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@gmail.com> wrote:
Hi Bruno,
On Mon, Sep 15, 2014 at 7:58 PM, Bruno Villasenor <br1villasen@gmail.com> 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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