Issues with loading old data and scalar product computation (f * u) after updating Oceananigans #3978
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simone-silvestri
Alisa-Shikanyan
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Issues with loading old data and scalar product computation (f * u) after updating Oceananigans
#3978
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Hello everyone. I recently updated both Julia (to version 1.10.7) and Oceananigans (to the latest version 0.94.3). Previously, I had installed Oceananigans about a year ago, but unfortunately, I don’t remember the exact version I was using. After the updates, I’ve encountered a couple of issues:
Now, when I try to load this data using FieldTimeSeries, it fails with the following error:
I attempted to compute the scalar product f * u using this line (here is an example for t = 5): This code worked in the previous version, but now it fails with the following error: I apologize for including such long error messages and detailed examples, but I hope they help clarify the issues I'm encountering. I would greatly appreciate any guidance on how to resolve these problems or adapt my workflow to the current version of the library. Thank you so much for your time and assistance! |
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Answered by
simone-silvestri
Dec 9, 2024
Replies: 1 comment 4 replies
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Unfortunately, loading data saved with previous versions of Oceananigans is not always possible automatically because of compatibility issues with new and old types saved in the JLD2 files. You can always open the old datafile manually with file = jldopen("/path")and inspect the saved data that should be under the file["timeseries"]With regards to the second issue, I think you are missing the field constructor, try with: u_forcing_field = Oceananigans.field((Face, Center, Center), u_forcing, u_timeseries. grid) |
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4 replies
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Thanks a lot for your help! The second point was definitely my mistake, and your suggestion fixed it right away. Regarding the first point, I was wondering if it's possible to create the FieldTimeSeries manually from this "file"? I'm not quite sure how to set it up properly. One of the documentation pages has an empty page and the other doesn't have examples, so I keep running into errors. I'd really appreciate any help on how I could manually extract and create the FieldTimeSeries, if that's possible. |
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@Alisa-Shikanyan you want to use the first constructor for help?> FieldTimeSeries
search: FieldTimeSeries
FieldTimeSeries{LX, LY, LZ}(grid::AbstractGrid [, times=()]; kwargs...)
Construct a FieldTimeSeries on grid and at times.
Keyword arguments
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• indices: spatial indices
• backend: backend, InMemory(indices=Colon()) or OnDisk()
• path: path to data for backend = OnDisk()
• name: name of field for backend = OnDisk()
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
FieldTimeSeries(path, name;
backend = InMemory(),
architecture = nothing,
grid = nothing,
location = nothing,
boundary_conditions = UnspecifiedBoundaryConditions(),
time_indexing = Linear(),
iterations = nothing,
times = nothing,
reader_kw = Dict{Symbol, Any}())
Return a FieldTimeSeries containing a time-series of the field name load from JLD2 output located at path.
Keyword arguments
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• backend: InMemory() to load data into a 4D array, OnDisk() to lazily load data from disk when indexing into
FieldTimeSeries.
• grid: A grid to associate with the data, in the case that the native grid was not serialized properly.
• iterations: Iterations to load. Defaults to all iterations found in the file.
• times: Save times to load, as determined through an approximate floating point comparison to recorded save times.
Defaults to times associated with iterations. Takes precedence over iterations if times is specified.
• reader_kw: A dictionary of keyword arguments to pass to the reader (currently only JLD2) to be used when opening files.
julia>Create the set!(fts, path, name)where Alternatively you have to load the data from the |
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Here's an example: u_fts = FieldTimeSeries{Face, Center, Center}(grid, times) |
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Thanks for your help and clear answers! Everything is clear now, and I don’t have any more questions. |
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Unfortunately, loading data saved with previous versions of Oceananigans is not always possible automatically because of compatibility issues with new and old types saved in the JLD2 files.
You can always open the old datafile manually with
and inspect the saved data that should be under the
timeserieskeyfile["timeseries"]With regards to the second issue, I think you are missing the field constructor, try with: