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PyPSA / atlite

Atlite: A Lightweight Python Package for Calculating Renewable Power Potentials and Time Series
https://atlite.readthedocs.io
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Unable to generate SARAH cutouts #369

Open rdcarr2 opened 1 month ago

rdcarr2 commented 1 month ago

Version Checks (indicate both or one)

Issue Description

Hey everyone, I'm trying to create SARAH cutouts for later use in producing PyPSA-Eur networks for different climate years, but keep getting the same error message after running cutout.prepare():

"ValueError: dimension lat on 0th function argument to apply_ufunc with dask='parallelized' consists of multiple chunks, but is also a core dimension. To fix, either rechunk into a single array chunk along this dimension, i.e., .chunk(dict(lat=-1)), or pass allow_rechunk=True in dask_gufunc_kwargs but beware that this may significantly increase memory usage."

I've tried the rechunking method suggested, but keep getting the same error regardless. I'm stuck now and not sure what to do, and ChatGPT is sending me in circles. Anyone experienced this issue and managed to find a solution?

Reproducible Example

import atlite
import logging

logging.basicConfig(level=logging.INFO)

cutout_2015_sarah = atlite.Cutout(
    path="europe-2015-sarah.nc",
    module=["sarah", "era5"],
    sarah_dir="/Users/robertcarr/Documents/HZB/Modelling/SARAH data/2014_2016",
    x=slice(-16.5, 40.5),
    y=slice(32.70, 75),
    time=slice("2015-01-01", "2015-02-01")
)

# Rechunk along the 'y' dimension
cutout_2015_sarah.data = cutout_2015_sarah.data.chunk(dict(y=-1))
cutout_2015_sarah.prepare()

Expected Behavior

Screenshot 2024-08-09 at 16 54 10

Installed Versions

name: pypsa-eur-RDC channels: - bioconda - defaults - conda-forge dependencies: - affine=2.4.0=pyhd8ed1ab_0 - ampl-mp=3.1.0=hbec66e7_1006 - amply=0.1.6=pyhd8ed1ab_0 - appdirs=1.4.4=pyh9f0ad1d_0 - appnope=0.1.4=pyhd8ed1ab_0 - argparse-dataclass=2.0.0=pyhd8ed1ab_0 - asttokens=2.4.1=pyhd8ed1ab_0 - atk-1.0=2.38.0=hd03087b_2 - atlite=0.2.13=pyhd8ed1ab_0 - attrs=23.2.0=pyh71513ae_0 - aws-c-auth=0.7.22=h8a62e84_10 - aws-c-cal=0.7.1=h94d0942_1 - aws-c-common=0.9.23=h99b78c6_0 - aws-c-compression=0.2.18=h94d0942_7 - aws-c-event-stream=0.4.2=hb74cd8f_15 - aws-c-http=0.8.2=had1507a_6 - aws-c-io=0.14.10=hcdb10ff_1 - aws-c-mqtt=0.10.4=h856d8ab_8 - aws-c-s3=0.6.0=ha9fd6de_2 - aws-c-sdkutils=0.1.16=h94d0942_3 - aws-checksums=0.1.18=h94d0942_7 - aws-crt-cpp=0.27.3=h9d3339c_2 - aws-sdk-cpp=1.11.329=he6360a2_9 - azure-core-cpp=1.12.0=hd01fc5c_0 - azure-identity-cpp=1.8.0=h0a11218_1 - azure-storage-blobs-cpp=12.11.0=h77cc766_1 - azure-storage-common-cpp=12.6.0=h7024f69_1 - azure-storage-files-datalake-cpp=12.10.0=h64d02d0_1 - beautifulsoup4=4.12.3=pyha770c72_0 - blosc=1.21.6=h5499902_0 - bokeh=3.5.0=pyhd8ed1ab_0 - bottleneck=1.4.0=py311h5d790af_1 - branca=0.7.2=pyhd8ed1ab_0 - brotli=1.1.0=hb547adb_1 - brotli-bin=1.1.0=hb547adb_1 - brotli-python=1.1.0=py311ha891d26_1 - bzip2=1.0.8=h99b78c6_7 - c-ares=1.32.3=h99b78c6_0 - c-blosc2=2.15.0=h5063078_1 - ca-certificates=2024.7.4=hf0a4a13_0 - cads-api-client=1.1.0=pyhd8ed1ab_0 - cairo=1.18.0=hc6c324b_2 - cartopy=0.23.0=py311h4b4568b_1 - cdsapi=0.7.0=pyhd8ed1ab_0 - certifi=2024.7.4=pyhd8ed1ab_0 - cffi=1.16.0=py311h4a08483_0 - cfgv=3.3.1=pyhd8ed1ab_0 - cfitsio=4.4.1=h793ed5c_0 - cftime=1.6.4=py311h5d790af_0 - charset-normalizer=3.3.2=pyhd8ed1ab_0 - click=8.1.7=unix_pyh707e725_0 - click-plugins=1.1.1=py_0 - cligj=0.7.2=pyhd8ed1ab_1 - cloudpickle=3.0.0=pyhd8ed1ab_0 - coin-or-cbc=2.10.11=h700c273_0 - coin-or-cgl=0.60.7=hf050ae7_0 - coin-or-clp=1.17.8=h65c2c7c_0 - coin-or-osi=0.108.10=h0dc0bf9_0 - coin-or-utils=2.11.11=hafd1a81_1 - coincbc=2.10.11=0_metapackage - colorama=0.4.6=pyhd8ed1ab_0 - comm=0.2.2=pyhd8ed1ab_0 - conda-inject=1.3.2=pyhd8ed1ab_0 - configargparse=1.7=pyhd8ed1ab_0 - connection_pool=0.0.3=pyhd3deb0d_0 - contourpy=1.2.1=py311hcc98501_0 - country_converter=1.2=pyhd8ed1ab_0 - cppad=20240000.5=h00cdb27_0 - cycler=0.12.1=pyhd8ed1ab_0 - cytoolz=0.12.3=py311h05b510d_0 - dask=2024.7.1=pyhd8ed1ab_0 - dask-core=2024.7.1=pyhd8ed1ab_0 - dask-expr=1.1.9=pyhd8ed1ab_0 - datrie=0.8.2=py311heffc1b2_7 - debugpy=1.8.2=py311hb9542d7_0 - decorator=5.1.1=pyhd8ed1ab_0 - deprecation=2.1.0=pyh9f0ad1d_0 - descartes=1.1.0=py_4 - distlib=0.3.8=pyhd8ed1ab_0 - distributed=2024.7.1=pyhd8ed1ab_0 - docutils=0.21.2=pyhd8ed1ab_0 - dpath=2.2.0=pyha770c72_0 - entsoe-py=0.6.8=pyhd8ed1ab_0 - et_xmlfile=1.1.0=pyhd8ed1ab_0 - exceptiongroup=1.2.2=pyhd8ed1ab_0 - executing=2.0.1=pyhd8ed1ab_0 - expat=2.6.2=hebf3989_0 - filelock=3.15.4=pyhd8ed1ab_0 - fiona=1.9.6=py311hf75b9fa_3 - fmt=10.2.1=h2ffa867_0 - folium=0.17.0=pyhd8ed1ab_0 - font-ttf-dejavu-sans-mono=2.37=hab24e00_0 - font-ttf-inconsolata=3.000=h77eed37_0 - font-ttf-source-code-pro=2.038=h77eed37_0 - font-ttf-ubuntu=0.83=h77eed37_2 - fontconfig=2.14.2=h82840c6_0 - fonts-conda-ecosystem=1=0 - fonts-conda-forge=1=0 - fonttools=4.53.1=py311hd3f4193_0 - freetype=2.12.1=hadb7bae_2 - freexl=2.0.0=hfbad9fb_0 - fribidi=1.0.10=h27ca646_0 - fsspec=2024.6.1=pyhff2d567_0 - gdal=3.9.1=py311h08b0975_8 - gdk-pixbuf=2.42.12=h7ddc832_0 - geographiclib=2.0=pyhd8ed1ab_0 - geojson-rewind=1.1.0=pyhd8ed1ab_0 - geopandas=1.0.1=pyhd8ed1ab_0 - geopandas-base=1.0.1=pyha770c72_0 - geopy=2.4.1=pyhd8ed1ab_1 - geos=3.12.2=h00cdb27_1 - geotiff=1.7.3=h7e5fb84_1 - gflags=2.2.2=hc88da5d_1004 - giflib=5.2.2=h93a5062_0 - gitdb=4.0.11=pyhd8ed1ab_0 - gitpython=3.1.43=pyhd8ed1ab_0 - glog=0.7.1=heb240a5_0 - glpk=5.0=h6d7a090_0 - gmp=6.3.0=h7bae524_2 - graphite2=1.3.13=hebf3989_1003 - graphviz=11.0.0=h9bb9bc9_0 - gtk2=2.24.33=h91d5085_5 - gts=0.7.6=he42f4ea_4 - h2=4.1.0=pyhd8ed1ab_0 - harfbuzz=9.0.0=h1836168_0 - hdf4=4.2.15=h2ee6834_7 - hdf5=1.14.3=nompi_hec07895_105 - hpack=4.0.0=pyh9f0ad1d_0 - humanfriendly=10.0=pyhd8ed1ab_6 - hyperframe=6.0.1=pyhd8ed1ab_0 - icu=73.2=hc8870d7_0 - identify=2.6.0=pyhd8ed1ab_0 - idna=3.7=pyhd8ed1ab_0 - immutables=0.20=py311heffc1b2_1 - importlib-metadata=8.1.0=pyha770c72_0 - importlib_metadata=8.1.0=hd8ed1ab_0 - importlib_resources=6.4.0=pyhd8ed1ab_0 - iniconfig=2.0.0=pyhd8ed1ab_0 - ipopt=3.14.16=h387674d_4 - ipykernel=6.29.5=pyh57ce528_0 - ipython=8.26.0=pyh707e725_0 - jedi=0.19.1=pyhd8ed1ab_0 - jinja2=3.1.4=pyhd8ed1ab_0 - joblib=1.4.2=pyhd8ed1ab_0 - json-c=0.17=he54c16a_1 - jsonschema=4.23.0=pyhd8ed1ab_0 - jsonschema-specifications=2023.12.1=pyhd8ed1ab_0 - jupyter_client=8.6.2=pyhd8ed1ab_0 - jupyter_core=5.7.2=py311h267d04e_0 - kealib=1.5.3=h848a2d4_1 - kiwisolver=1.4.5=py311he4fd1f5_1 - krb5=1.21.3=h237132a_0 - lcms2=2.16=ha0e7c42_0 - lerc=4.0.0=h9a09cb3_0 - libabseil=20240116.2=cxx17_h00cdb27_1 - libaec=1.1.3=hebf3989_0 - libarchive=3.7.4=h83d404f_0 - libarrow=17.0.0=h2a00445_0_cpu - libarrow-acero=17.0.0=h00cdb27_0_cpu - libarrow-dataset=17.0.0=h00cdb27_0_cpu - libarrow-substrait=17.0.0=hc68f6b8_0_cpu - libblas=3.9.0=23_osxarm64_openblas - libbrotlicommon=1.1.0=hb547adb_1 - libbrotlidec=1.1.0=hb547adb_1 - libbrotlienc=1.1.0=hb547adb_1 - libcblas=3.9.0=23_osxarm64_openblas - libcrc32c=1.1.2=hbdafb3b_0 - libcurl=8.9.0=hfd8ffcc_0 - libcxx=18.1.8=h167917d_0 - libdeflate=1.20=h93a5062_0 - libedit=3.1.20191231=hc8eb9b7_2 - libev=4.33=h93a5062_2 - libevent=2.1.12=h2757513_1 - libexpat=2.6.2=hebf3989_0 - libffi=3.4.2=h3422bc3_5 - libgd=2.3.3=hfdf3952_9 - libgdal=3.9.1=hce30654_8 - libgdal-core=3.9.1=hf00468f_8 - libgdal-fits=3.9.1=h7a7a030_8 - libgdal-grib=3.9.1=hdd4b840_8 - libgdal-hdf4=3.9.1=h94124bd_8 - libgdal-hdf5=3.9.1=hf90b89a_8 - libgdal-jp2openjpeg=3.9.1=h54bcb16_8 - libgdal-kea=3.9.1=hacb1b3e_8 - libgdal-netcdf=3.9.1=h1723b65_8 - libgdal-pdf=3.9.1=h4cf08c4_8 - libgdal-pg=3.9.1=h7d28298_8 - libgdal-postgisraster=3.9.1=h7d28298_8 - libgdal-tiledb=3.9.1=hbb20944_8 - libgdal-xls=3.9.1=hb39617b_8 - libgfortran=5.0.0=13_2_0_hd922786_3 - libgfortran5=13.2.0=hf226fd6_3 - libglib=2.80.3=h59d46d9_1 - libgoogle-cloud=2.26.0=hfe08963_0 - libgoogle-cloud-storage=2.26.0=h1466eeb_0 - libgrpc=1.62.2=h9c18a4f_0 - libhwloc=2.11.1=default_h7685b71_1000 - libiconv=1.17=h0d3ecfb_2 - libintl=0.22.5=h8fbad5d_2 - libjpeg-turbo=3.0.0=hb547adb_1 - libkml=1.3.0=h00ed6cc_1020 - liblapack=3.9.0=23_osxarm64_openblas - liblapacke=3.9.0=23_osxarm64_openblas - libnetcdf=4.9.2=nompi_he469be0_114 - libnghttp2=1.58.0=ha4dd798_1 - libopenblas=0.3.27=openmp_h517c56d_1 - libparquet=17.0.0=hcf52c46_0_cpu - libpng=1.6.43=h091b4b1_0 - libpq=16.3=h7afe498_0 - libprotobuf=4.25.3=hbfab5d5_0 - libre2-11=2023.09.01=h7b2c953_2 - librsvg=2.58.2=h1db61d3_1 - librttopo=1.1.0=h31fb324_16 - libscotch=7.0.4=h7c38b86_5 - libsodium=1.0.18=h27ca646_1 - libspatialite=5.1.0=hf7a34df_8 - libsqlite=3.46.0=hfb93653_0 - libssh2=1.11.0=h7a5bd25_0 - libthrift=0.19.0=h026a170_1 - libtiff=4.6.0=h07db509_3 - libutf8proc=2.8.0=h1a8c8d9_0 - libwebp=1.4.0=h54798ee_0 - libwebp-base=1.4.0=h93a5062_0 - libxcb=1.16=hf2054a2_0 - libxml2=2.12.7=h9a80f22_3 - libxslt=1.1.39=h223e5b9_0 - libzip=1.10.1=ha0bc3c6_3 - libzlib=1.3.1=hfb2fe0b_1 - linopy=0.3.13=pyhd8ed1ab_0 - llvm-openmp=18.1.8=hde57baf_0 - locket=1.0.0=pyhd8ed1ab_0 - lxml=5.2.2=py311hf9a6a72_0 - lz4=4.3.3=py311hd44b8e9_0 - lz4-c=1.9.4=hb7217d7_0 - lzo=2.10=h93a5062_1001 - mapclassify=2.6.1=pyhd8ed1ab_0 - markupsafe=2.1.5=py311h05b510d_0 - matplotlib=3.9.1=py311ha1ab1f8_0 - matplotlib-base=3.9.1=py311hba6b155_0 - matplotlib-inline=0.1.7=pyhd8ed1ab_0 - memory_profiler=0.61.0=pyhd8ed1ab_0 - metis=5.1.0=h13dd4ca_1007 - minizip=4.0.7=h27ee973_0 - mpfr=4.2.1=h41d338b_1 - msgpack-python=1.0.8=py311h6bde47b_0 - multiurl=0.3.1=pyhd8ed1ab_0 - mumps-include=5.7.2=hce30654_0 - mumps-seq=5.7.2=hab9b160_0 - munkres=1.1.4=pyh9f0ad1d_0 - nbformat=5.10.4=pyhd8ed1ab_0 - ncurses=6.5=hb89a1cb_0 - nest-asyncio=1.6.0=pyhd8ed1ab_0 - netcdf4=1.7.1=nompi_py311h42682c7_101 - networkx=3.3=pyhd8ed1ab_1 - nodeenv=1.9.1=pyhd8ed1ab_0 - nspr=4.35=hb7217d7_0 - nss=3.102=hc42bcbf_0 - numexpr=2.10.0=py311h4b4568b_0 - numpy=1.26.4=py311h7125741_0 - openjdk=22.0.1=h363fedd_1 - openjpeg=2.5.2=h9f1df11_0 - openpyxl=3.1.4=py311h1fc4b72_0 - openssl=3.3.1=hfb2fe0b_2 - orc=2.0.1=h47ade37_1 - packaging=24.1=pyhd8ed1ab_0 - pandas=2.2.2=py311h4b4568b_1 - pango=1.54.0=h9ee27a3_1 - parso=0.8.4=pyhd8ed1ab_0 - partd=1.4.2=pyhd8ed1ab_0 - patsy=0.5.6=pyhd8ed1ab_0 - pcre2=10.44=h297a79d_0 - pexpect=4.9.0=pyhd8ed1ab_0 - pickleshare=0.7.5=py_1003 - pillow=10.4.0=py311hd7951ec_0 - pip=24.0=pyhd8ed1ab_0 - pixman=0.43.4=hebf3989_0 - pkgutil-resolve-name=1.3.10=pyhd8ed1ab_1 - plac=1.4.3=pyhd8ed1ab_0 - platformdirs=4.2.2=pyhd8ed1ab_0 - pluggy=1.5.0=pyhd8ed1ab_0 - ply=3.11=pyhd8ed1ab_2 - polars=1.2.1=py311h9e175c1_0 - poppler=24.07.0=h9787579_0 - poppler-data=0.4.12=hd8ed1ab_0 - postgresql=16.3=hdfa2ec6_0 - powerplantmatching=0.5.15=pyhd8ed1ab_0 - pre-commit=3.7.1=pyha770c72_0 - progressbar2=4.4.2=pyhd8ed1ab_0 - proj=9.4.1=hfb94cee_0 - prompt-toolkit=3.0.47=pyha770c72_0 - psutil=6.0.0=py311hd3f4193_0 - pthread-stubs=0.4=h27ca646_1001 - ptyprocess=0.7.0=pyhd3deb0d_0 - pulp=2.8.0=py311h267d04e_0 - pure_eval=0.2.3=pyhd8ed1ab_0 - py-cpuinfo=9.0.0=pyhd8ed1ab_0 - pyarrow=17.0.0=py311h35c05fe_0 - pyarrow-core=17.0.0=py311hf5072a7_0_cpu - pyarrow-hotfix=0.6=pyhd8ed1ab_0 - pycountry=24.6.1=pyhd8ed1ab_0 - pycparser=2.22=pyhd8ed1ab_0 - pygments=2.18.0=pyhd8ed1ab_0 - pyogrio=0.8.0=py311he661659_2 - pyomo=6.6.1=py311ha891d26_0 - pyparsing=3.1.2=pyhd8ed1ab_0 - pyproj=3.6.1=py311h5e0e26b_7 - pypsa=0.28.0=pyhd8ed1ab_0 - pyscipopt=5.1.1=py311hb9542d7_0 - pyshp=2.3.1=pyhd8ed1ab_0 - pysocks=1.7.1=pyha2e5f31_6 - pytables=3.9.2=py311h5d6d252_3 - pytest=8.3.1=pyhd8ed1ab_0 - python=3.11.9=h932a869_0_cpython - python-dateutil=2.9.0=pyhd8ed1ab_0 - python-fastjsonschema=2.20.0=pyhd8ed1ab_0 - python-tzdata=2024.1=pyhd8ed1ab_0 - python-utils=3.8.2=pyhd8ed1ab_0 - python_abi=3.11=4_cp311 - pytz=2024.1=pyhd8ed1ab_0 - pyxlsb=1.0.10=pyhd8ed1ab_0 - pyyaml=6.0.1=py311heffc1b2_1 - pyzmq=26.0.3=py311h9bed540_0 - qhull=2020.2=h420ef59_5 - rasterio=1.3.10=py311he66545a_4 - 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euronion commented 3 weeks ago

Hey there!

I haven't seen the issue before. I think the underlying rechunk would need to happen on the SARAH data, not on the cutout. A wild guess would be that you could you try to pass the chunk argument to the prepare(...) function similarly as shown in the example here:

https://atlite.readthedocs.io/en/latest/examples/create_cutout_SARAH.html#Specifying-the-cutout