[yt-users] rockstar exception message
Bruno Villasenor
br1villasen at gmail.com
Thu Sep 18 12:22:56 PDT 2014
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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>> > yt-users at lists.spacepope.org
>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >
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