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

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

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

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

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

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

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

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

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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

Hi Carla, I'm out of ideas for what could be the cause of this lack of halos. It could be an issue with the initial conditions or the simulation. It's hard to say without knowing more about the simulation setup. Britton On Mon, Jun 14, 2021 at 10:58 AM C Bernhardt <bernhardt.phd@gmail.com> wrote:

Hi Britton (and yt-users),

Thanks for your help on this a few months back. Your last email finally got things working with rockstar.

However, even after redoing the rockstar analysis, then redoing the simulation itself and the rockstar analysis, I am still finding there seems to be some lower limit to finding halos below 1e+8 Msun/h. I get the same range of smallest halos whether I have a particle mass of 8.41072e+06 Msun/h or 1.31418e+05 Msun/h. The smallest halo I see in any output is about 1.4e+08 Msun/h. What could possibly be preventing me from finding smaller halos?

Thanks, Carla

Am Do., 29. Apr. 2021 um 13:19 Uhr schrieb Britton Smith < brittonsmith@gmail.com>:

...

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

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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