Error loading active particles
Hi all, I am trying to read enzo dataset with active particles and getting the following error. There are active particles as indicated by print statement prior to datadump but yt immediately raises this error after loading it. Any help in this regard will be appreciated. yt : [INFO ] 2020-04-13 19:39:50,444 Parameters: current_time = 12.774511689726 yt : [INFO ] 2020-04-13 19:39:50,444 Parameters: domain_dimensions = [256 256 256] yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: domain_left_edge = [0. 0. 0.] yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: domain_right_edge = [1. 1. 1.] yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: cosmological_simulation = 1 yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: current_redshift = 23.138771212879 yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: omega_lambda = 0.6911 yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: omega_matter = 0.3089 yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: hubble_constant = 0.6774 Parsing Hierarchy : 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1771/1771 [00:00<00:00, 4770.60it/s] yt : [INFO ] 2020-04-13 19:39:50,937 Gathering a field list (this may take a moment.) Traceback (most recent call last): File "ytdiv.py", line 20, in <module> print(ds.derived_field_list) File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py", line 216, in ireq self.index File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py", line 509, in index self, dataset_type=self.dataset_type) File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/frontends/enzo/data_structures.py", line 195, in __init__ GridIndex.__init__(self, ds, dataset_type) File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/geometry/geometry_handler.py", line 58, in __init__ self._detect_output_fields() File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/frontends/enzo/data_structures.py", line 429, in _detect_output_fields ap_fields = self._detect_active_particle_fields() File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/frontends/enzo/data_structures.py", line 388, in _detect_active_particle_fields node = handle["/Grid%08i/Particles/" % g.id] File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/h5py/_hl/group.py", line 262, in __getitem__ oid = h5o.open(self.id, self._e(name), lapl=self._lapl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5o.pyx", line 190, in h5py.h5o.open KeyError: "Unable to open object (object 'Particles' doesn't exist)" Best wishes, Latif
Hi Latif, I assume that you're using the latest version of Enzo 2.6. This PR addressed the updates to Enzo's active particle I/O. https://github.com/yt-project/yt/pull/2107 At the time, the I/O changes weren't merged into the master branch, so it wasn't accepted. It's only one commit. Could you merge it into your fork and test it out on your data? Thanks, John On 4/13/2020 12:07, Muhammad Latif wrote:
Hi all,
I am trying to read enzo dataset with active particles and getting the following error. There are active particles as indicated by print statement prior to datadump but yt immediately raises this error after loading it. Any help in this regard will be appreciated.
yt : [INFO ] 2020-04-13 19:39:50,444 Parameters: current_time = 12.774511689726
yt : [INFO ] 2020-04-13 19:39:50,444 Parameters: domain_dimensions = [256 256 256]
yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: domain_left_edge = [0. 0. 0.]
yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: domain_right_edge = [1. 1. 1.]
yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: cosmological_simulation = 1
yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: current_redshift = 23.138771212879
yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: omega_lambda = 0.6911
yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: omega_matter = 0.3089
yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: hubble_constant = 0.6774
Parsing Hierarchy : 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1771/1771 [00:00<00:00, 4770.60it/s]
yt : [INFO ] 2020-04-13 19:39:50,937 Gathering a field list (this may take a moment.)
Traceback (most recent call last):
File "ytdiv.py", line 20, in <module>
print(ds.derived_field_list)
File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py", line 216, in ireq
self.index
File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py", line 509, in index
self, dataset_type=self.dataset_type)
File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/frontends/enzo/data_structures.py", line 195, in __init__
GridIndex.__init__(self, ds, dataset_type)
File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/geometry/geometry_handler.py", line 58, in __init__
self._detect_output_fields()
File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/frontends/enzo/data_structures.py", line 429, in _detect_output_fields
ap_fields = self._detect_active_particle_fields()
File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/frontends/enzo/data_structures.py", line 388, in _detect_active_particle_fields
node = handle["/Grid%08i/Particles/" % g.id <http://g.id/>]
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/h5py/_hl/group.py", line 262, in __getitem__
oid = h5o.open(self.id <http://self.id/>, self._e(name), lapl=self._lapl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5o.pyx", line 190, in h5py.h5o.open
KeyError: "Unable to open object (object 'Particles' doesn't exist)"
Best wishes, Latif
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
-- John Wise Associate Professor of Physics Center for Relativistic Astrophysics, Georgia Tech http://cosmo.gatech.edu
Hi John, Thank you.Yes, I am using enzo 2.6 and it works after suggested merge. best regards Latif Hi Latif,
I assume that you're using the latest version of Enzo 2.6. This PR addressed the updates to Enzo's active particle I/O.
https://github.com/yt-project/yt/pull/2107
At the time, the I/O changes weren't merged into the master branch, so it wasn't accepted. It's only one commit. Could you merge it into your fork and test it out on your data?
Thanks, John
On 4/13/2020 12:07, Muhammad Latif wrote:
Hi all,
I am trying to read enzo dataset with active particles and getting the following error. There are active particles as indicated by print statement prior to datadump but yt immediately raises this error after loading it. Any help in this regard will be appreciated.
yt : [INFO ] 2020-04-13 19:39:50,444 Parameters: current_time = 12.774511689726
yt : [INFO ] 2020-04-13 19:39:50,444 Parameters: domain_dimensions = [256 256 256]
yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: domain_left_edge = [0. 0. 0.]
yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: domain_right_edge = [1. 1. 1.]
yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: cosmological_simulation = 1
yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: current_redshift = 23.138771212879
yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: omega_lambda = 0.6911
yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: omega_matter = 0.3089
yt : [INFO ] 2020-04-13 19:39:50,445 Parameters: hubble_constant = 0.6774
Parsing Hierarchy :
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████|
1771/1771 [00:00<00:00, 4770.60it/s]
yt : [INFO ] 2020-04-13 19:39:50,937 Gathering a field list (this may take a moment.)
Traceback (most recent call last):
File "ytdiv.py", line 20, in <module>
print(ds.derived_field_list)
File
"/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py",
line 216, in ireq
self.index
File
"/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/data_objects/static_output.py",
line 509, in index
self, dataset_type=self.dataset_type)
File
"/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/frontends/enzo/data_structures.py",
line 195, in __init__
GridIndex.__init__(self, ds, dataset_type)
File
"/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/geometry/geometry_handler.py",
line 58, in __init__
self._detect_output_fields()
File
"/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/frontends/enzo/data_structures.py",
line 429, in _detect_output_fields
ap_fields = self._detect_active_particle_fields()
File
"/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/yt/frontends/enzo/data_structures.py",
line 388, in _detect_active_particle_fields
node = handle["/Grid%08i/Particles/" % g.id <http://g.id/>]
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File
"/home/malatif/YT_DEV/yt-conda/lib/python3.7/site-packages/h5py/_hl/group.py",
line 262, in __getitem__
oid = h5o.open(self.id <http://self.id/>, self._e(name), lapl=self._lapl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5o.pyx", line 190, in h5py.h5o.open
KeyError: "Unable to open object (object 'Particles' doesn't exist)"
Best wishes, Latif
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
-- John Wise Associate Professor of Physics Center for Relativistic Astrophysics, Georgia Tech http://cosmo.gatech.edu _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
participants (2)
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John Wise -
Muhammad Latif