[yt-users] rockstar exception message

Hilary Egan hilaryye at gmail.com
Thu Sep 18 13:07:11 PDT 2014


Hi Bruno,

I'm not able to recreate you issue with any of my test datasets, so having
access to some of your data might make debugging a little bit easier. If
you could share a test dataset (via dropbox, google drive, etc), I'll take
a look at this!

-Hilary

On Thu, Sep 18, 2014 at 1:22 PM, Bruno Villasenor <br1villasen at gmail.com>
wrote:

> Hi,
>
> I just tested the change and it works fine, this is the new output
>
> ########################################
> P000 yt : [INFO     ] 2014-09-18 13:55:50,652
> http://adsabs.harvard.edu/abs/2013ApJ...762..109B
> P002 yt : [INFO     ] 2014-09-18 13:55:50,652 Rockstar is using 1 readers
> and 1 writers
> P001 yt : [INFO     ] 2014-09-18 13:55:50,652 Rockstar is using 1 readers
> and 1 writers
> P000 yt : [INFO     ] 2014-09-18 13:55:50,652 Rockstar is using 1 readers
> and 1 writers
> P001 yt : [WARNING  ] 2014-09-18 13:55:50,719 Total Particle Count:
> 3.154e+05
> [     0s] Accepting connections...
> [     1s] Accepted all reader / writer connections.
> [     1s] Verified all reader / writer connections.
> [     1s] Transmitted all client connection info.
> [     1s] 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...
> [     2s] Analyzing for halos / subhalos...
> [     3s] Loading merger tree information...
> [     3s] Constructing merger tree...
> [     3s] [Success] Done with snapshot 0.
> [     3s] [Finished]
> P001 yt : [INFO     ] 2014-09-18 13:55:53,597 Parameters: current_time
>          = 2.44801700503e+17 s
> P001 yt : [INFO     ] 2014-09-18 13:55:53,597 Parameters:
> domain_dimensions         = [2 2 2]
> P001 yt : [INFO     ] 2014-09-18 13:55:53,597 Parameters: domain_left_edge
>          = [ 0.  0.  0.]
> P001 yt : [INFO     ] 2014-09-18 13:55:53,598 Parameters:
> domain_right_edge         = [  1.12666939e+23   1.12666939e+23
> 1.12666939e+23]
> P001 yt : [INFO     ] 2014-09-18 13:55:53,598 Parameters:
> cosmological_simulation   = 1
> P001 yt : [INFO     ] 2014-09-18 13:55:53,598 Parameters: current_redshift
>          = 0.6
> P001 yt : [INFO     ] 2014-09-18 13:55:53,598 Parameters: omega_lambda
>          = 0.699999988079
> P001 yt : [INFO     ] 2014-09-18 13:55:53,598 Parameters: omega_matter
>          = 0.300000011921
> P001 yt : [INFO     ] 2014-09-18 13:55:53,599 Parameters: hubble_constant
>           = 0.699999988079
> P000 yt : [INFO     ] 2014-09-18 13:55:53,603 Parameters: current_time
>          = 2.44801700503e+17 s
> P000 yt : [INFO     ] 2014-09-18 13:55:53,604 Parameters:
> domain_dimensions         = [2 2 2]
> P000 yt : [INFO     ] 2014-09-18 13:55:53,604 Parameters: domain_left_edge
>          = [ 0.  0.  0.]
> P000 yt : [INFO     ] 2014-09-18 13:55:53,605 Parameters:
> domain_right_edge         = [  1.12666939e+23   1.12666939e+23
> 1.12666939e+23]
> P000 yt : [INFO     ] 2014-09-18 13:55:53,605 Parameters:
> cosmological_simulation   = 1
> P000 yt : [INFO     ] 2014-09-18 13:55:53,605 Parameters: current_redshift
>          = 0.6
> P000 yt : [INFO     ] 2014-09-18 13:55:53,605 Parameters: omega_lambda
>          = 0.699999988079
> P000 yt : [INFO     ] 2014-09-18 13:55:53,605 Parameters: omega_matter
>          = 0.300000011921
> P000 yt : [INFO     ] 2014-09-18 13:55:53,605 Parameters: hubble_constant
>           = 0.699999988079
> P000 yt : [INFO     ] 2014-09-18 13:55:53,614 Allocating for 0.000e+00
> particles
> P002 yt : [INFO     ] 2014-09-18 13:55:53,615 Allocating for 0.000e+00
> particles
> P001 yt : [INFO     ] 2014-09-18 13:55:53,615 Allocating for 0.000e+00
> particles
> P000 yt : [WARNING  ] 2014-09-18 13:55:53,618 No halos were found for
> galaxy.00300
> P002 yt : [WARNING  ] 2014-09-18 13:55:53,619 No halos were found for
> galaxy.00300
> P000 yt : [INFO     ] 2014-09-18 13:55:53,619 Saving halo catalog (0
> halos) to halo_catalogs/catalog/catalog.
> P002 yt : [INFO     ] 2014-09-18 13:55:53,619 Saving halo catalog (0
> halos) to halo_catalogs/catalog/catalog.
> P001 yt : [WARNING  ] 2014-09-18 13:55:53,623 No halos were found for
> galaxy.00300
> P001 yt : [INFO     ] 2014-09-18 13:55:53,623 Saving halo catalog (0
> halos) to halo_catalogs/catalog/catalog.
> ###################################################
>
>
> Thanks a lot for the quick fix.
>
> There's something else, I don't understand why Rockstar is not finding any
> halos. (when I use "hop finder_method" it finds a bunch of them),
> does the exception message below means that the finder is looking for
> something that I should be creating for a TipsyDataset?
> ########################################
> Exception yt.utilities.exceptions.YTFieldNotFound: YTFieldNotFound() in
> 'yt.analysis_modules.halo_finding.rockstar.rockstar_interface.rh_read_particles'
> ignored
> ########################################
>
> I'm an undergraduate student who just very recently started using yt, so
> if someone has any suggestion I will really appreciate it.
>
> Thanks in advance.
>
> Best Regards
> Bruno
>
>
>
> 2014-09-18 11:40 GMT-05:00 Nathan Goldbaum <nathan12343 at gmail.com>:
>
> 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>
>>> 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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>>> >
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