On Thu, Sep 16, 2021 at 2:39 PM Nick Gnedin <gnedin@fnal.gov> wrote:

Britton,

I tried your methods 1 and 2 and RS (Rockstar-Galaxies Version:
0.99.9-RC3-newA) runs with both to the end. However, I discovered a
weird thing - the actual value for the particle mass has no effect. I
ran it both with the default value and with the changed value, both
values are correctly listed in corresponding out_0.list files:
#Particle mass: 4.22991e+06 Msun/h [default value]
#Particle mass: 5.02229e+06 Msun/h [assigned correct value]

However, the produced mass functions are the same in both runs, and they
differ by the OmegaM/OmegaDM factor (the ratio of
5.02229e+06/4.22991e+06) from the mass function that I consider correct
(obtained with the old RS (Rockstar Version: 0.99.9-RC3) as implemented
in yt '3.7.dev0' in yt.analysis_modules.halo_finding.rockstar.api, which
also agrees with the analytical fit from hmf.py).

Perhaps yt sets the RS particle mass correctly but feeds the actual
particle data with the default mass?

Nick

On 9/10/2021 4:51 AM, Britton Smith wrote:
> Hi Nick,
>
> Thanks for sending the script; I can see why my solution didn't work.
> The time series object does not have a unit registry like a loaded
> dataset. I issued a pull request to yt_astro_analysis which should fix
> this by allowing you to do what you should have been able to all along.
> https://github.com/yt-project/yt_astro_analysis/pull/84
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_yt-2Dproject_yt-5Fastro-5Fanalysis_pull_84&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=B-7bLI_gVkNbVTTL6WLE_jBPCCUxcykB81atg_VPNZk&s=W5CyZgXekUT6Tj6afPdEBapaE3i0lR5cnwbDmUCiaoU&e=>
>
> With this PR, you can now give the particle mass in three ways:
> 1. as a regular float. This will assume units of Msun/h. This was the
> original way that was broken and should now be fixed again.
> 2. as a tuple of (value, unit) for example (5.02229e+06,"Msun/h").
> 3. as a unyt_quantity
>
> To make the 3rd option work, you would do
> ts[0].quan(5.02229e+06,"Msun/h"), since ts[0] will be the first dataset.
> The first two should work as is.
>
> Let me know if this works and I'll get the PR merged.
>
> Britton
>
> On Thu, Sep 9, 2021 at 4:25 PM Nick Gnedin <gnedin@fnal.gov
> <mailto:gnedin@fnal.gov>> wrote:
>
>
> 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, 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@fnal.gov
> <mailto:gnedin@fnal.gov>
> > <mailto:gnedin@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=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=B-7bLI_gVkNbVTTL6WLE_jBPCCUxcykB81atg_VPNZk&s=2_fGkJLumDq8tWLAVMj7QFVdHuAKvqfJdzqYGdfURJk&e=>
> >
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__unit-5Fexpr.name&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=cMSuy1wk_MnvGpsaSr0UGNuBY7jsbP9G0peOd1GSxxo&s=fQnOScv-s6bWFuDrdnIHjeC3QNVz06iWIzq9luu8NMY&e= <https://urldefense.proofpoint.com/v2/url?u=http-3A__unit-5Fexpr.name&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=cMSuy1wk_MnvGpsaSr0UGNuBY7jsbP9G0peOd1GSxxo&s=fQnOScv-s6bWFuDrdnIHjeC3QNVz06iWIzq9luu8NMY&e=>>,
> > 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@fnal.gov <mailto:gnedin@fnal.gov>
> > <mailto:gnedin@fnal.gov <mailto:gnedin@fnal.gov>>
> > > <mailto:gnedin@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#rockstar-galaxies
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.readthedocs.io_en_latest_halo-5Ffinding.html-23rockstar-2Dgalaxies&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=B-7bLI_gVkNbVTTL6WLE_jBPCCUxcykB81atg_VPNZk&s=rioH0Z4sPMCDJmzXuh6042cebm2-lT_STAfR_16PT7M&e=>
> >
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.readthedocs.io_en_latest_halo-5Ffinding.html-23rockstar-2Dgalaxies&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=cMSuy1wk_MnvGpsaSr0UGNuBY7jsbP9G0peOd1GSxxo&s=9YZq_c61MCYtqrvrjbgYZdjNx1lLYQheFyuRa6YIf_Q&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.readthedocs.io_en_latest_halo-5Ffinding.html-23rockstar-2Dgalaxies&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=cMSuy1wk_MnvGpsaSr0UGNuBY7jsbP9G0peOd1GSxxo&s=9YZq_c61MCYtqrvrjbgYZdjNx1lLYQheFyuRa6YIf_Q&e=>>
> > >
> >
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.readthedocs.io_en_latest_halo-5Ffinding.html-23rockstar-2Dgalaxies&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=91a-YxIolKtcnV0IqQEf1J21gbPSR5m03nK26IzbbmU&s=zkLfKb5t7rANzwoPnoBa3eM_eYdF_1zIuOiSO4ALaDY&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.readthedocs.io_en_latest_halo-5Ffinding.html-23rockstar-2Dgalaxies&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=91a-YxIolKtcnV0IqQEf1J21gbPSR5m03nK26IzbbmU&s=zkLfKb5t7rANzwoPnoBa3eM_eYdF_1zIuOiSO4ALaDY&e=> <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.readthedocs.io_en_latest_halo-5Ffinding.html-23rockstar-2Dgalaxies&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=91a-YxIolKtcnV0IqQEf1J21gbPSR5m03nK26IzbbmU&s=zkLfKb5t7rANzwoPnoBa3eM_eYdF_1zIuOiSO4ALaDY&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.readthedocs.io_en_latest_halo-5Ffinding.html-23rockstar-2Dgalaxies&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=91a-YxIolKtcnV0IqQEf1J21gbPSR5m03nK26IzbbmU&s=zkLfKb5t7rANzwoPnoBa3eM_eYdF_1zIuOiSO4ALaDY&e=>>>
> > >
> > > 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.
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> > >
> >
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=91a-YxIolKtcnV0IqQEf1J21gbPSR5m03nK26IzbbmU&s=a1Qa5dFGi8B4e2_dD7eGB_nlkGuO5Zvb9dpFAQBr8hk&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=91a-YxIolKtcnV0IqQEf1J21gbPSR5m03nK26IzbbmU&s=a1Qa5dFGi8B4e2_dD7eGB_nlkGuO5Zvb9dpFAQBr8hk&e=> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=91a-YxIolKtcnV0IqQEf1J21gbPSR5m03nK26IzbbmU&s=a1Qa5dFGi8B4e2_dD7eGB_nlkGuO5Zvb9dpFAQBr8hk&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.avg.com&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=91a-YxIolKtcnV0IqQEf1J21gbPSR5m03nK26IzbbmU&s=a1Qa5dFGi8B4e2_dD7eGB_nlkGuO5Zvb9dpFAQBr8hk&e=>>>
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> > > Member address: brittonsmith@gmail.com
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> > >
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>
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