ClimateCompatibleGrowth / GeoH2

Geospatial analysis of green hydrogen production costs.
MIT License
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optimized_hydrogen_plant cause get_weather_data error #22

Open Bachirou06 opened 1 week ago

Bachirou06 commented 1 week ago

Again, as i copy the data_year.nc downloaded from the previous version instead of using the snakefile -j get_weather.py because when using the later the algorithm download the .nc file in the temp folder without combining them in one single file in the Cutouts folder. below is the snaphot:

Probable cause could be maybe the location of the temp file path, which need more specification on where the temp file should be path ((# TEMPDIR DEFINITION IS NEW TO FIX ERROR # ??))

first error hex_lcoh: /GeoH2-main_new_NE$ snakemake -j 1 Resources/hex_lcoh_NE_2023.geojson Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Job stats: job count


get_weather_data 1 optimize_hydrogen_plant 1 total 2

Select jobs to execute...

[Fri Oct 25 06:17:08 2024] rule get_weather_data: input: Data/hexagons_with_country_NE.geojson output: Cutouts/NE_2023.nc jobid: 1 reason: Missing output files: Cutouts/NE_2023.nc wildcards: country=NE, weather_year=2023 resources: tmpdir=/tmp

INFO:atlite.cutout:Building new cutout Cutouts/NE_2023.nc INFO:atlite.data:Storing temporary files in temp INFO:atlite.data:Calculating and writing with module era5: Traceback (most recent call last): File "/home/bachirou/GeoH2-main_new_NE/.snakemake/scripts/tmpa7157ab8.get_weather_data.py", line 58, in cutout.prepare(tmpdir="temp") # TEMPDIR DEFINITION IS NEW TO FIX ERROR # /home/bachirou/GeoH2-main_new_NE/temp/ C:\Users\hp\AppData\Local\Temp snakemake -j [NUMBER OF CORES TO BE USED] Resources/hextransport[COUNTRY ISO CODE].geojson # C:\Users\hp\AppData\Local\Temp\tmpaynbmwwm File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/atlite/data.py", line 98, in wrapper res = func(*args, *kwargs) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/atlite/data.py", line 164, in cutout_prepare ds = get_features(cutout, module, missing_features, tmpdir=tmpdir) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/atlite/data.py", line 46, in get_features datasets = compute(datasets) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/dask/base.py", line 662, in compute results = schedule(dsk, keys, kwargs) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/atlite/datasets/era5.py", line 352, in get_data "area": _area(coords), File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/atlite/datasets/era5.py", line 227, in _area x0, x1 = coords["x"].min().item(), coords["x"].max().item() File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/_aggregations.py", line 1581, in min return self.reduce( File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/dataarray.py", line 3834, in reduce var = self.variable.reduce(func, dim, axis, keep_attrs, keepdims, kwargs) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/variable.py", line 1666, in reduce result = super().reduce( File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/namedarray/core.py", line 912, in reduce data = func(self.data, kwargs) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/duck_array_ops.py", line 447, in f return func(values, axis=axis, kwargs) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/nanops.py", line 71, in nanmin return nputils.nanmin(a, axis=axis) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/nputils.py", line 232, in f result = bn_func(values, axis=axis, **kwargs) ValueError: numpy.nanmin raises on a.size==0 and axis=None; So Bottleneck too. [Fri Oct 25 06:17:10 2024] Error in rule get_weather_data: jobid: 1 input: Data/hexagons_with_country_NE.geojson output: Cutouts/NE_2023.nc

RuleException: CalledProcessError in file /home/bachirou/GeoH2-main_new_NE/Snakefile, line 41: Command 'set -euo pipefail; /home/bachirou/miniconda3/envs/geoh2s/bin/python3.10 /home/bachirou/GeoH2-main_new_NE/.snakemake/scripts/tmpa7157ab8.get_weather_data.py' returned non-zero exit status 1. File "/home/bachirou/GeoH2-main_new_NE/Snakefile", line 41, in __rule_get_weather_data File "/home/bachirou/miniconda3/envs/geoh2s/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/2024-10-25T061707.897314.snakemake.log

second error get_weather_data /GeoH2-main_new_NE$ snakemake -j 1 Cutouts/NE_2023.nc Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Job stats: job count


get_weather_data 1 total 1

Select jobs to execute...

[Fri Oct 25 06:18:27 2024] rule get_weather_data: input: Data/hexagons_with_country_NE.geojson output: Cutouts/NE_2023.nc jobid: 0 reason: Missing output files: Cutouts/NE_2023.nc wildcards: country=NE, weather_year=2023 resources: tmpdir=/tmp

INFO:atlite.cutout:Building new cutout Cutouts/NE_2023.nc INFO:atlite.data:Storing temporary files in temp INFO:atlite.data:Calculating and writing with module era5: Traceback (most recent call last): File "/home/bachirou/GeoH2-main_new_NE/.snakemake/scripts/tmpey999h_0.get_weather_data.py", line 58, in cutout.prepare(tmpdir="temp") # TEMPDIR DEFINITION IS NEW TO FIX ERROR # File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/atlite/data.py", line 98, in wrapper res = func(*args, *kwargs) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/atlite/data.py", line 164, in cutout_prepare ds = get_features(cutout, module, missing_features, tmpdir=tmpdir) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/atlite/data.py", line 46, in get_features datasets = compute(datasets) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/dask/base.py", line 662, in compute results = schedule(dsk, keys, kwargs) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/atlite/datasets/era5.py", line 352, in get_data "area": _area(coords), File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/atlite/datasets/era5.py", line 227, in _area x0, x1 = coords["x"].min().item(), coords["x"].max().item() File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/_aggregations.py", line 1581, in min return self.reduce( File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/dataarray.py", line 3834, in reduce var = self.variable.reduce(func, dim, axis, keep_attrs, keepdims, kwargs) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/variable.py", line 1666, in reduce result = super().reduce( File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/namedarray/core.py", line 912, in reduce data = func(self.data, kwargs) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/duck_array_ops.py", line 447, in f return func(values, axis=axis, kwargs) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/nanops.py", line 71, in nanmin return nputils.nanmin(a, axis=axis) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/nputils.py", line 232, in f result = bn_func(values, axis=axis, **kwargs) ValueError: numpy.nanmin raises on a.size==0 and axis=None; So Bottleneck too. [Fri Oct 25 06:18:29 2024] Error in rule get_weather_data: jobid: 0 input: Data/hexagons_with_country_NE.geojson output: Cutouts/NE_2023.nc

RuleException: CalledProcessError in file /home/bachirou/GeoH2-main_new_NE/Snakefile, line 41: Command 'set -euo pipefail; /home/bachirou/miniconda3/envs/geoh2s/bin/python3.10 /home/bachirou/GeoH2-main_new_NE/.snakemake/scripts/tmpey999h_0.get_weather_data.py' returned non-zero exit status 1. File "/home/bachirou/GeoH2-main_new_NE/Snakefile", line 41, in __rule_get_weather_data File "/home/bachirou/miniconda3/envs/geoh2s/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/2024-10-25T061827.048691.snakemake.log

samiyhanaqvi commented 1 week ago

Hi,

Thank you for sharing this issue that you're facing. Hopefully we can solve this quickly and easily!

A couple of notes: Firstly, the error is just from the get_weather_data rule and is the same error, not two separate ones. This is due to the optimize_hydrogen_plant rule requiring the nc file and if it is not there, snakemake will run the get_weather_data rule before running the optimize_hydrogen_plant rule.

Secondly, when it runs successfully the rule should download a bunch of files into a "temp" folder and then in the end it will output the desired, complete nc file in the "Cutouts" folder. Unfortunately, your runs are getting interrupted with an error and so you've just been left with the temp files and not the end file.

Things to get me up to speed with what is going on on your side, as I have just ran this and it's not an issue with the code:

samiyhanaqvi commented 1 week ago

This issue could be with the package versions that we have in our current environment file. I had been testing the new cdsapi and updated versions locally without updating the repo.

If you could try git pull, as I've just updated, and run the get_weather_data rule again. I hope this will solve the issue!

Bachirou06 commented 1 week ago

Hi @samiyhanaqvi ,

Thanks for your time.

So far, I have followed the instructions you stated. I have checked the URL and token; everything seems fine. I have also updated the athlete to 0.2.14, as I am still facing the same issue. Please kindly have a look below at the installed packages of the environment.

mamba list

packages in environment at /home/bachirou/miniconda3/envs/geoh:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge affine 2.4.0 pyhd8ed1ab_0 conda-forge aioeasywebdav 2.4.0 pyha770c72_0 conda-forge aiohappyeyeballs 2.4.3 pyhd8ed1ab_0 conda-forge aiohttp 3.10.10 py310h89163eb_0 conda-forge aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge alsa-lib 1.2.8 h166bdaf_0 conda-forge amply 0.1.6 pyhd8ed1ab_0 conda-forge annotated-types 0.7.0 pyhd8ed1ab_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge arrow-cpp 10.0.1 h3e2b116_4_cpu conda-forge async-timeout 4.0.3 pyhd8ed1ab_0 conda-forge atlite 0.2.14 pyhd8ed1ab_0 conda-forge attr 2.5.1 h166bdaf_1 conda-forge attrs 24.2.0 pyh71513ae_0 conda-forge aws-c-auth 0.6.21 h774e2f3_1 conda-forge aws-c-cal 0.5.20 hd3b2fe5_3 conda-forge aws-c-common 0.8.5 h166bdaf_0 conda-forge aws-c-compression 0.2.16 hf5f93bc_0 conda-forge aws-c-event-stream 0.2.16 h52dae97_0 conda-forge aws-c-http 0.6.29 hf21410f_0 conda-forge aws-c-io 0.13.11 h4f448d1_2 conda-forge aws-c-mqtt 0.7.13 hefb3e95_10 conda-forge aws-c-s3 0.2.1 h2b8044a_2 conda-forge aws-c-sdkutils 0.1.7 hf5f93bc_0 conda-forge aws-checksums 0.1.14 h6027aba_0 conda-forge aws-crt-cpp 0.18.16 h89864ff_5 conda-forge aws-sdk-cpp 1.9.379 hc894300_6 conda-forge bcrypt 4.2.0 py310h505e2c1_1 conda-forge blosc 1.21.5 h0f2a231_0 conda-forge bokeh 3.6.0 pyhd8ed1ab_0 conda-forge boost-cpp 1.78.0 h5adbc97_2 conda-forge boto3 1.35.49 pyhd8ed1ab_0 conda-forge botocore 1.35.49 pyge310_1234567_0 conda-forge bottleneck 1.4.2 py310hf462985_0 conda-forge branca 0.7.2 pyhd8ed1ab_0 conda-forge brotli 1.0.9 h166bdaf_9 conda-forge brotli-bin 1.0.9 h166bdaf_9 conda-forge brotli-python 1.0.9 py310hd8f1fbe_9 conda-forge bzip2 1.0.8 h4bc722e_7 conda-forge c-ares 1.32.3 h4bc722e_0 conda-forge ca-certificates 2024.9.24 h06a4308_0
cachetools 5.5.0 pyhd8ed1ab_0 conda-forge cads-api-client 1.4.7 pyhd8ed1ab_0 conda-forge cairo 1.16.0 ha61ee94_1014 conda-forge cartopy 0.24.0 py310h5eaa309_0 conda-forge cdsapi 0.7.4 pyhd8ed1ab_0 conda-forge certifi 2024.8.30 py310h06a4308_0
cffi 1.17.1 py310h8deb56e_0 conda-forge cfitsio 4.1.0 hd9d235c_0 conda-forge cftime 1.6.4 py310hf462985_1 conda-forge charset-normalizer 3.4.0 pyhd8ed1ab_0 conda-forge click 8.1.7 unix_pyh707e725_0 conda-forge click-plugins 1.1.1 py_0 conda-forge cligj 0.7.2 pyhd8ed1ab_1 conda-forge cloudpickle 3.1.0 pyhd8ed1ab_1 conda-forge coin-or-cbc 2.10.12 h8b142ea_1 conda-forge coin-or-cgl 0.60.7 h516709c_0 conda-forge coin-or-clp 1.17.8 h1ee7a9c_0 conda-forge coin-or-osi 0.108.10 haf5fa05_0 conda-forge coin-or-utils 2.11.11 hee58242_0 conda-forge coincbc 2.10.12 1_metapackage conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge coloredlogs 15.0.1 pyhd8ed1ab_3 conda-forge configargparse 1.7 pyhd8ed1ab_0 conda-forge connection_pool 0.0.3 pyhd3deb0d_0 conda-forge contourpy 1.3.0 py310h3788b33_2 conda-forge cryptography 39.0.0 py310h65dfdc0_0 conda-forge curl 7.86.0 h7bff187_1 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge cytoolz 1.0.0 py310ha75aee5_1 conda-forge dask 2024.8.1 pyhd8ed1ab_0 conda-forge dask-core 2024.8.1 pyhd8ed1ab_0 conda-forge dask-expr 1.1.11 pyhd8ed1ab_0 conda-forge datrie 0.8.2 py310ha75aee5_8 conda-forge dbus 1.13.6 h5008d03_3 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge deprecation 2.1.0 pyh9f0ad1d_0 conda-forge distributed 2024.8.1 pyhd8ed1ab_0 conda-forge docutils 0.21.2 pyhd8ed1ab_0 conda-forge dpath 2.2.0 pyha770c72_0 conda-forge dropbox 12.0.2 pyhd8ed1ab_0 conda-forge eido 0.2.4 pyhd8ed1ab_0 conda-forge et_xmlfile 2.0.0 pyhd8ed1ab_0 conda-forge exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge expat 2.6.3 h5888daf_0 conda-forge fftw 3.3.10 nompi_hf1063bd_110 conda-forge filechunkio 1.8 py_2 conda-forge fiona 1.8.22 py310ha325b7b_5 conda-forge folium 0.18.0 pyhd8ed1ab_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 h77eed37_3 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.54.1 py310h89163eb_1 conda-forge freetype 2.12.1 h267a509_2 conda-forge freexl 1.0.6 h166bdaf_1 conda-forge frozenlist 1.5.0 py310ha75aee5_0 conda-forge fsspec 2024.10.0 pyhff2d567_0 conda-forge ftputil 5.1.0 pyhd8ed1ab_0 conda-forge gdal 3.6.0 py310hb7951cf_1 conda-forge geographiclib 2.0 pyhd8ed1ab_0 conda-forge geopandas 0.14.4 pyhd8ed1ab_0 conda-forge geopandas-base 0.14.4 pyha770c72_0 conda-forge geopy 2.4.1 pyhd8ed1ab_1 conda-forge geos 3.11.0 h27087fc_0 conda-forge geotiff 1.7.1 ha76d385_4 conda-forge gettext 0.22.5 he02047a_3 conda-forge gettext-tools 0.22.5 he02047a_3 conda-forge gflags 2.2.2 h5888daf_1005 conda-forge giflib 5.2.2 hd590300_0 conda-forge gitdb 4.0.11 pyhd8ed1ab_0 conda-forge gitpython 3.1.43 pyhd8ed1ab_0 conda-forge glib 2.80.2 hf974151_0 conda-forge glib-tools 2.80.2 hb6ce0ca_0 conda-forge glog 0.6.0 h6f12383_0 conda-forge google-api-core 2.21.0 pyhd8ed1ab_0 conda-forge google-api-python-client 2.149.0 pyhff2d567_0 conda-forge google-auth 2.35.0 pyhff2d567_0 conda-forge google-auth-httplib2 0.2.0 pyhd8ed1ab_0 conda-forge google-cloud-core 2.4.1 pyhd8ed1ab_0 conda-forge google-cloud-storage 2.18.2 pyhff2d567_0 conda-forge google-crc32c 1.1.2 py310hd027165_6 conda-forge google-resumable-media 2.7.2 pyhd8ed1ab_1 conda-forge googleapis-common-protos 1.65.0 pyhd8ed1ab_0 conda-forge grpcio 1.51.1 py310h5b20944_0 conda-forge gst-plugins-base 1.21.3 h4243ec0_1 conda-forge gstreamer 1.21.3 h25f0c4b_1 conda-forge gstreamer-orc 0.4.40 hb9d3cd8_0 conda-forge h2 4.1.0 pyhd8ed1ab_0 conda-forge hdf4 4.2.15 h9772cbc_5 conda-forge hdf5 1.12.2 nompi_h2386368_100 conda-forge hpack 4.0.0 pyh9f0ad1d_0 conda-forge httplib2 0.22.0 pyhd8ed1ab_0 conda-forge humanfriendly 10.0 pyhd8ed1ab_6 conda-forge hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge icu 70.1 h27087fc_0 conda-forge idna 3.10 pyhd8ed1ab_0 conda-forge importlib-metadata 8.5.0 pyha770c72_0 conda-forge importlib_metadata 8.5.0 hd8ed1ab_0 conda-forge importlib_resources 6.4.5 pyhd8ed1ab_0 conda-forge iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge jack 1.9.22 h11f4161_0 conda-forge jinja2 3.1.4 pyhd8ed1ab_0 conda-forge jmespath 1.0.1 pyhd8ed1ab_0 conda-forge joblib 1.4.2 pyhd8ed1ab_0 conda-forge jpeg 9e h0b41bf4_3 conda-forge json-c 0.16 hc379101_0 conda-forge jsonschema 4.23.0 pyhd8ed1ab_0 conda-forge jsonschema-specifications 2024.10.1 pyhd8ed1ab_0 conda-forge jupyter_core 5.7.2 pyh31011fe_1 conda-forge kealib 1.4.15 ha7026e8_1 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.7 py310h3788b33_0 conda-forge krb5 1.19.3 h3790be6_0 conda-forge lame 3.100 h166bdaf_1003 conda-forge lcms2 2.14 h6ed2654_0 conda-forge ld_impl_linux-64 2.43 h712a8e2_2 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libabseil 20220623.0 cxx17_h05df665_6 conda-forge libarrow 10.0.1 hee49ebd_4_cpu conda-forge libasprintf 0.22.5 he8f35ee_3 conda-forge libasprintf-devel 0.22.5 he8f35ee_3 conda-forge libblas 3.9.0 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Bachirou06 commented 1 week ago

Hi @samiyhanaqvi

To confirm whether the issue is from the atlite I have run the get_weather_data.py on the previous without the snakemake the algorithm create the temp and some tempwcxz.nc file inside while enabling to combine those file in one single country.nc file in Cut.couts.

Maybe we need to look at if the issue is not related to snakmake python get_weather_data.py INFO:atlite.cutout:Building new cutout Cutouts/Niger-2023.nc INFO:atlite.data:Storing temporary files in temp INFO:atlite.data:Calculating and writing with module era5: INFO:atlite.datasets.era5:Requesting data for feature wind... INFO:atlite.datasets.era5:Requesting data for feature height... INFO:atlite.datasets.era5:Requesting data for feature temperature... INFO:atlite.datasets.era5:Requesting data for feature influx... ......... .... ...

download

mamba activate geoh2s (geoh2s) bachirou@djibo:~/GeoH2-main_new_NE$ snakemake -j 2 Cutouts/NE_2023.nc Building DAG of jobs... Using shell: /bin/bash Provided cores: 2 Rules claiming more threads will be scaled down. Job stats: job count


get_weather_data 1 total 1

Select jobs to execute...

[Wed Oct 30 22:23:07 2024] rule get_weather_data: input: Data/hexagons_with_country_NE.geojson output: Cutouts/NE_2023.nc jobid: 0 reason: Missing output files: Cutouts/NE_2023.nc wildcards: country=NE, weather_year=2023 resources: tmpdir=/tmp

INFO:atlite.cutout:Building new cutout Cutouts/NE_2023.nc INFO:atlite.data:Storing temporary files in temp INFO:atlite.data:Calculating and writing with module era5: Traceback (most recent call last): File "/home/bachirou/GeoH2-main_new_NE/.snakemake/scripts/tmpl7v6rffm.get_weather_data.py", line 58, in cutout.prepare(tmpdir="temp") # TEMPDIR DEFINITION IS NEW TO FIX ERROR File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/atlite/data.py", line 98, in wrapper res = func(*args, *kwargs) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/atlite/data.py", line 164, in cutout_prepare ds = get_features(cutout, module, missing_features, tmpdir=tmpdir) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/atlite/data.py", line 46, in get_features datasets = compute(datasets) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/dask/base.py", line 662, in compute results = schedule(dsk, keys, kwargs) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/atlite/datasets/era5.py", line 352, in get_data "area": _area(coords), File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/atlite/datasets/era5.py", line 227, in _area x0, x1 = coords["x"].min().item(), coords["x"].max().item() File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/_aggregations.py", line 1581, in min return self.reduce( File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/dataarray.py", line 3834, in reduce var = self.variable.reduce(func, dim, axis, keep_attrs, keepdims, kwargs) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/variable.py", line 1666, in reduce result = super().reduce( File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/namedarray/core.py", line 912, in reduce data = func(self.data, kwargs) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/duck_array_ops.py", line 447, in f return func(values, axis=axis, kwargs) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/nanops.py", line 71, in nanmin return nputils.nanmin(a, axis=axis) File "/home/bachirou/miniconda3/envs/geoh2s/lib/python3.10/site-packages/xarray/core/nputils.py", line 232, in f result = bn_func(values, axis=axis, **kwargs) ValueError: numpy.nanmin raises on a.size==0 and axis=None; So Bottleneck too. [Wed Oct 30 22:23:21 2024] Error in rule get_weather_data: jobid: 0 input: Data/hexagons_with_country_NE.geojson output: Cutouts/NE_2023.nc

RuleException: CalledProcessError in file /home/bachirou/GeoH2-main_new_NE/Snakefile, line 41: Command 'set -euo pipefail; /home/bachirou/miniconda3/envs/geoh2s/bin/python3.10 /home/bachirou/GeoH2-main_new_NE/.snakemake/scripts/tmpl7v6rffm.get_weather_data.py' returned non-zero exit status 1. File "/home/bachirou/GeoH2-main_new_NE/Snakefile", line 41, in __rule_get_weather_data File "/home/bachirou/miniconda3/envs/geoh2s/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/2024-10-30T222258.256910.snakemake.log

samiyhanaqvi commented 1 week ago

Hi,

I need to look through the packages and see if there are any compatibility issues there. I wanted to reply to clear up that there is not an issue with snakemake. Snakemake has just notified us of the issue that is happening when you run the get_weather_data.py file.

Just to make sure we're on the same page - did you update Atlite in your old environment file and then run the old get_weather_data.py file and it worked?

You should have two environments and if it's working with one and not the other, I suspect that there is an issue with the environment and the package versions. It would be helpful if you could run the following for both environments. (It will produce a file with the file name given at the end, make sure to change that for each environment.)

mamba env export --no-builds | grep -v "prefix" > file1.yaml

Could you then attach both to your reply and I can then compare them to see if the issue is there.

Bachirou06 commented 5 days ago

Hi @samiyhanaqvi,

Thanks for clarifying regarding the snakemake. It seems the old environment is requesting to update some package. So i updated and run the env2 the attached file.ymal is below. I have also tested something that would be helpful to resolve the issue, i have copied the get_weather_data.py and weather_parameters.xlsx from the previous versions folder and pasted into the new version (ven2 folder) then i runs the python get_weahther_data.py in env 2 it downloaded the NE_2023.nc successfully.

file1 (1).txt

Bachirou06 commented 5 days ago

Then i run again the snakemake -j 1 Cutouts/country_2022.nc snakemake check all the required files are downloaded in the temp folder and cutouts, then confirmed the successful this step.

samiyhanaqvi commented 3 days ago

Does the new version with snakemake work with your new environment (which is the one in the attached file?)?

Bachirou06 commented 3 days ago

The new version with snakmake does not work with the new environment when apply for get_weather_data.py rule.

samiyhanaqvi commented 3 days ago

I think something might have gone wrong with your environment, as it seems you have updated packages which could then cause some incompatibility. In its current state, the environment should work and should display some update suggestions as "warnings", but you should ignore those, as they will and need to be looked into to ensure that updating will not cause any issues with other packages.

It seems best to make sure you've got the most up-to-date repo using git pull and then re-creating the environment with mamba env create -f environment.yaml.

I know this might seem counter-intuitive, but I have just checked the environment on mine and it works with the get_weather_data.py rule. This is all seeming to be an environment issue.