Error when creating a new case #62
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Hi developers, I encountered an error when I followed the tutorial Setup section "Create Scripts". Using the command ./create_elm-fates-singlepoint-1pft_bci_invinit.sh within the container terminal, it started to run and build.
2024-09-17 18:47:11 PRE_RUN_CHECK HAS FINISHED I checked the log info and it shows: NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. I checked the paramfiles within the container elm-fates, it only includes a README.md without the fates_params_default-1pft.nc', I am not sure whether that induced the error. I only found that there is one fates_params_default.cdl under the fates/parameter_files in the github fates page, I import it and modified my create script, but the error changed to : I am stuck here now and not sure which step is wrong. Thanks for your attention! Best, |
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Replies: 3 comments 6 replies
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The file fates_params_default.cdl is a human-readable version of a netcdf file. FATES uses a parameter file ending in .nc. After downloading the file " fates_params_default.cdl ", you need to convert it to .nc (do this inside the folder "paramfiles" in docker): ncgen -o fates_params_default.nc fates_params_default.cdlThe next step is to define 1 pft, following: ./FatesPFTIndexSwapper.py --fin=fates_params_default.nc --fout=fates_params_default-1pft.nc
--pft-indices=1The file ./FatesPFTIndexSwapper.py is located in: cp ../E3SM/components/elm/src/external_models/fates/tools/FatesPFTIndexSwapper.py . |
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Thank you so much! That works to create the fates_params_default-1pft.nc. |
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Thanks for the question @YidongTong and for the answer @jamedina09. I've made a new issue #63 to help address this for future users. |
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Thanks! After adding the fates_params_default-1pft.nc and modifying the create scripts, i tried again. Then I got an error again. Thank you for your assistance! |
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Thank you for sharing your logs and error messages. Would you take a look in your case |
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Sure! The lnd.log shows "Error reading. Var:fates_landuse_pprodharv10_forest_mean. " It seems that the problem is still about the params? |
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Hi @glemieux , I took a look at the ln.log and share the .txt file below. |
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@YidongTong this error is stating that the model is looking for particular variable name in the parameter file, but doesn't see it. Can you open the parameter file and search to see if Note that the parameter file that should be used with the tutorial can be found in the |
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@glemieux Thank you so much!! It solved! |
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The file fates_params_default.cdl is a human-readable version of a netcdf file. FATES uses a parameter file ending in .nc.
After downloading the file " fates_params_default.cdl ", you need to convert it to .nc (do this inside the folder "paramfiles" in docker):
The next step is to define 1 pft, following:
The file ./FatesPFTIndexSwapper.py is located in:
cp ../E3SM/components/elm/src/external_models/fates/tools/FatesPFTIndexSwapper.py .