[yt-users] rockstar exception message
Nathan Goldbaum
nathan12343 at gmail.com
Thu Sep 18 09:40:54 PDT 2014
Looks like Hillary just opened a PR to fix this:
https://bitbucket.org/yt_analysis/yt/pull-request/1213/bugfix-catch-no-halos-found-error-before/diff
Bruno if you could test this, that would be great. Let us know if you have
any questions about how to locally test a pull request.
On Thursday, September 18, 2014, Matthew Turk <matthewturk at gmail.com> wrote:
> Hi Bruno,
>
> On Mon, Sep 15, 2014 at 7:58 PM, Bruno Villasenor <br1villasen at gmail.com
> <javascript:;>> wrote:
> > Hi all,
> >
> > I'm trying to run the RockstarHaloFinder via the HaloCatalog function on
> a
> > TIPSY file.
> > When I run the HaloCatalog function I get the following rockstar output:
> >
> > ########################################################################
> > P002 yt : [INFO ] 2014-09-15 19:36:11,382 Rockstar is using 1 readers
> > and 1 writers
> > P000 yt : [INFO ] 2014-09-15 19:36:11,382 The citation for the
> Rockstar
> > halo finder can be found at
> > P001 yt : [INFO ] 2014-09-15 19:36:11,382 Rockstar is using 1 readers
> > and 1 writers
> > P000 yt : [INFO ] 2014-09-15 19:36:11,382
> > http://adsabs.harvard.edu/abs/2013ApJ...762..109B
> > P000 yt : [INFO ] 2014-09-15 19:36:11,383 Rockstar is using 1 readers
> > and 1 writers
> > P001 yt : [WARNING ] 2014-09-15 19:36:41,582 Total Particle Count:
> > 4.862e+07
> > [ 0s] Accepting connections...
> > [ 1s] Accepted all reader / writer connections.
> > [ 1s] Verified all reader / writer connections.
> > [ 1s] Transmitted all client connection info.
> > [ 2s] Reading 1 blocks for snapshot 0...
> > Exception yt.utilities.exceptions.YTFieldNotFound: YTFieldNotFound() in
> >
> 'yt.analysis_modules.halo_finding.rockstar.rockstar_interface.rh_read_particles'
> > ignored
> > [ 2s] Transferring particles to writers...
> > [ 2s] Analyzing for FoF groups...
> > [ 2s] Transferring boundary particles between writers...
> > [ 2s] Linking boundary particles...
> > [ 3s] Analyzing for halos / subhalos...
> > [ 3s] Loading merger tree information...
> > [ 3s] Constructing merger tree...
> > [ 3s] [Success] Done with snapshot 0.
> > [ 3s] [Finished]
> > #######################################################################
> >
> > followed by the next YT output
> >
> > #######################################################################
> > P001 yt : [INFO ] 2014-09-15 19:36:44,986 Parameters: current_time
> > = 2.44801700503e+17 s
> > P001 yt : [INFO ] 2014-09-15 19:36:44,987 Parameters:
> domain_dimensions
> > = [2 2 2]
> > P000 yt : [INFO ] 2014-09-15 19:36:44,994 Parameters: current_time
> > = 2.44801700503e+17 s
> > P000 yt : [INFO ] 2014-09-15 19:36:44,994 Parameters:
> domain_dimensions
> > = [2 2 2]
> > P000 yt : [INFO ] 2014-09-15 19:36:44,994 Parameters:
> domain_left_edge
> > = [ 0. 0. 0.]
> > P000 yt : [INFO ] 2014-09-15 19:36:45,012 Parameters:
> domain_right_edge
> > = [ 0.00207136 0.00207136 0.00207136]
> > P000 yt : [INFO ] 2014-09-15 19:36:45,013 Parameters:
> > cosmological_simulation = 1
> > P000 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters:
> current_redshift
> > = 0.6
> > P001 yt : [INFO ] 2014-09-15 19:36:44,987 Parameters:
> domain_left_edge
> > = [ 0. 0. 0.]
> > P000 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters: omega_lambda
> > = 0.699999988079
> > P000 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters: omega_matter
> > = 0.300000011921
> > P000 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters: hubble_constant
> > = 0.699999988079
> > P001 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters:
> domain_right_edge
> > = [ 0.00207136 0.00207136 0.00207136]
> > P001 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters:
> > cosmological_simulation = 1
> > P001 yt : [INFO ] 2014-09-15 19:36:45,015 Parameters:
> current_redshift
> > = 0.6
> > P001 yt : [INFO ] 2014-09-15 19:36:45,015 Parameters: omega_lambda
> > = 0.699999988079
> > P001 yt : [INFO ] 2014-09-15 19:36:45,015 Parameters: omega_matter
> > = 0.300000011921
> > P001 yt : [INFO ] 2014-09-15 19:36:45,015 Parameters: hubble_constant
> > = 0.699999988079
> > P000 yt : [INFO ] 2014-09-15 19:36:45,070 Allocating for 0.000e+00
> > particles
> > P001 yt : [INFO ] 2014-09-15 19:36:45,070 Allocating for 0.000e+00
> > particles
> > P002 yt : [INFO ] 2014-09-15 19:36:45,070 Allocating for 0.000e+00
> > particles
> > Traceback (most recent call last):
> > File "simple_rockstar.py", line 44, in <module>
> > Traceback (most recent call last):
> > File "simple_rockstar.py", line 44, in <module>
> > Traceback (most recent call last):
> > File "simple_rockstar.py", line 44, in <module>
> > hc.create()
> > File
> >
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",
> > line 297, in create
> > hc.create()
> > File
> >
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",
> > line 297, in create
> > hc.create()
> > File
> >
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",
> > line 297, in create
> > self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic)
> > File
> >
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
> > line 248, in barrierize
> > self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic)
> > self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic)
> > File
> >
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
> > line 248, in barrierize
> > File
> >
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
> > line 248, in barrierize
> > retval = func(*args, **kwargs)
> > File
> >
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",
> > line 367, in _run
> > self.halos_ds.index
> > AttributeError: 'NoneType' object has no attribute 'index'
> > retval = func(*args, **kwargs)
> > File
> >
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",
> > line 367, in _run
> > self.halos_ds.index
> > retval = func(*args, **kwargs)
> > AttributeError: 'NoneType' object has no attribute 'index'
> > File
> >
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",
> > line 367, in _run
> > self.halos_ds.index
> > AttributeError: 'NoneType' object has no attribute 'index'
>
> This does indeed look like an internal error. It looks to me like the
> halos_ds is not being created -- even if R* finds something, I think
> this should be created. Britton and/or Hilary, have you seen this
> error before?
>
> -Matt
>
> >
> #######################################################################################
> >
> > It seems to me like rockstar is not finding anything (Exception message)
> and
> > then when yt load and save to disk it fails.
> > The simplest working version of my code is the next one:
> >
> >
> #######################################################################################
> > import yt
> > from yt.mods import *
> > from yt.analysis_modules.halo_analysis.api import HaloCatalog
> > from yt.data_objects.particle_filters import add_particle_filter
> > from mpi4py import MPI
> > import numpy as np
> >
> > dataDir = "/home/bruno/Desktop/data/yt/"
> > dataFile = 'DM.Only.tipsy/dwf1.6144.01280'
> > ts = DatasetSeries([dataDir + dataFile])
> > data_ds = ts[0]
> > #data_ds = yt.load( dataDir + dataFile )
> > data_ds.set_units( )
> >
> > #Add symbol "Mpccm"
> > data_ds.unit_registry.add( 'Mpccm',
> > float(units.Mpc.in_cgs().v),
> > units.dimensions.length)
> >
> > #Create particle filter to filter to filter a single mass particle type
> > def low_mass(pfilter, data):
> > filter = data["all", "Mass"] < 1.3e-12 * units.Msun
> > return filter
> > add_particle_filter("low_mass", function=low_mass,
> > filtered_type='all',
> > requires=["Mass"])
> > data_ds.add_particle_filter("low_mass")
> >
> > #Set cosmology parameters
> > data_ds.hubble_constant = 0.7
> > data_ds.omega_matter = 0.3
> > data_ds.current_redshift = 0.6
> > data_ds.omega_lambda = 0.7
> >
> > #Arguments for RockstarHoloFinder
> > rockstar_kwargs = {
> > 'particle_type': 'low_mass',
> > 'force_res': 1e-4 #100pc
> > }
> >
> > hc = HaloCatalog(data_ds=data_ds,
> > finder_method='rockstar',
> > finder_kwargs = rockstar_kwargs)
> > hc.create()
> > ##################################################################
> >
> > If someone has any suggestion I would really appreciate it.
> >
> > Thanks,
> > Bruno
> >
> > _______________________________________________
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> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
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