Errors within batch c2rcc using bash file

Optical Toolbox
#1

Hi All,

I have been using the bash file for batch processing of c2rcc on S2 files. While the output does puts out a file with appropriate bands, there are a fair amount of warnings in the terminal during file creation. Since I am not 100% familiar with all of the lingo, I just wanted to check and make sure that the files it is outputting are appropriate for scientific use, since I am not sure what these warnings really mean. Within the process I am also using the resample tool (10m) prior to c2rcc and the reprojection tool after (to epsg 4326). Thank you for any insight! Below is an example of the errors received during one iteration:

INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Incompatible GDAL 3.4.1 found on system. Internal GDAL 3.2.1 from distribution will be used.
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Incompatible GDAL 3.4.1 found on system. Internal GDAL 3.2.1 from distribution will be used.
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Internal GDAL 3.2.1 set to be used by SNAP.
INFO: org.esa.snap.core.util.EngineVersionCheckActivator: Please check regularly for new updates for the best SNAP experience.
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Internal GDAL 3.2.1 set to be used by SNAP.
Executing processing graph
INFO: org.esa.s2tbx.dataio.s2.ortho.S2OrthoProductReaderPlugIn: Building product reader - EPSG:32610
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [metadata_level] does not exist
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [granuleidentifier] does not exist
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
INFO: org.hsqldb.persist.Logger: dataFileCache open start
INFO: org.esa.s3tbx.c2rcc.ancillary.AtmosphericAuxdataBuilder: Atmospheric auxdata product can’t be used. At least one is not specified. Using constant values for ozone (330.0) and surface pressure (1000.0).
…10%…20%…30%…40%…50%…60%…70%…80%…90% done.
INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Incompatible GDAL 3.4.1 found on system. Internal GDAL 3.2.1 from distribution will be used.
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Incompatible GDAL 3.4.1 found on system. Internal GDAL 3.2.1 from distribution will be used.
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Internal GDAL 3.2.1 set to be used by SNAP.
INFO: org.esa.snap.core.util.EngineVersionCheckActivator: Please check regularly for new updates for the best SNAP experience.
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Internal GDAL 3.2.1 set to be used by SNAP.
Executing processing graph
INFO: org.esa.s2tbx.dataio.s2.ortho.S2OrthoProductReaderPlugIn: Building product reader - EPSG:32610
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [metadata_level] does not exist
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [granuleidentifier] does not exist
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
INFO: org.hsqldb.persist.Logger: dataFileCache open start
INFO: org.esa.s3tbx.c2rcc.ancillary.AtmosphericAuxdataBuilder: Atmospheric auxdata product can’t be used. At least one is not specified. Using constant values for ozone (330.0) and surface pressure (1000.0).
…10%…20%…30%…40%…50%…60%…70%…80%…90% done.

#2

You can safely use the generated output.
The warnings are not harmful.

INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Incompatible GDAL 3.4.1 found on system. Internal GDAL 3.2.1 from distribution will be used.
This explains the situation quite well. You have a GDAL version 3.4.1 installed, but SNAP will use the internally provided version 3.2.1. In most cases when using SNAP the GDAL library will not be used at all. Usually, you need to use it explicitly.

WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [*****] does not exist
The missing metadata elements were contained in older S2 MSI products, but not anymore in later version of the data.
Actually, those messages shouldn’t be printed any more.

INFO: org.esa.s3tbx.c2rcc.ancillary.AtmosphericAuxdataBuilder: Atmospheric auxdata product can’t be used. At least one is not specified. Using constant values for ozone (330.0) and surface pressure (1000.0).
This only tells you that the provided values for ozone and surface pressure are used, because auxiliary data products are note provided.

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