Hi! I am running a C2RCC operator for Sentinel-2 image. Whenever I specify output format as NetCDF4-CF I am getting an error. It does not happen when the output format is BEAM-DIMAP. The error is as follows:
# A fatal error has been detected by the Java Runtime Environment:
# SIGSEGV (0xb) at pc=0x00007fece4b78089, pid=522790, tid=522860
# JRE version: OpenJDK Runtime Environment (21.0.6+10) (build 21.0.6+10-LTS)
# Java VM: OpenJDK 64-Bit Server VM (21.0.6+10-LTS, mixed mode, tiered, compressed class ptrs, g1 gc, linux-amd64)
# Problematic frame:
# C [libc.so.6+0x1a1089]
# Core dump will be written. Default location: Core dumps may be processed with "/usr/lib/systemd/systemd-coredump %P %u %g %s %t %c %h" (or dumping to /processor/snap_gdal_processing/core.522790)
# An error report file with more information is saved as:
# /processor/snap_gdal_processing/hs_err_pid522790.log
[16.022s][warning][os] Loading hsdis library failed
# If you would like to submit a bug report, please visit:
# https://bell-sw.com/support
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
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.
[main] INFO hdf.hdflib.HDFLibrary - HDF4 library:
[main] INFO hdf.hdflib.HDFLibrary - successfully loaded.
[main] INFO hdf.hdf5lib.H5 - HDF5 library:
[main] INFO hdf.hdf5lib.H5 - successfully loaded.
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).
[main] INFO serverStartup - Nc4Iosp: NetCDF-4 C library loaded (jna_path='/mnt/vol/snapuser/auxdata/netcdf_natives/13.0.0/amd64', libname='netcdf').
[main] INFO serverStartup - NetcdfLoader: set log level: old=0 new=0
[main] INFO serverStartup - Nc4Iosp: set log level: old=0 new=0
It seems to be related to other threads like Java error "invalid memory access" or NetCDF-CF writing: Segmentation fault and metadata issues with SNAP v9.0.4+ but whatever worked in these cases does not help. The image that I am using does not have the mentioned metadata structure, so there is nothing to delete. Is there any workaround or potential fix?
Additional logs from JVM: 1.log (201.8 KB)
The graph: c2rcc_msi_graph.xml (1.5 KB)
You should be able to recreate this with any Sentinel-2 image but I was using: S2C_MSIL1C_20250710T104041_N0511_R008_T32VNM_20250710T141929.SAFE