Mailman 3 September 2021 - yt-users

website not available?
by Slavin, Jonathan Sept. 15, 2021

Sept. 15, 2021

Hi, It seems that yt-project.org is unreachable right now. Is that others' experience? Jon -- Jonathan D. Slavin Astrophysicist - High Energy Astrophysics Division Center for Astrophysics | Harvard & Smithsonian Office: (617) 496-7981 | Cell: (781) 363-0035 60 Garden Street | MS 83 | Cambridge, MA 02138

2 1

Re: Rockstar is not working
by Nick Gnedin Sept. 10, 2021

Sept. 10, 2021

Britton, Actually, your suggestion does not work: File "rs-hfc.py", line 19, in <module> ts.unit_registry.add("h", 0.6814, dimensionless) P010 yt : [ERROR ] 2021-09-09 10:23:11,397 AttributeError: 'DatasetSeries' object has no attribute 'unit_registry' Here is my script (based on your suggestion from a couple of years back): sets = glob.glob(root+"/"+dir+"/rei20c1_a*/*.art") sets.sort() ts = yt.DatasetSeries(sets) ts.unit_registry.add("h", 0.6814, … [View More]dimensionless) rh = HaloCatalog(data_ds=ts, finder_method='rockstar', finder_kwargs={"num_readers":n, "num_writers":4, "outbase":root+"/"+dir+"/rstest1", "particle_type":"N-BODY_0", "particle_mass":yt.YTQuantity(5.02229e+06,"Msun/h")}) rh.create() del rh del ts On 9/9/2021 9:01 AM, Britton Smith wrote: > Hi Nick, > > Rockstar wants particle masses in units of Msun/h, so it's trying to do > that conversion. If your dataset doesn't have h defined, you can do > something like this: > > from unyt.dimensions import dimensionless > > ds = yt.load(...) > ds.unit_registry.add("h", VALUE, dimensionless) > > Hopefully, that does the trick. > > Britton > > > On Tue, Sep 7, 2021 at 8:57 PM Nick Gnedin <gnedin(a)fnal.gov > <mailto:gnedin@fnal.gov>> wrote: > > > Britton, > > You were right, when I updated yt and yt_astro_analysis to the latest > versions (and downgraded matplotlib to circumvent the matplotlib._png > bug), Rockstar now runs, but I encounter a unit error: > > File "rs-hfc.py", line 21, in <module> > rh.create() > File "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis > ... > File > "/data/gnedin/soft/anaconda3/envs/yt/lib/python3.8/site-packages/unyt/unit_object.py", > > line 972, in _get_unit_data_from_expr > return _lookup_unit_symbol(unit_expr.name > <https://urldefense.proofpoint.com/v2/url?u=http-3A__unit-5Fexpr.name&d=DwMF…>, > unit_symbol_lut) > File > "/data/gnedin/soft/anaconda3/envs/yt/lib/python3.8/site-packages/unyt/unit_registry.py", > > line 330, in _lookup_unit_symbol > raise UnitParseError( > P011 yt : [ERROR ] 2021-09-07 14:39:16,965 UnitParseError: Could not > find unit symbol 'h' in the provided symbols. > > I removed any reference to h in my script, so I am flabbergasted by > that > error. Here is my script: > > import yt, yt.funcs > import glob, sys, os.path > yt.enable_parallelism() > from yt.extensions.astro_analysis.halo_analysis import HaloCatalog > > root = > "/data/gnedin/REI/D/Cai.B20.N128L2.sf=1_uv=0.15_bw=10_res=100.WC1" > n = 16 > dirs = ( "A", ) > for dir in dirs: > sets = glob.glob(root+"/"+dir+"/rei20c1_a*/*.art") > sets.sort() > ts = yt.DatasetSeries(sets) > rh = HaloCatalog(data_ds=ts, finder_method='rockstar', > finder_kwargs={"num_readers":n, "num_writers":4, > "outbase":root+"/"+dir+"/rscor", "particle_type":"N-BODY_0", > "particle_mass":yt.YTQuantity(5.02229e+06/0.6814,"Msun")}) > rh.create() > del rh > del ts > ## > > > Nick > > > On 9/6/2021 10:00 AM, Britton Smith wrote: > > Hi Nick, > > > > I was not able to reproduce this error using the latest dev yt and > > yt_astro_analysis installed. The call to ytcfg.get looks > correct to me. > > The error looks to me like the older yt config parser syntax, so > the yt > > installation may be out of date. > > > > Britton > > > > On Thu, Sep 2, 2021 at 1:40 AM Nick Gnedin <gnedin(a)fnal.gov > <mailto:gnedin@fnal.gov> > > <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov>>> wrote: > > > > > > Folks, > > > > I am trying to run rockstar using your instructions on > > > > > https://yt-astro-analysis.readthedocs.io/en/latest/halo_finding.html#rockst… > <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.…> > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.… <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.…>> > > > > and I am getting the following error almost immediately: > > > > Traceback (most recent call last): > > File "rs-hfc.py", line 24, in <module> > > hc.create() > > File > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py", > > > > line 333, in create > > self._run(save_halos, save_output, > > File > > > "/data/gnedin/soft/anaconda3/lib/python3.8/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", > > > > line 301, in barrierize > > return func(*args, **kwargs) > > File > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py", > > > > line 224, in _run > > self.finder_method(self) > > File > > > "/home/gnedin/ART/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 > > > "/home/gnedin/ART/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 > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py", > > > > line 214, in __init__ > > self.runner = InlineRunner() > > File > > > "/home/gnedin/ART/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 > > > "/data/gnedin/soft/anaconda3/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 > > > > Nick Gnedin > > > > > > -- > > This email has been checked for viruses by AVG. > > https://www.avg.com > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c…> > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c… <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c…>> > > > > _______________________________________________ > > yt-users mailing list -- yt-users(a)python.org > <mailto:yt-users@python.org> > > <mailto:yt-users@python.org <mailto:yt-users@python.org>> > > To unsubscribe send an email to yt-users-leave(a)python.org > <mailto:yt-users-leave@python.org> > > <mailto:yt-users-leave@python.org > <mailto:yt-users-leave@python.org>> > > https://mail.python.org/mailman3/lists/yt-users.python.org/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.python.org_mailma…> > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.python.org_mailma… <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.python.org_mailma…>> > > Member address: brittonsmith(a)gmail.com > <mailto:brittonsmith@gmail.com> <mailto:brittonsmith@gmail.com > <mailto:brittonsmith@gmail.com>> > > > -- This email has been checked for viruses by AVG. https://www.avg.com [View Less]

2 1

Re: Rockstar is not working
by Nick Gnedin Sept. 9, 2021

Sept. 9, 2021

Britton, Thank you so much. I wonder why it happens now - it does work with my previous installation of yt ('3.7.dev0'). I am using ARTIO frontend that does have h defined. Nick On 9/9/2021 9:01 AM, Britton Smith wrote: > Hi Nick, > > Rockstar wants particle masses in units of Msun/h, so it's trying to do > that conversion. If your dataset doesn't have h defined, you can do > something like this: > > from unyt.dimensions import dimensionless > > ds = yt.… [View More]load(...) > ds.unit_registry.add("h", VALUE, dimensionless) > > Hopefully, that does the trick. > > Britton > > > On Tue, Sep 7, 2021 at 8:57 PM Nick Gnedin <gnedin(a)fnal.gov > <mailto:gnedin@fnal.gov>> wrote: > > > Britton, > > You were right, when I updated yt and yt_astro_analysis to the latest > versions (and downgraded matplotlib to circumvent the matplotlib._png > bug), Rockstar now runs, but I encounter a unit error: > > File "rs-hfc.py", line 21, in <module> > rh.create() > File "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis > ... > File > "/data/gnedin/soft/anaconda3/envs/yt/lib/python3.8/site-packages/unyt/unit_object.py", > > line 972, in _get_unit_data_from_expr > return _lookup_unit_symbol(unit_expr.name > <https://urldefense.proofpoint.com/v2/url?u=http-3A__unit-5Fexpr.name&d=DwMF…>, > unit_symbol_lut) > File > "/data/gnedin/soft/anaconda3/envs/yt/lib/python3.8/site-packages/unyt/unit_registry.py", > > line 330, in _lookup_unit_symbol > raise UnitParseError( > P011 yt : [ERROR ] 2021-09-07 14:39:16,965 UnitParseError: Could not > find unit symbol 'h' in the provided symbols. > > I removed any reference to h in my script, so I am flabbergasted by > that > error. Here is my script: > > import yt, yt.funcs > import glob, sys, os.path > yt.enable_parallelism() > from yt.extensions.astro_analysis.halo_analysis import HaloCatalog > > root = > "/data/gnedin/REI/D/Cai.B20.N128L2.sf=1_uv=0.15_bw=10_res=100.WC1" > n = 16 > dirs = ( "A", ) > for dir in dirs: > sets = glob.glob(root+"/"+dir+"/rei20c1_a*/*.art") > sets.sort() > ts = yt.DatasetSeries(sets) > rh = HaloCatalog(data_ds=ts, finder_method='rockstar', > finder_kwargs={"num_readers":n, "num_writers":4, > "outbase":root+"/"+dir+"/rscor", "particle_type":"N-BODY_0", > "particle_mass":yt.YTQuantity(5.02229e+06/0.6814,"Msun")}) > rh.create() > del rh > del ts > ## > > > Nick > > > On 9/6/2021 10:00 AM, Britton Smith wrote: > > Hi Nick, > > > > I was not able to reproduce this error using the latest dev yt and > > yt_astro_analysis installed. The call to ytcfg.get looks > correct to me. > > The error looks to me like the older yt config parser syntax, so > the yt > > installation may be out of date. > > > > Britton > > > > On Thu, Sep 2, 2021 at 1:40 AM Nick Gnedin <gnedin(a)fnal.gov > <mailto:gnedin@fnal.gov> > > <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov>>> wrote: > > > > > > Folks, > > > > I am trying to run rockstar using your instructions on > > > > > https://yt-astro-analysis.readthedocs.io/en/latest/halo_finding.html#rockst… > <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.…> > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.… <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.…>> > > > > and I am getting the following error almost immediately: > > > > Traceback (most recent call last): > > File "rs-hfc.py", line 24, in <module> > > hc.create() > > File > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py", > > > > line 333, in create > > self._run(save_halos, save_output, > > File > > > "/data/gnedin/soft/anaconda3/lib/python3.8/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", > > > > line 301, in barrierize > > return func(*args, **kwargs) > > File > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py", > > > > line 224, in _run > > self.finder_method(self) > > File > > > "/home/gnedin/ART/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 > > > "/home/gnedin/ART/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 > > > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py", > > > > line 214, in __init__ > > self.runner = InlineRunner() > > File > > > "/home/gnedin/ART/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 > > > "/data/gnedin/soft/anaconda3/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 > > > > Nick Gnedin > > > > > > -- > > This email has been checked for viruses by AVG. > > https://www.avg.com > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c…> > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c… <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c…>> > > > > _______________________________________________ > > yt-users mailing list -- yt-users(a)python.org > <mailto:yt-users@python.org> > > <mailto:yt-users@python.org <mailto:yt-users@python.org>> > > To unsubscribe send an email to yt-users-leave(a)python.org > <mailto:yt-users-leave@python.org> > > <mailto:yt-users-leave@python.org > <mailto:yt-users-leave@python.org>> > > https://mail.python.org/mailman3/lists/yt-users.python.org/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.python.org_mailma…> > > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.python.org_mailma… <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.python.org_mailma…>> > > Member address: brittonsmith(a)gmail.com > <mailto:brittonsmith@gmail.com> <mailto:brittonsmith@gmail.com > <mailto:brittonsmith@gmail.com>> > > > -- This email has been checked for viruses by AVG. https://www.avg.com [View Less]

1 0

Re: Rockstar is not working
by Nick Gnedin Sept. 9, 2021

Sept. 9, 2021

Britton, You were right, when I updated yt and yt_astro_analysis to the latest versions (and downgraded matplotlib to circumvent the matplotlib._png bug), Rockstar now runs, but I encounter a unit error: File "rs-hfc.py", line 21, in <module> rh.create() File "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis ... File "/data/gnedin/soft/anaconda3/envs/yt/lib/python3.8/site-packages/unyt/unit_object.py", line 972, in _get_unit_data_from_expr return … [View More]_lookup_unit_symbol(unit_expr.name, unit_symbol_lut) File "/data/gnedin/soft/anaconda3/envs/yt/lib/python3.8/site-packages/unyt/unit_registry.py", line 330, in _lookup_unit_symbol raise UnitParseError( P011 yt : [ERROR ] 2021-09-07 14:39:16,965 UnitParseError: Could not find unit symbol 'h' in the provided symbols. I removed any reference to h in my script, so I am flabbergasted by that error. Here is my script: import yt, yt.funcs import glob, sys, os.path yt.enable_parallelism() from yt.extensions.astro_analysis.halo_analysis import HaloCatalog root = "/data/gnedin/REI/D/Cai.B20.N128L2.sf=1_uv=0.15_bw=10_res=100.WC1" n = 16 dirs = ( "A", ) for dir in dirs: sets = glob.glob(root+"/"+dir+"/rei20c1_a*/*.art") sets.sort() ts = yt.DatasetSeries(sets) rh = HaloCatalog(data_ds=ts, finder_method='rockstar', finder_kwargs={"num_readers":n, "num_writers":4, "outbase":root+"/"+dir+"/rscor", "particle_type":"N-BODY_0", "particle_mass":yt.YTQuantity(5.02229e+06/0.6814,"Msun")}) rh.create() del rh del ts ## Nick On 9/6/2021 10:00 AM, Britton Smith wrote: > Hi Nick, > > I was not able to reproduce this error using the latest dev yt and > yt_astro_analysis installed. The call to ytcfg.get looks correct to me. > The error looks to me like the older yt config parser syntax, so the yt > installation may be out of date. > > Britton > > On Thu, Sep 2, 2021 at 1:40 AM Nick Gnedin <gnedin(a)fnal.gov > <mailto:gnedin@fnal.gov>> wrote: > > > Folks, > > I am trying to run rockstar using your instructions on > > https://yt-astro-analysis.readthedocs.io/en/latest/halo_finding.html#rockst… > <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.…> > > and I am getting the following error almost immediately: > > Traceback (most recent call last): > File "rs-hfc.py", line 24, in <module> > hc.create() > File > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py", > > line 333, in create > self._run(save_halos, save_output, > File > "/data/gnedin/soft/anaconda3/lib/python3.8/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", > > line 301, in barrierize > return func(*args, **kwargs) > File > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py", > > line 224, in _run > self.finder_method(self) > File > "/home/gnedin/ART/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 > "/home/gnedin/ART/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 > "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py", > > line 214, in __init__ > self.runner = InlineRunner() > File > "/home/gnedin/ART/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 > "/data/gnedin/soft/anaconda3/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 > > Nick Gnedin > > > -- > This email has been checked for viruses by AVG. > https://www.avg.com > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c…> > > _______________________________________________ > yt-users mailing list -- yt-users(a)python.org > <mailto:yt-users@python.org> > To unsubscribe send an email to yt-users-leave(a)python.org > <mailto:yt-users-leave@python.org> > https://mail.python.org/mailman3/lists/yt-users.python.org/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.python.org_mailma…> > Member address: brittonsmith(a)gmail.com <mailto:brittonsmith@gmail.com> > [View Less]

2 1

How to change the center of a plot without changing the coordinate
by Karen Yang Sept. 8, 2021

Sept. 8, 2021

Hi! This seems to be a simple task but I didn't manage to find an answer in the threads. Sorry if I missed something obvious. I was trying to to plot a slice shifted along the z-axis from the center of the simulation domain. Say the center of the simulation domain is (0,0,0). Doing p = yt.SlicePlot(ds, 'x', 'density', width=20) p.set_center(0., 10.) would yield the region I want. However, the coordinate in the resulting plot would show z ranges of (-10, 10) instead of the original … [View More]

3 4

Rockstar is not working
by Nick Gnedin Sept. 6, 2021

Sept. 6, 2021

Folks, I am trying to run rockstar using your instructions on https://yt-astro-analysis.readthedocs.io/en/latest/halo_finding.html#rockst… and I am getting the following error almost immediately: Traceback (most recent call last): File "rs-hfc.py", line 24, in <module> hc.create() File "/home/gnedin/ART/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py", line 333, in create self._run(save_halos, save_output, File "/data/gnedin/soft/… [View More]

2 1