OceanBioME / OceanBioME.jl

🌊 🦠 🌿 A fast and flexible modelling environment written in Julia for modelling the coupled interactions between ocean biogeochemistry, carbonate chemistry, and physics
https://oceanbiome.github.io/OceanBioME.jl/
MIT License
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Added `adapt_structure` method for NPZD #88

Closed jagoosw closed 1 year ago

jagoosw commented 1 year ago

Solves #86

jagoosw commented 1 year ago

@iuryt @zwei961120 I've just tested on GPU and it seems to work now!

codecov-commenter commented 1 year ago

Codecov Report

Patch coverage has no change and project coverage change: -0.26 :warning:

Comparison is base (f9ea0e3) 53.04% compared to head (0a57fdb) 52.78%.

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #88 +/- ## ========================================== - Coverage 53.04% 52.78% -0.26% ========================================== Files 26 26 Lines 1018 1023 +5 ========================================== Hits 540 540 - Misses 478 483 +5 ``` | [Impacted Files](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/88?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME) | Coverage Δ | | |---|---|---| | [src/Models/AdvectedPopulations/LOBSTER/LOBSTER.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/88?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL01vZGVscy9BZHZlY3RlZFBvcHVsYXRpb25zL0xPQlNURVIvTE9CU1RFUi5qbA==) | `80.48% <0.00%> (ø)` | | | [src/Models/AdvectedPopulations/NPZD.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/88?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL01vZGVscy9BZHZlY3RlZFBvcHVsYXRpb25zL05QWkQuamw=) | `0.00% <0.00%> (ø)` | | | [src/OceanBioME.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/88?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL09jZWFuQmlvTUUuamw=) | `0.00% <ø> (ø)` | | | [src/Utils/sinking\_velocity\_fields.jl](https://app.codecov.io/gh/OceanBioME/OceanBioME.jl/pull/88?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OceanBioME#diff-c3JjL1V0aWxzL3NpbmtpbmdfdmVsb2NpdHlfZmllbGRzLmps) | `50.00% <0.00%> (ø)` | |

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jagoosw commented 1 year ago

Anyone mind if I just merge this without the docs working? I can't work out why they won't run, but this PR doesn't make any changes to the docs

zwei961120 commented 1 year ago

Anyone mind if I just merge this without the docs working? I can't work out why they won't run, but this PR doesn't make any changes to the docs

Thanks for your efforts!After updating the branch, I was able to run NPZD model on the GPU smoothly. In fact, when I run the code in the Jupyter Notebook, I also run into problems like Package Strided does not have StridedViews in its dependencies: - You may have a partially installed environment. Try 'pg.instantiate ()' , image but when run from the command line, everything becomes normal. image

jagoosw commented 1 year ago

Anyone mind if I just merge this without the docs working? I can't work out why they won't run, but this PR doesn't make any changes to the docs

Thanks for your efforts!After updating the branch, I was able to run NPZD model on the GPU smoothly. In fact, when I run the code in the Jupyter Notebook, I also run into problems like Package Strided does not have StridedViews in its dependencies: - You may have a partially installed environment. Try 'pg.instantiate ()' , ...

Great! No worries, I'm glad its of help to you.

This is helpful to know because thats the same error the documentation run is giving, thank you!