Mailman 3 - yt-users

updating list of yt extensions and external frontends
by Chris Havlin Feb. 21, 2024

Feb. 21, 2024

Hi there! Do you use or maintain a yt extension or externally packaged frontend that is not part of the main yt package? I'm working on updating the docs to include a more current list so if you're aware of any not yet listed in https://github.com/yt-project/yt/issues/4824 I'd appreciate a note! Best, Chris

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Error in Loading vtk Files
by A. Lam Feb. 13, 2024

Feb. 13, 2024

Dear yt Dev Team, Hope this email finds you well! I am writing to seek assistance regarding an issue I encountered while attempting to load vtk files. Specifically, I am trying to extract data from vtk files generated by athena simulations using the ds.load function. However, the code returned the following error message, Traceback (most recent call last): File "/home/wkal2/rds/hpc-work/project/code/plot.py", line 13, in <module> ds = yt.load(vtk_filename,parameters=parameters) File "/home/wkal2/ENTER/envs/ml/lib/python3.9/site-packages/yt/_maintenance/deprecation.py", line 69, in inner return func(*args, **kwargs) File "/home/wkal2/ENTER/envs/ml/lib/python3.9/site-packages/yt/loaders.py", line 144, in load return cls(fn, *args, **kwargs) File "/home/wkal2/ENTER/envs/ml/lib/python3.9/site-packages/yt/frontends/athena/data_structures.py", line 488, in __init__ Dataset.__init__( File "/home/wkal2/ENTER/envs/ml/lib/python3.9/site-packages/yt/data_objects/static_output.py", line 293, in __init__ self._parse_parameter_file() File "/home/wkal2/ENTER/envs/ml/lib/python3.9/site-packages/yt/frontends/athena/data_structures.py", line 572, in _parse_parameter_file self.domain_dimensions[2] = np.int32(1) ValueError: assignment destination is read-only I would greatly appreciate any insights you can provide on what might be causing this issue with the code. For your reference, I am using yt version 4.3.0. Thank you for your attention and I look forward to hearing from you! Best regards, Amelie Lam

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Follow-Up: Error in Loading vtk Files - Urgent Response Needed
by A. Lam Feb. 13, 2024

Feb. 13, 2024

Dear yt Dev Team, Hope this email finds you well! I am reaching out to follow up on my previous email with the subject "Error in Loading vtk Files." Unfortunately, I have not received any response thus far, except for an automated message stating that my email is pending approval from the list moderator. Given the urgency of the matter at hand, I kindly request your prompt attention to this issue. Your assistance in addressing this matter would be greatly appreciated. If there are any additional details or information needed from my end to expedite the process, please do not hesitate to let me know. Thank you for your understanding and I look forward to hearing from you soon! Best regards, Amelie Lam

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Loading a SWIFT .hdf5 snapshot using latest version of yt
by hannah.obrennan.2021＠mumail.ie Jan. 30, 2024

Jan. 30, 2024

Has anyone recently been able to load a SWIFT snapshot using yt.load? I created a conda env using python=3. I installed the latest version of yt using: conda install -c conda-forge yt I installed h5py using: conda install h5py I also installed yt_astro_analysis (to use HaloCatalog later) using: git clone https://github.com/yt-project/yt_astro_analysis; cd yt_astro_analysis; python -m pip install -e . I attempted to create a Dataset using yt.load("SWIFT_filename.hdf5") and found the following error: Traceback (most recent call last): File "/data/regan_data/Hannah_WS/Halo_mass_function_project/2023-10_11_12/FOF_Rockstar_comparison/hc_creation.py", line 62, in <module> data_ds = yt.load(dir_name) ^^^^^^^^^^^^^^^^^ File "/home/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/yt/_maintenance/deprecation.py", line 69, in inner return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/yt/loaders.py", line 144, in load return cls(fn, *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/yt/frontends/swift/data_structures.py", line 36, in __init__ super().__init__( File "/home/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/yt/frontends/sph/data_structures.py", line 34, in __init__ super().__init__( File "/home/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/yt/data_objects/static_output.py", line 2123, in __init__ super().__init__( File "/home/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/yt/data_objects/static_output.py", line 293, in __init__ self._parse_parameter_file() File "/home/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/yt/frontends/swift/data_structures.py", line 100, in _parse_parameter_file runtime_parameters = self._get_info_attributes("RuntimePars") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/yt/frontends/swift/data_structures.py", line 84, in _get_info_attributes header = dict(handle[dataset].attrs) ~~~~~~^^^^^^^^^ 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/hannah/anaconda3/envs/yt-10_01_2024/lib/python3.12/site-packages/h5py/_hl/group.py", line 357, 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 'RuntimePars' doesn't exist)" When I examine the keys from the .hdf5 file in python, I find: >>> import h5py >>> f = h5py.File('../SWIFT__0.5_cMpc_h/N_512/RedshiftOutput0002.hdf5') >>> list(f.keys()) ['Cells', 'Code', 'Cosmology', 'DMParticles', 'GravityScheme', 'Header', 'InternalCodeUnits', 'Parameters', 'PartType1', 'PhysicalConstants', 'Policy', 'SubgridScheme', 'Units', 'UnusedParameters'] 'RuntimePars' is not one of the keys listed. Strangely, I was able to load the snapshot successfully on 12/12/2023 but cannot now, nor can I load any others. This is the same error found by Romeel Davé (January 2022) in https://mail.python.org/archives/list/yt-users@python.org/message/NUKRAWV7J… Any help with would be much appreciated, thank you! - Hannah

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help
by 张小霞 Dec. 13, 2023

Dec. 13, 2023

Hi, I have a problem when using yt to obtain the X-ray luminosity of a simulated region. I found that yt 4.3 and yt 4.4 give very different results, i.e., about 5 vs. 10 (* 1e39 erg/s). Do you know what causes this difference? Here is the code. Thanks! import yt ds = yt.load('snapshot_155.hdf5') xray_fields = yt.add_xray_emissivity_field(ds, 0.5, 2.0, table_type='apec', metallicity=1.0) sp = ds.sphere("c", (100.0, "kpc")) shpere= sp.quantities.total_quantity("xray_luminosity_0.5_2.0_keV") print(shpere) Best, Dr. Xiaoxia Zhang (张小霞) Department of Astronomy Xiamen University

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Key error: 'particle_posx'
by piyush.suneet＠gmail.com Nov. 9, 2023

Nov. 9, 2023

I am post processing some MHD simulations done with FLASH using yt (yt version 4.3.0). Initially, the simulation has no particles, but over time, we add some (sink) particles to it. I would like to use the boolean ds.particles_exist to check if a given FLASH HDF5 particle file has any particles in it or not. It works fine when there are particles, but gives a key error when there are no particles, instead of returning False. The same issue also occurs with an earlier version of yt (4.0.4). Traceback below: In [1]: yt.__version__ Out[1]: '4.3.0' In [4]: ds=yt.load('FLASH_part_0050') yt : [INFO ] 2023-10-24 11:01:22,508 Parameters: current_time = 50966272658115.96 yt : [INFO ] 2023-10-24 11:01:22,508 Parameters: domain_dimensions = [1 1 1] yt : [INFO ] 2023-10-24 11:01:22,508 Parameters: domain_left_edge = [-3.703e+18 -3.703e+18 -3.703e+18] yt : [INFO ] 2023-10-24 11:01:22,508 Parameters: domain_right_edge = [3.703e+18 3.703e+18 3.703e+18] yt : [INFO ] 2023-10-24 11:01:22,509 Parameters: cosmological_simulation = 0 In [5]: ds.particles_exist yt : [INFO ] 2023-10-24 11:01:26,270 Allocating for 3 particles Out[5]: True In [6]: ds=yt.load('FLASH_part_0000') yt : [INFO ] 2023-10-24 11:01:41,713 Parameters: current_time = 0.0 yt : [INFO ] 2023-10-24 11:01:41,713 Parameters: domain_dimensions = [1 1 1] yt : [INFO ] 2023-10-24 11:01:41,714 Parameters: domain_left_edge = [-3.703e+18 -3.703e+18 -3.703e+18] yt : [INFO ] 2023-10-24 11:01:41,714 Parameters: domain_right_edge = [3.703e+18 3.703e+18 3.703e+18] yt : [INFO ] 2023-10-24 11:01:41,714 Parameters: cosmological_simulation = 0 In [7]: ds.particles_exist --------------------------------------------------------------------------- KeyError Traceback (most recent call last) Input In [7], in <cell line: 1>() ----> 1 ds.particles_exist File ~/.local/lib/python3.9/site-packages/yt/data_objects/static_output.py:1238, in Dataset.particles_exist(self) 1236 @property 1237 def particles_exist(self): -> 1238 for pt, f in itertools.product(self.particle_types_raw, self.field_list): 1239 if pt == f[0]: 1240 return True File ~/.local/lib/python3.9/site-packages/yt/data_objects/static_output.py:657, in Dataset.field_list(self) 655 @property 656 def field_list(self): --> 657 return self.index.field_list File ~/.local/lib/python3.9/site-packages/yt/data_objects/static_output.py:606, in Dataset.index(self) 603 @property 604 def index(self): 605 if self._instantiated_index is None: --> 606 self._instantiated_index = self._index_class( 607 self, dataset_type=self.dataset_type 608 ) 609 # Now we do things that we need an instantiated index for 610 # ...first off, we create our field_info now. 611 oldsettings = np.geterr() File ~/.local/lib/python3.9/site-packages/yt/geometry/particle_geometry_handler.py:72, in ParticleIndex.__init__(self, ds, dataset_type) 70 self.dataset = weakref.proxy(ds) 71 self.float_type = np.float64 ---> 72 super().__init__(ds, dataset_type) 73 self._initialize_index() File ~/.local/lib/python3.9/site-packages/yt/geometry/geometry_handler.py:42, in Index.__init__(self, ds, dataset_type) 39 self._setup_geometry() 41 mylog.debug("Initializing data grid data IO") ---> 42 self._setup_data_io() 44 # Note that this falls under the "geometry" object since it's 45 # potentially quite expensive, and should be done with the indexing. 46 mylog.debug("Detecting fields.") File ~/.local/lib/python3.9/site-packages/yt/geometry/geometry_handler.py:124, in Index._setup_data_io(self) 122 if getattr(self, "io", None) is not None: 123 return --> 124 self.io = io_registry[self.dataset_type](self.dataset) File ~/.local/lib/python3.9/site-packages/yt/frontends/flash/io.py:224, in IOHandlerFLASHParticle.__init__(self, ds) 222 self._handle = ds._handle 223 self._particle_fields = determine_particle_fields(self._handle) --> 224 self._position_fields = [ 225 self._particle_fields[f"particle_pos{ax}"] for ax in "xyz" 226 ] File ~/.local/lib/python3.9/site-packages/yt/frontends/flash/io.py:225, in <listcomp>(.0) 222 self._handle = ds._handle 223 self._particle_fields = determine_particle_fields(self._handle) 224 self._position_fields = [ --> 225 self._particle_fields[f"particle_pos{ax}"] for ax in "xyz" 226 ] KeyError: 'particle_posx'

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ANN: unyt 3.0.1 is now available
by Clément Robert Nov. 2, 2023

Nov. 2, 2023

We're happy to announce the release of unyt 3.0.1 ! This version (as compared with 2.9.5) brings a major improvement: the implementation of "array functions” (as defined by [NEP 18](https://numpy.org/neps/nep-0018-array-function-protocol.html)), bringing unyt more in line with astropy.units. In short, this means that a lot more of numpy functions are now unyt-aware and should behave more intuitively when passed unyt_array instances, including - np.dot - np.inner - np.histogram - np.concatenate - np.stack - functions from np.linalg and np.fft - np.isclose - and many more ! This also means that existing applications *may* break around these functions, as the return value suddendly have dimensionally accurate units they previously didn't, which is why the *major* version number was bumped from 2 to 3. Despite our efforts to make this release as stable as possible, some unintented breakage may still happen, so please report any supsicious behaviour you encounter. Another major feature in unyt 3.0 is first class support for unyt-aware dask arrays. See our documentation for details on how to use it https://unyt.readthedocs.io/en/latest/usage.html#working-with-dask-arrays Note that it isn't recommended to use unyt 3 with current yt (4.3.0), but the next yt release will be compatible with both unyt 2.9 and 3.0, so yt users will be allowed to switch back to the historical behaviour and transition more smoothly. For a more complete description of changes in this release, including bug fixes, see our changelog https://unyt.readthedocs.io/en/latest/history.html

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issues with hop
by ocvirk Oct. 27, 2023

Oct. 27, 2023

Hi all, I am trying to run halo finding on a dataset, using hop via yt. Im getting weird results in particular slowdowns and a weird message. Up to here everything looks ok: P002 yt : [INFO ] 2023-10-27 04:31:09,841 Parsing outputs Calling regroup... No minimum group size specified. Assuming 10 particles. ngroups = 53540 and then it takes a while and finally I see something like: P002 yt : [INFO ] 2023-10-25 11:52:40,201 Saving 1 halos: ./info_000065/info_000065.2.h5. and the output file is very large (saving particles by defaut). So Im guessing that somehow the regroup routine is making one huge halo regrouping the 53450 groups... which may be why it is so slow…. Do you know if there is any way to control mingroupsize from yt? It does not seem like this is a parameter of the fof halo finder method that can be tuned from yt. Also, I have no idea if that would fix the problem. Here Im using parallel (8 proc) but the problem is the same with 1 proc. NB: this is ramses, everything looks fine on the ramses test data (output_00101). Any help would be welcome! Cheers, Pierre ============================================================ Pierre OCVIRK Observatoire Astronomique de Strasbourg 11 rue de l'Universite 67000 STRASBOURG FRANCE tel: +33 (0)3 68 85 24 40 fax: +33 (0)3 68 85 24 25 pierre.ocvirk(a)astro.unistra.fr ============================================================

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Error concerning 'ewah_bool_utils' while installing yt
by Braňo Rabatin Aug. 15, 2023

Aug. 15, 2023

Hello, I tried to install yt from the install script on Ubuntu. I changed a couple of things in the script: INST_YT_SOURCE = 1 INST_SCIPY = 1 INST_ASTROPY = 1 Everything installed successfully until the message "Building yt from source", where an error occurred, copied below: *Installing sympyInstalling netcdf4Building yt from sourceSetting YT_DIR=/home/rabatinb/yt-conda/src/yt-git******************************************** FAILURE REPORT:********************************************EXECUTING: /home/rabatinb/yt-conda/bin/git -C /home/rabatinb/yt-conda/src/yt-git checkout mainAlready on 'main'Your branch is up to date with 'origin/main'.Traceback (most recent call last): File "/home/rabatinb/yt-conda/src/yt-git/setup.py", line 8, in <module> from setupext import ( File "/home/rabatinb/yt-conda/src/yt-git/setupext.py", line 16, in <module> import ewah_bool_utilsModuleNotFoundError: No module named 'ewah_bool_utils'****************************************************************************************Failure. Check /home/rabatinb/yt-conda/yt_install.log. The last 10 lines are above.* What could be the issue and how can I fix this? Thank you, Branislav Rabatin.

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YT-startup
by arnavl0711＠gmail.com Aug. 11, 2023

Aug. 11, 2023

Hey guys, I'm new to YT and I wanted to download it so I can analyze data and make images from the FIRE simulator, but its not downloading for some reason. Its saying I need something called a git I do not know what that is. Someone pls help me!

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