Mailman 3 - yt-users

Key error: 'particle_posx'
by piyush.suneet＠gmail.com 09 Nov '23

09 Nov '23

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 02 Nov '23

02 Nov '23

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 27 Oct '23

27 Oct '23

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 15 Aug '23

15 Aug '23

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 11 Aug '23

11 Aug '23

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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Problem with yt.ProjectionPlot
by ssp202311＠asiaa.sinica.edu.tw 08 Aug '23

08 Aug '23

Hi all, I encountered the 'RuntimeError' when use yt.ProjectionPlot like below: Traceback (most recent call last): File "/scratch/data/hnguyen/gas/gas/lss_pro.py", line 3, in <module> p = yt.ProjectionPlot(gas, 'z', ('gas', 'density'),data_source = gas.all_data(),buff_size=(100, 100)) File "/tiara/home/hnguyen/.local/miniconda3/lib/python3.9/site-packages/yt/visualization/plot_window.py", line 2069, in __init__ proj = ds.proj( File "/tiara/home/hnguyen/.local/miniconda3/lib/python3.9/site-packages/yt/data_objects/construction_data_containers.py", line 551, in __init__ self.get_data(field) File "/tiara/home/hnguyen/.local/miniconda3/lib/python3.9/site-packages/yt/data_objects/construction_data_containers.py", line 283, in get_data self._handle_chunk(chunk, fields + sfields, tree) File "/tiara/home/hnguyen/.local/miniconda3/lib/python3.9/site-packages/yt/data_objects/construction_data_containers.py", line 638, in _handle_chunk ilevel = chunk.ires * self.ds.ires_factor File "/tiara/home/hnguyen/.local/miniconda3/lib/python3.9/site-packages/yt/data_objects/static_output.py", line 1266, in ires_factor raise RuntimeError RuntimeError But when I use yt.SlicePlot, my code works. Is there any idea to solve this problem? I really need ProjectionPlot for my visualization. Thank you. Best regards, Huy

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some questions about particleprojectionplot
by 34820221153820＠stu.xmu.edu.cn 07 Aug '23

07 Aug '23

Hello I am new about YT. I want to use YT to make some analysis and get some projection plots. The data that will be used is from Arepo code. The output files are same as Gadget that the format of them is HDF5. I have used YT to produce the stellar particles projection plots using yt.ParticleProjectionPlot(). However, I found that if I use yt.ParticleProjectionPlot(), I cannot use contour . (error information:yt.utilities.exceptions.YTUnsupportedPlotCallback: The `Particle` class currently doesn't support the `annotate_contour` method.) So, I want to learn how to add the contour if I just want to plot the N-body partciles. Additionally, in my simulation, my galaxy model is not aligned with the descartes system.In other words, the disc of the galaxy is not parallel to any plane of the coordinate system.I found I can set the normal vector L as showed in examples,but how I could know the real normal vector if I want to make the face-on galaxy plot? Thank everyone very much for answering my questions !And I will be sorry if I miss the important imformation which is showed in YT home website.Please tell me!

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Problems installing yt with non-standard library locations
by Anne Noer Kolborg 21 Jul '23

21 Jul '23

Hi yt community, I’m encountering errors when running python -c “import yt”. Background: I’m working in a python set-up on a shared linux system to which I do not have root access and the system wide python installation is older than what I need for the version of yt I’d like to run. So, I’m working with a set-up in a non-standard location and I think this may be the cause of the problems, but I don’t know how to proceed to fix it. My first approach was to pip install, as described on the yt install page. That failed with "segmentation fault (core dumped)” error, when testing the installation (python -c “import yt”). I tried all possible combinations of Python 3.11.4, Python 3.10.12 and yt 4.2.1 and yt 4.2.0, they all caused this issue. (Including when installing yt[full]). Because my other python libraries work without problems and the path to the yt executable is on the search PATH, I figure this is perhaps related to some non-python libraries required by yt. My next step was to install yt from source, which seems to confirm my suspicion: in this case python -c “import yt” yields a more informative error message: < Leaving out a long traceback > File "yt/geometry/selection_routines.pyx", line 1, in init yt.geometry.selection_routines # distutils: include_dirs = LIB_DIR ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /PATH/TO/YT/yt/utilities/lib/image_samplers.cpython-310-x86_64-linux-gnu.so) I checked that CXXABI_1.3.9 does indeed exist on the system and the path to it is included in the LD_LIBRARY_PATH in .bash_profile, however yt seems to look for it in the system wide folder (/lib64/) and not my local library folder ($HOME/GCC/lib64/). I would be grateful if someone has any ideas about how to get yt to use the correct (local) library path instead of the standard system wide path it is currently using. Sincerely Anne

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Changing the "center" field parameter in radial velocity calculation
by Samuel Patrick 28 Jun '23

28 Jun '23

Hi, I have a region of space I'm trying to perform an OffAxisSlicePlot of, with the field in question being the gas velocity towards a specific predetermined point within that space. How do I effectively change the "center" parameter within the ('gas', 'velocity_spherical_radius') field to achieve this, so that the normal vector is pointing between the gas coordinates and the point in question? Many thanks, Sam Patrick The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

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yt-napari tutorial series and live virtual events
by Chris Havlin 26 Jun '23

26 Jun '23

Some exciting yt-napari announcements! -------------------------------------- yt-napari video tutorial series -------------------------------------- The first two videos in the yt-napari tutorial series are now available, covering introductions to napari and yt-napari. 1. Intro to napari for yt users: https://youtu.be/tNdIetamf98 2. Tour of the yt-napari plugin: https://youtu.be/ta7rBOYNpmg Future videos will cover more advanced napari and yt-napari usage and will be added to the yt-napari playlist here: https://www.youtube.com/playlist?list=PLqbhAmYZU5KxuAcnNBIxyBkivUEiKswq1 --------------------------- yt-napari live events --------------------------- I'll be convening some live weekly events: starting off with a drop-in virtual help and discussion session on zoom on Thursday June 29 at 10am central time. Come with questions or development ideas! Zoom link will be posted in the #yt-napari channel of the yt slack (remember, you can join the yt slack via the link at https://yt-project.org/community.html ). ----------------------------- other ways to get help ----------------------------- - join the #yt-napari channel in the yt slack and ask there - post in the general yt help channel and ping me (@Chris Havlin) - send me a direct message on slack (@Chris Havlin) Happy visualizing! Chris

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