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conda-incubator / condacolab

Install Conda and friends on Google Colab, easily
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possible problem with gdal #9

Closed crsnao closed 3 years ago

crsnao commented 3 years ago

Hello,

I am using google colab to work on a model calibration and I few weeks ago I was able to run the code properly (thanks to condacolab!!), but now colab throws some errors like ValueError: Could not open ('my_file',) as a gdal.OF_RASTER and AttributeError: module 'osgeo.osr' has no attribute 'OAMS_TRADITIONAL_GIS_ORDER'. While downloading GDAL the only possible issue I detected is the massenge failed with initial frozen solve. Retrying with flexible solve. And from this comments in stackoverflow there seems to be a problem with installing GDAL with conda. So I was wondering if you could help me.

here is the link to my colab notebook if you want to reproduce the errors

And if needed this is the link to the calibration user guide (the author share the github repository with data and the steps to calibrate the model)

Regards, Carson

jaimergp commented 3 years ago

Hi, thanks for using condacolab!

Mixing conda and pip can be tricky specially if there are lot of compiled libraries involved. I have added some packages to your conda install command so pip can find them installed already. That way we ensure everything was compiled in the same way at conda-forge.

By the way, condacolab installs Mamba too, which is way faster. In short, replace your conda install call with this one:

#Installing request packages for ucm calibration
! mamba install -q 'gdal<3.0' rtree 'shapely<1.7.0' dask  click fiona numpy 'scipy<1.5.0,>=0.16.1' rasterio scikit-learn shapely simanneal xarray

The rest should "just work". At least the error you mentioned is no longer there!

jaimergp commented 3 years ago 
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
 Temperature        Energy    Accept   Improve     Elapsed   Remaining
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
not precalculated (calculate T air (5)), Task hash exists, but there are these mismatches: Modified times don't match cached: (1623336373.625049) actual: (1623336376.147265)
not precalculated (area kernel (6)), Task hash exists, but there are these mismatches: Modified times don't match cached: (1623336373.640050) actual: (1623336376.165267)
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
proj_create: Open of /usr/local/share/proj failed
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
ERROR 4: Unable to open EPSG support file gcs.csv.  Try setting the GDAL_DATA environment variable to point to the directory containing EPSG csv files.
2021-06-10 14:46:48,239 - invest_ucm_calibration.cli.main - INFO - Best solution [522.6477531359949, 101.02038626027505, 0.817957072756969, 0.0678115218350912, 0.11423140540793983] with cost 0.9166748510692126
2021-06-10 14:46:48,239 - invest_ucm_calibration.cli.main - INFO - Dumped calibrated parameters to calibrated-params.json

This is what I get!

crsnao commented 3 years ago

A LIFESAVER @jaimergp I cant thank you enough.

Any idea what these errors might mean to the actual result? Could the result be wrong? This link https://rasterio.readthedocs.io/en/latest/faq.html says I should "unset GDAL_DATA if it exists and see if that eliminates the error condition and the message." but I also found some solutions to this problem in stackoverflow that involve creating or changing an environment (which is not possible in colab). D you have any suggestions?

Once again: I cant thank you enough for the help and for condacolab!

jaimergp commented 3 years ago

The condacolab base installation is pretty much a fresh environment, so you don't have those env pollution problems that can appear locally.

You might need to set GDAL_DATA mimicking what conda activate would do. See here.

The problem is that you are executing a subprocess instead of using the running Python kernel, so some env variables are not exported / ingested as it would happen on your local installation. Hence the rough edges, but nothing that cannot be worked around.

I think you can do this:

# calibrating parameters with data
! . /usr/local/etc/profile.d/conda.sh && \
  conda activate && \
  python $(which invest-ucm-calibration) lulc.tif biophysical-table.csv factors \
            --ref-et-raster-filepaths ./ref_et0.tif --t-raster-filepaths T0.tif \
            --num-steps 10 --num-update-logs 10 \
            --dst-filepath calibrated-params.json

, which returns:

 Temperature        Energy    Accept   Improve     Elapsed   Remaining
not precalculated (calculate T air (5)), Task hash exists, but there are these mismatches: Modified times don't match cached: (1623425922.024089) actual: (1623425926.348463)
not precalculated (area kernel (6)), Task hash exists, but there are these mismatches: Modified times don't match cached: (1623425922.045091) actual: (1623425926.368464)
not precalculated (calculate T air (5)), Task hash exists, but there are these mismatches: Modified times don't match cached: (1623425919.792896) actual: (1623425928.489648)
not precalculated (area kernel (6)), Task hash exists, but there are these mismatches: Modified times don't match cached: (1623425919.810898) actual: (1623425928.507649)
2021-06-11 15:38:51,552 - invest_ucm_calibration.cli.main - INFO - Best solution [283.4410558918151, 201.31728096380257, 0.7370114483513446, 0.15413894061108285, 0.10884961103757256] with cost 0.919217426494883
2021-06-11 15:38:51,552 - invest_ucm_calibration.cli.main - INFO - Dumped calibrated parameters to calibrated-params.json
crsnao commented 3 years ago

Amazing! Thank you so much @jaimergp !!