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' ####################################################################################### 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
Hi Bruno, On Mon, Sep 15, 2014 at 7:58 PM, Bruno Villasenor <br1villasen@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 yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Looks like Hillary just opened a PR to fix this: https://bitbucket.org/yt_analysis/yt/pull-request/1213/bugfix-catch-no-halos... 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@gmail.com> wrote:
Hi Bruno,
On Mon, Sep 15, 2014 at 7:58 PM, Bruno Villasenor <br1villasen@gmail.com <javascript:;>> 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 yt-users@lists.spacepope.org <javascript:;> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <javascript:;> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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...
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@gmail.com> wrote:
Hi Bruno,
On Mon, Sep 15, 2014 at 7:58 PM, Bruno Villasenor <br1villasen@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 yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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@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...
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@gmail.com> wrote:
Hi Bruno,
On Mon, Sep 15, 2014 at 7:58 PM, Bruno Villasenor <br1villasen@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 yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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@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@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...
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@gmail.com> wrote:
Hi Bruno,
On Mon, Sep 15, 2014 at 7:58 PM, Bruno Villasenor < br1villasen@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 yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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@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@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@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...
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@gmail.com> wrote:
Hi Bruno,
On Mon, Sep 15, 2014 at 7:58 PM, Bruno Villasenor < br1villasen@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 yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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@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@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@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@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...
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@gmail.com> wrote: Hi Bruno,
On Mon, Sep 15, 2014 at 7:58 PM, Bruno Villasenor <br1villasen@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 yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
participants (6)
-
B.W. Keller -
Bruno Villasenor -
Bruno Villasenor Alvarez -
Hilary Egan -
Matthew Turk -
Nathan Goldbaum