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January 2024

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Loading a SWIFT .hdf5 snapshot using latest version of yt
by hannah.obrennan.2021＠mumail.ie 30 Jan '24

30 Jan '24

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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