Smith < brittonsmith@gmail.com>:
Hi Carla,
I'm sorry to hear that. The last stable releases of both yt and yt_astro_analysis should work together. If you start from a fresh conda environment and do: pip install yt pip install yt-astro-analysis
that should give you the older version. Unfortunately, I'm unable to provide a version of the yt-astro documentation from that version. You can build that locally if you do the following in a different conda environment:
git clone https://github.com/yt-project/yt_astro_analysis git checkout yt_astro_analysis-1.0.0 pip install -e .[dev] cd doc make html
If you then open the file in your yt-astro repo doc/build/html/index.html in a web browser, you'll get the old docs.
Britton
On Mon, Apr 12, 2021 at 9:46 AM C Bernhardt <bernhardt.phd@gmail.com> wrote:
Hi Britton,
Thanks for all your help. I have now tried several times and ways of installing yt from source and had no success, even our IT support couldn't make it work. Is there a way I can go to an older version of rockstar to be able to use it with the stable version of yt? I still want to resolve the original issue of not getting small enough halos ...
Thanks, Carla
Am Mo., 29. März 2021 um 17:03 Uhr schrieb Britton Smith < brittonsmith@gmail.com>:
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 <bernhardt.phd@gmail.com> 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 <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 >>>>> >>>> _______________________________________________ >>>> 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
_______________________________________________ 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