Mailman 3 October 2022 - yt-users

enzo-mrp-music/get_halo_initial_extent.py not working with yt 4.0.1
by C Bernhardt June 2, 2023

June 2, 2023

Dear yt users, I just updated yt to 4.0.1 and now I get this error message when trying to run enzo-mrp-music.py from John Wise on https://github.com/jwise77/enzo-mrp-music. Traceback (most recent call last): File "enzo-mrp-music/enzo-mrp-music.py", line 264, in <module> params = find_lagrangian_region(params) File "enzo-mrp-music/enzo-mrp-music.py", line 177, in find_lagrangian_region get_center_and_extent(params["halo_info"], File "enzo-mrp-music/get_halo_initial_extent.py", line 147, in get_center_and_extent halo_indices, halo_com, shifted = get_halo_indices(my_halo, final_dataset, File "enzo-mrp-music/get_halo_initial_extent.py", line 119, in get_halo_indices get_halo_sphere_particles(my_halo, dataset, radius_factor=radius_factor) File "enzo-mrp-music/get_halo_initial_extent.py", line 73, in get_halo_sphere_particles my_sphere = pf.h.sphere(my_halo_data['center'], radius_factor * r_200) AttributeError: 'EnzoDataset' object has no attribute 'h' I am honestly not sure what the attribute 'h' does in this case, so I didn't know what to try to adjust. Any suggestions for getting around this? Or how can I go back to yt 3? Kind regards, -- Carla Bernhardt PhD Student Universität Heidelberg ZAH Institut für Theoretische Astrophysik

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problem creating point object
by Slavin, Jonathan Oct. 18, 2022

Oct. 18, 2022

Hi, I have some FLASH data from a 2-D simulation (cylindrical symmetry, R-Z) and I was trying to get point objects following the approach on the web page: https://yt-project.org/doc/analyzing/objects.html?highlight=interpolate There it indicates that you can do something like: ds = yt.load(file) pt = ds.r[(10.0, "km"), (200, "m"), (1.0, "km")] In my case I just give 0 for the last value since it doesn't matter in 2D. However if I try that I get the error message: --------------------------------------------------------------------------- YTDimensionalityError Traceback (most recent call last) Cell In [4], line 1 ----> 1 pt = ds.r[(rinit,'pc'), (zinit,'pc'), (0.,'pc')] File /export/slavin/anaconda3/envs/py38/lib/python3.8/site-packages/yt/data_objects/region_expression.py:67, in RegionExpression.__getitem__(self, item) 61 item.insert(idx, slice(None)) 63 if len(item) != self.ds.dimensionality: 64 # Not the right specification, and we don't want to do anything 65 # implicitly. Note that this happens *after* the implicit expansion 66 # of a single slice. ---> 67 raise YTDimensionalityError(len(item), self.ds.dimensionality) 69 # OK, now we need to look at our slices. How many are a specific 70 # coordinate? 72 nslices = sum(isinstance(v, slice) for v in item) YTDimensionalityError: Dimensionality specified was 3 but we need 2 So I thought this might be due to the data being 2D. Then I tried pt = ds.r[(rinit,'pc'), (zinit,'pc')] but that leads to a TypeError - the message ends with: File /export/slavin/anaconda3/envs/py38/lib/python3.8/site-packages/yt/funcs.py:1119, in validate_3d_array(obj) 1117 def validate_3d_array(obj): 1118 if not is_sequence(obj) or len(obj) != 3: -> 1119 raise TypeError( 1120 "Expected an array of size (3,), received '%s' of " 1121 "length %s" % (str(type(obj)).split("'")[1], len(obj)) 1122 ) TypeError: Expected an array of size (3,), received 'list' of length 2 So is there any way around this? (By the way, I'm using yt 4.1.1 and got the same issue with 4.0.5.) Thanks in advance for any help. Regards, Jon -- Jonathan D. Slavin (he/him) Astrophysicist - High Energy Astrophysics Division Center for Astrophysics | Harvard & Smithsonian Office: (617) 496-7981 | Cell: (781) 363-0035 60 Garden Street | MS 04 | Cambridge, MA 02138

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ANN: yt 4.1.1 is available
by Clément Robert Oct. 18, 2022

Oct. 18, 2022

yt 4.1.1 is out ! It fixes a couple important bugs that were discovered after the 4.1.0 release, including the octree memory leak recently discussed on the user mailing list. See the release notes on github for details : https://github.com/yt-project/yt/releases/tag/yt-4.1.1 Happy analysis! Clément, on behalf of the yt team

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Potential memory leak in Ramses frontend
by Anne Noer Kolborg Oct. 12, 2022

Oct. 12, 2022

Dear yt community, I am have encountered an out-of-memory problem (potential memory leak) when using yt to load and process several Ramses outputs in a row. Each simulation output is approximately 3 GB, but the RAM usage easily exceeds 16 GB in ~30 mins of computation time (single threaded computation time). When allocated more RAM the computation continues for longer but ultimately always runs out the memory before the end of the data-processing. I have created a minimal working example that triggers this problem. It is uploaded here: http://paste.yt-project.org/show/404/ <http://paste.yt-project.org/show/404/> Log of the memory usage over time while running that script is here: http://paste.yt-project.org/show/406/ <http://paste.yt-project.org/show/405/> As you can see the total memory usage simply grows for each round of the loop. I suspect that the memory allocated to the dataset does not get cleared. Simulation output to test the code is uploaded here: http://use.yt/upload/1ace6072 <http://use.yt/upload/1ace6072> The del and clear_data() statements in line 18 and 19 do not impact the memory usage when commented in. I tested the same bit of code using the “HiresIsolatedGalaxy” Enzo dataset from the sample datasets (https://yt-project.org/data/ <https://yt-project.org/data/>). It is similar in size to the outputs I am trying to process and runs without issues. Therefore, I suspect it might be the ramses frontend causing the memory leak. Any advice or pointers on how to debug this further, alternative ways to handle this or suggestions for how to use yt more efficiently are most welcome! Best regards, Anne Version lists: Yt version 4.1.dev, changeset = 39949fb6bfba. (cloned from GitHub about a week ago) - the stable version 4.0.1 also produces the same issue. Python version 3.8.12 Gcc 4.8.5 CentOS Linux release 7.9.2009 // Linux 3.10.0 (x86-64 architecture)

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Quiver Keys in annotate velocity
by daniellin456＠gmail.com Oct. 10, 2022

Oct. 10, 2022

Hi, Is that possible to add quiver key in the plot when using the annotate_velocity? Thank you

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ANN: yt 4.1.0 is available
by Clément Robert Oct. 7, 2022

Oct. 7, 2022

yt 4.1.0 is out ! This release represents more than a year worth of work form 30 contributors, and contains many improvements as well as new features. See the release notes on github for details : https://github.com/yt-project/yt/releases/tag/yt-4.1.0 Happy analysis! Clément, on behalf of the yt team

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_fill_fields raise RuntimeError in Derived fields
by hyf＠stu.pku.edu.cn Oct. 4, 2022

Oct. 4, 2022

Hi Everyone, I met RuntimeError when I tried to plot Derived fields, such as vorticity field derived from velocity field It seems that "tot" calculated from the function "fill_region" raising the "RuntimeError" (See the corresponding yt source code part below) I wonder how to fix up this error and will appreciate if anyone can help me~ -------------------------------------------------------- Here is the plotting vorticity field code PART ONE function 144 def vort_z_func(field, data): 145 return ( 146 + data['boxlib', 'v_gradient_x'] 147 - data['boxlib', 'u_gradient_y'] 148 ) PART TWO main 59 u_gradient = ds.add_gradient_fields(("boxlib","u")) 60 v_gradient = ds.add_gradient_fields(("boxlib","v")) 61 62 derived_fields = [ # field name, units, displayname 63 ('vort_z', '1 / cm', 'Vorticity in z direction') 64 ] 65 for name, unitstr, dispname in derived_fields: 66 ds.add_field( 67 ('boxlib', name), 68 units = unitstr, 69 function = eval(name + '_func'), 70 sampling_type = 'cell', 71 display_name = dispname 72 ) 73 ds.periodicity = (True, True, True) 74 slc = yt.SlicePlot(ds, 'z', 'vort_z', width=((chang,'cm'),(kuan,'cm')),center=([xcent,ycent,0.001],'cm')) -------------------------------------------------------------------------------------------------- Here is the error info: 1084 File "vorfield.py", line 143, in <module> 1085 slc = yt.SlicePlot(ds, 'z', 'vort_z', width=((chang,'cm'),(kuan,'cm')),center=([xcent,ycent,0.001],'cm')) 1086 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/visualization/plot_window.py", line 1986, in SlicePlot 1087 return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs) 1088 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/visualization/plot_window.py", line 1282, in __init__ 1089 slc.get_data(fields) 1090 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1583, in get_data 1091 self._generate_fields(fields_to_generate) 1092 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1603, in _generate_fields 1093 fd = self._generate_field(field) 1094 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 293, in _generate_field 1095 tr = self._generate_fluid_field(field) 1096 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 311, in _generate_fluid_field 1097 rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) 1098 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 341, in _generate_spatial_fluid 1099 gz[field][ngz:-ngz, ngz:-ngz, ngz:-ngz], 1100 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 256, in __getitem__ 1101 self.get_data(f) 1102 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/construction_data_containers.py", line 691, in get_data 1103 if len(fill) > 0: self._fill_fields(fill) 1104 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/construction_data_containers.py", line 1060, in _fill_fields 1105 raise RuntimeError --------------------------------------------------------------------------------------------------- Here is the corresponding yt source code part 1053 for chunk in ls.data_source.chunks(fields, "io"): 1054 chunk[fields[0]] 1055 input_fields = [chunk[field] for field in fields] 1056 tot -= fill_region(input_fields, ls.fields, ls.current_level, 1057 ls.global_startindex, chunk.icoords, 1058 chunk.ires, domain_dims, refine_by) 1059 if level == 0 and tot != 0: 1060 raise RuntimeError 1061 self._update_level_state(ls) Best wishes, He Yifeng

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