[yt-users] rockstar exception message
Bruno Villasenor
br1villasen at gmail.com
Thu Sep 18 23:08:40 PDT 2014
Hi Hilary,
Fist, thank you very much for your help, I really appreciate it.
Sorry for the delay, the dataset took a while to upload.
Here is a dropbok link to the dataset I'm using, its a TIPSY binary file,
you can also find the the most fundamental version of my code there:
https://www.dropbox.com/sh/tgtd3b57jkpvyjc/AACnx4QFO99TxUpF2qadXMDWa?dl=0
I think that the problem is that I'm not setting the mass and length
conversion factors for the TipsyDataset correctly (I haven't figured out
how to do this).
Again, thanks a lot for your help, let me know if I can help with something
else.
-Bruno
2014-09-18 15:07 GMT-05:00 Hilary Egan <hilaryye at gmail.com>:
> 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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