[yt-users] rockstar exception message
B.W. Keller
kellerbw at mcmaster.ca
Fri Sep 19 05:31:56 PDT 2014
Hi Bruno,
Do you have a parameter file sitting in the same directory as your binary
TIPSY file? Usually, yt will read the mass/length units from a parameter
file as the parameters:
dKpcUnit = SOMETHING
dMsolUnit = SOMETHING
Ben
On Fri, Sep 19, 2014 at 2:08 AM, Bruno Villasenor <br1villasen at gmail.com>
wrote:
> 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
>>>>> >
>>>>> > _______________________________________________
>>>>> > yt-users mailing list
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>>>>> >
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