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.

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 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:

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

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.

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
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Carla Bernhardt
PhD Student
Universität Heidelberg
ZAH Institut für Theoretische Astrophysik
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--
Carla Bernhardt
PhD Student
Universität Heidelberg
ZAH Institut für Theoretische Astrophysik
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--
Carla Bernhardt
PhD Student
Universität Heidelberg
ZAH Institut für Theoretische Astrophysik
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--
Carla Bernhardt
PhD Student
Universität Heidelberg
ZAH Institut für Theoretische Astrophysik
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--
Carla Bernhardt
PhD Student
Universität Heidelberg
ZAH Institut für Theoretische Astrophysik
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--
Carla Bernhardt
PhD Student
Universität Heidelberg
ZAH Institut für Theoretische Astrophysik
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--
Carla Bernhardt
PhD Student
Universität Heidelberg
ZAH Institut für Theoretische Astrophysik
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