[yt-users] rockstar exception message
Bruno Villasenor Alvarez
cobaltscience at gmail.com
Fri Sep 19 07:40:49 PDT 2014
Hi Ben,
I don't have the parameter file that you mention, do yo have one that I could use as a template or do you know where can I get one?.
Thanks.
-Bruno
On Sep 19, 2014, at 7:31 AM, B.W. Keller <kellerbw at mcmaster.ca> wrote:
> 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
> >
> > _______________________________________________
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