Issue with c2rcc.msi

snap
1

Hi,

I am processing a series of S2 L1C files with the c2rcc.msi operator in gpt. Most files (~90%) work just fine, but some of the files do not process and an empty L2 file is produced. I’m not sure what the issue might be.

Example L1C file (produces empty output product):
S2B_MSIL1C_20190301T145729_N0500_R039_T20QLE_20221112T211949.SAFE
S2MSI_C2RCC_graph_vUSVI.xml (2.2 KB)
hs_err_pid151964.log (226.5 KB)

The gpt xml graph file and error log are attached.

Thanks.

2

Here are the error messages I get that seem snap related:

WARNING: org.esa.snap.core.util.ServiceLoader: org.esa.snap.core.gpf.OperatorSpi: Provider eu.esa.opt.meris.sdr.aerosol.AerosolMergerOp$Spi not found
WARNING: org.esa.snap.core.util.ServiceLoader: org.esa.snap.core.gpf.OperatorSpi: Provider eu.esa.opt.meris.sdr.aerosol.ModisAerosolOp$Spi not found
INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters
INFO: org.esa.snap.core.util.EngineVersionCheckActivator: Please check regularly for new updates for the best SNAP experience.
INFO: eu.esa.opt.dataio.s2.ortho.S2OrthoProductReaderPlugIn: Building product reader - EPSG:32620
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
ERROR 1: libpq.so.5: cannot open shared object file: No such file or directory
ERROR 1: libpq.so.5: cannot open shared object file: No such file or directory
ERROR 1: libpq.so.5: cannot open shared object file: No such file or directory
ERROR 1: libpq.so.5: cannot open shared object file: No such file or directory
INFO: eu.esa.opt.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).
19411 [main] INFO serverStartup - Nc4Iosp: NetCDF-4 C library loaded (jna_path=‘/home/jovyan/.snap/auxdata/netcdf_natives/10.0.0/amd64’, libname=‘netcdf’).
19416 [main] INFO serverStartup - NetcdfLoader: set log level: old=0 new=0
19416 [main] INFO serverStartup - Nc4Iosp: set log level: old=0 new=0

3

Hi Daniel,

Are you experiencing the same error with SNAP 12 ?

4

Hi. I’m using 10 right now so I’m not sure. I will update and test w/SNAP12. Thanks.

5

Hi Diana,

I have updated my system to SNAP 12 and am still getting errors, although the error messages are a bit different than before. I have used the API to get S2 L1C files for 2025 over the US Virgin Islands, so files are all from the same tile. Most files process just fine, but it seems that around 10% of the files do not produce usable output. When a file fails, an output file is created, but it is empty.
The error message I get is this:
Error message: INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters
INFO: org.esa.snap.core.util.EngineVersionCheckActivator: Please check regularly for new updates for the best SNAP experience.
INFO: eu.esa.opt.dataio.s2.ortho.S2OrthoProductReaderPlugIn: Building product reader - EPSG:32620
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: eu.esa.opt.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).
45229 [main] INFO serverStartup - Nc4Iosp: NetCDF-4 C library loaded (jna_path=‘/home/jovyan/.snap/auxdata/netcdf_natives/12.0.0/amd64’, libname=‘netcdf’).
45235 [main] INFO serverStartup - NetcdfLoader: set log level: old=0 new=0
45235 [main] INFO serverStartup - Nc4Iosp: set log level: old=0 new=0

The file name and ID are here:
ID: 863dec6f-f3c3-411d-827d-05cc9947fe53, Name: S2A_MSIL1C_20250405T145741_N0511_R039_T20QLE_20250406T144114.SAFE

The graph I am using is in this thread above in the original post.
The error log is here:
hs_err_pid3102731.log (262.6 KB)

Any ideas on why some of these files are failing is much appreciated.

Thanks,
Dan

6

I think this is related to the following reports:

There is also a ticket in the issue tracker: [SNAP-3509] Invalid memory access error occurs when writing NetCDF-CF file

In the ticket it said the dev team doesn’t want to fix this.
You can save to a different file format, or you can try to remove the metadata with the subset op.

7

Yes. This solves the problem. Strange that only some products were failing. I have changed the output format to “NetCDF-BEAM”, although suppressing the metadata output works as well. Thanks!

8

The number of metadata elements varies. Some exceed the limit, other not.