ValueError: coords is not dict-like, but it has 3 items, which does not match the 4 dimensions of the data

[Constable1819]

I have started the process from the beginning. I got this error for the tutorial that was even running before.

ValueError: coords is not dict-like, but it has 3 items, which does not match the 4 dimensions of the data

[ekatef]

I have started the process from the beginning. I got this error for the tutorial that was even running before.

ValueError: coords is not dict-like, but it has 3 items, which does not match the 4 dimensions of the data

Hello @Constable1819, thanks for the report. Could you please post the whole error traceback?

Just to be sure: have you removed all the previous output of the workflow before running the tutorial? (It sounds very trivial but interactions with the old output are a quite frequent source of errors

[Constable1819]

ValueError: coords is not dict-like, but it has 3 items, which does not match the 4 dimensions of the data
[Mon Sep 30 22:58:41 2024]
Error in rule build_renewable_profiles:
jobid: 18
input: resources/natura.tiff, data/copernicus/PROBAV_LC100_global_v3.0.1_2019-nrt_Discrete-Classification-map_EPSG-4326.tif, data/gebco/GEBCO_2021_TID.nc, resources/shapes/country_shapes.geojson, resources/shapes/offshore_shapes.geojson, data/hydro_capacities.csv, data/eia_hydro_annual_generation.csv, resources/powerplants.csv, resources/bus_regions/regions_onshore.geojson, cutouts/cutout-2013-era5-tutorial.nc
output: resources/renewable_profiles/profile_solar.nc
log: logs/build_renewable_profile_solar.log (check log file(s) for error details)

RuleException:
CalledProcessError in file /Users/xxx/pypsa-earth/Snakefile, line 484:
Command 'set -euo pipefail; /opt/miniconda3/envs/pypsa-earth/bin/python3.10 /Users/xxx/pypsa-earth/.snakemake/scripts/tmp5_ny9xee.build_renewable_profiles.py' returned non-zero exit status 1.
File "/Users/xxx/pypsa-earth/Snakefile", line 484, in __rule_build_renewable_profiles
File "/opt/miniconda3/envs/pypsa-earth/lib/python3.10/concurrent/futures/thread.py", line 58, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-09-30T225500.825267.snakemake.log

[ekatef]

ValueError: coords is not dict-like, but it has 3 items, which does not match the 4 dimensions of the data [Mon Sep 30 22:58:41 2024] Error in rule build_renewable_profiles: jobid: 18 input: resources/natura.tiff, data/copernicus/PROBAV_LC100_global_v3.0.1_2019-nrt_Discrete-Classification-map_EPSG-4326.tif, data/gebco/GEBCO_2021_TID.nc, resources/shapes/country_shapes.geojson, resources/shapes/offshore_shapes.geojson, data/hydro_capacities.csv, data/eia_hydro_annual_generation.csv, resources/powerplants.csv, resources/bus_regions/regions_onshore.geojson, cutouts/cutout-2013-era5-tutorial.nc output: resources/renewable_profiles/profile_solar.nc log: logs/build_renewable_profile_solar.log (check log file(s) for error details)

RuleException: CalledProcessError in file /Users/xxx/pypsa-earth/Snakefile, line 484: Command 'set -euo pipefail; /opt/miniconda3/envs/pypsa-earth/bin/python3.10 /Users/xxx/pypsa-earth/.snakemake/scripts/tmp5_ny9xee.build_renewable_profiles.py' returned non-zero exit status 1. File "/Users/xxx/pypsa-earth/Snakefile", line 484, in __rule_build_renewable_profiles File "/opt/miniconda3/envs/pypsa-earth/lib/python3.10/concurrent/futures/thread.py", line 58, in run Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-09-30T225500.825267.snakemake.log

Thank you! Is it all the traceback you got? It would be great to see in which particular fragment of the code the error happens.

From the errors messages, I can guess that something is wrong with the cutout, like it doesn't cover the requested area or snapshots, but it would be great to have more details

[Constable1819]

[Mon Sep 30 22:58:19 2024]
rule build_renewable_profiles:
input: resources/natura.tiff, data/copernicus/PROBAV_LC100_global_v3.0.1_2019-nrt_Discrete-Classification-map_EPSG-4326.tif, data/gebco/GEBCO_2021_TID.nc, resources/shapes/country_shapes.geojson, resources/shapes/offshore_shapes.geojson, data/hydro_capacities.csv, data/eia_hydro_annual_generation.csv, resources/powerplants.csv, resources/bus_regions/regions_onshore.geojson, cutouts/cutout-2013-era5-tutorial.nc
output: resources/renewable_profiles/profile_solar.nc
log: logs/build_renewable_profile_solar.log
jobid: 18
benchmark: benchmarks/build_renewable_profiles_solar
reason: Missing output files: resources/renewable_profiles/profile_solar.nc; Input files updated by another job: cutouts/cutout-2013-era5-tutorial.nc, data/copernicus/PROBAV_LC100_global_v3.0.1_2019-nrt_Discrete-Classification-map_EPSG-4326.tif, data/gebco/GEBCO_2021_TID.nc, resources/shapes/offshore_shapes.geojson, resources/powerplants.csv, resources/bus_regions/regions_onshore.geojson, resources/shapes/country_shapes.geojson, resources/natura.tiff
wildcards: technology=solar
resources: tmpdir=/var/folders/r9/7fg7nyxj4m3_cb47j_qgsqw80000gn/T, mem_mb=20000, mem_mib=19074

/opt/miniconda3/envs/pypsa-earth/lib/python3.10/site-packages/pypsa/networkclustering.py:16: UserWarning: The namespace pypsa.networkclustering is deprecated and will be removed in PyPSA v0.24. Please use pypsa.clustering.spatial instead.
warnings.warn(
correction_factor is set as 0.854337
INFO:main:correction_factor is set as 0.854337
Calculate landuse availabilities...
INFO:main:Calculate landuse availabilities...
/opt/miniconda3/envs/pypsa-earth/lib/python3.10/site-packages/pypsa/networkclustering.py:16: UserWarning: The namespace pypsa.networkclustering is deprecated and will be removed in PyPSA v0.24. Please use pypsa.clustering.spatial instead.
warnings.warn(
Traceback (most recent call last):
File "/Users/xxx/pypsa-earth/.snakemake/scripts/tmp5_ny9xee.build_renewable_profiles.py", line 741, in
availability = cutout.availabilitymatrix(regions, excluder, **kwargs)
File "/opt/miniconda3/envs/pypsa-earth/lib/python3.10/site-packages/atlite/gis.py", line 761, in compute_availabilitymatrix
return xr.DataArray(availability, coords=coords)
File "/opt/miniconda3/envs/pypsa-earth/lib/python3.10/site-packages/xarray/core/dataarray.py", line 445, in init
coords, dims = _infer_coords_and_dims(data.shape, coords, dims)
File "/opt/miniconda3/envs/pypsa-earth/lib/python3.10/site-packages/xarray/core/dataarray.py", line 147, in _infer_coords_and_dims
raise ValueError(
ValueError: coords is not dict-like, but it has 3 items, which does not match the 4 dimensions of the data
[Mon Sep 30 22:58:41 2024]
Error in rule build_renewable_profiles:
jobid: 18
input: resources/natura.tiff, data/copernicus/PROBAV_LC100_global_v3.0.1_2019-nrt_Discrete-Classification-map_EPSG-4326.tif, data/gebco/GEBCO_2021_TID.nc, resources/shapes/country_shapes.geojson, resources/shapes/offshore_shapes.geojson, data/hydro_capacities.csv, data/eia_hydro_annual_generation.csv, resources/powerplants.csv, resources/bus_regions/regions_onshore.geojson, cutouts/cutout-2013-era5-tutorial.nc
output: resources/renewable_profiles/profile_solar.nc
log: logs/build_renewable_profile_solar.log (check log file(s) for error details)

RuleException:
CalledProcessError in file /Users/xxx/pypsa-earth/Snakefile, line 484:
Command 'set -euo pipefail; /opt/miniconda3/envs/pypsa-earth/bin/python3.10 /Users/xxx/pypsa-earth/.snakemake/scripts/tmp5_ny9xee.build_renewable_profiles.py' returned non-zero exit status 1.
File "/Users/xxx/pypsa-earth/Snakefile", line 484, in __rule_build_renewable_profiles
File "/opt/miniconda3/envs/pypsa-earth/lib/python3.10/concurrent/futures/thread.py", line 58, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-09-30T225500.825267.snakemake.log

[ekatef]

@Constable1819 thank you!! It appears that the reason is the mismatch between the requested countries and the cutout area and/or natura.tiff raster. Coild you please let know what is the list of countries you currently define in config.yaml?

[Constable1819]

@ekatef this is the tutorial config ["NG,BJ"], no edits have been made

[futuredataperson]

Halo @Constable1819 @ekatef I am getting a similar error for the tutorial too; coords is not dict-like, but it has 3 items, which does not match the 4 dimensions of the data. Have you found a solution?

[ekatef]

Hello @Constable1819 @futuredataperson, thanks for reporting the troubles. According the discussion in Support channel of PyPSA-meets-Earth server, the reason of these troubles is an update of rasterio version. Have created #1146 PR to fix that. Could you please test if using thisenvironment.yaml resolve the issue?

[Constable1819]

Hi @ekatef Yes it does. Thank you.

[ekatef]

Hi @ekatef Yes it does. Thank you.

Super, thank you so much for the confirmation