Back-Geocoding crashes with SNAP 8 (Alpine) about esa-snap

[neteler]

Hi Vincent,

this seems to be two issues:
a) libgfortran package missing
b) the problem you face with the Back-Geocoding operator

Concerning:
a) does this also apply to the latest SNAP 8.0 based docker image?
b) do you have a reproducible example for us to try here?

[neteler]

And yes, please attach the log file for inspection.

[vincentvaroquaux]

Hi Markus !
Thank you for your answer.

It's easy to reproduce using a Sentinel 1 SLC product with the two following SNAP commands:

/usr/local/snap/bin/gpt -x -J-Xmx9000m TOPSAR-Split -Psubswath=IW1 -PlastBurstIndex=1 -t output.dim S1A_IW_SLC__1SDV_20190103T170041_20190103T170108_025316_02CD10_2226.zip
/usr/local/snap/bin/gpt -x -J-Xmx9000m Back-Geocoding output.dim

It works well in the docker mundialis/esa-snap:s1tbx-7.0v2 (provided you add the missing library), but fails in the docker mundialis/esa-snap:s1tbx-8.0.

Output of mundialis/esa-snap:s1tbx-7.0v2 :

# /usr/local/snap/bin/gpt -x -J-Xmx9000m TOPSAR-Split -Psubswath=IW1 -PlastBurstIndex=1 -t output.dim S1A_IW_SLC__1SDV_20190103T170041_20190103T170108_025316_02CD10_2226.zip 
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.
WARNING: org.esa.snap.core.util.EngineVersionCheckActivator: A new SNAP version is available for download.
Currently installed 7.0, available is 8.0.0.
Please visit http://step.esa.int

INFO: org.hsqldb.persist.Logger: dataFileCache open start
INFO: org.esa.snap.core.gpf.common.WriteOp: Start writing product S1A_IW_SLC__1SDV_20190103T170041_20190103T170108_025316_02CD10_2226 to output.dim
Writing...
....10%....20%....30%....40%....50%....60%....70%....80%....90%....100% done.
INFO: org.esa.snap.core.gpf.common.WriteOp: End writing product output to output.dim
INFO: org.esa.snap.core.gpf.common.WriteOp: Time: 18.087 s total, 12.042 ms per line, 0.000526 ms per pixel

# /usr/local/snap/bin/gpt -x -J-Xmx9000m Back-Geocoding output.dim
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: org.hsqldb.persist.Logger: dataFileCache open start
INFO: org.esa.snap.core.gpf.common.WriteOp: Start writing product output_Stack to target.dim
Writing...
....10%....20%....30%....40%....50%....60%....70%....80%....90%.... done.
INFO: org.esa.snap.core.gpf.common.WriteOp: End writing product target to target.dim
INFO: org.esa.snap.core.gpf.common.WriteOp: Time:  2.023 s total,  1.347 ms per line, 0.000059 ms per pixel
-- org.jblas INFO Deleting /tmp/jblas2584424987876700331/libjblas_arch_flavor.so
-- org.jblas INFO Deleting /tmp/jblas2584424987876700331/libjblas.so
-- org.jblas INFO Deleting /tmp/jblas2584424987876700331

Output of mundialis/esa-snap:s1tbx-8.0 :

tBurstIndex=1 -t output.dim S1A_IW_SLC__1SDV_20190103T170041_20190103T170108_025
316_02CD10_2226.zip 
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: org.esa.s1tbx.io.sentinel1.Sentinel1Level1Directory: Less than 8K RAM. Using FileCacheImageInputStream
INFO: org.esa.s1tbx.io.sentinel1.Sentinel1Level1Directory: Less than 8K RAM. Using FileCacheImageInputStream
INFO: org.esa.s1tbx.io.sentinel1.Sentinel1Level1Directory: Less than 8K RAM. Using FileCacheImageInputStream
INFO: org.esa.s1tbx.io.sentinel1.Sentinel1Level1Directory: Less than 8K RAM. Using FileCacheImageInputStream
INFO: org.esa.s1tbx.io.sentinel1.Sentinel1Level1Directory: Less than 8K RAM. Using FileCacheImageInputStream
INFO: org.esa.s1tbx.io.sentinel1.Sentinel1Level1Directory: Less than 8K RAM. Using FileCacheImageInputStream
INFO: org.hsqldb.persist.Logger: dataFileCache open start
Executing operator...
20%....30%....40%....50%....60%....70%....80%....90%.... done.
INFO: org.esa.snap.core.gpf.common.WriteOp: Start writing product S1A_IW_SLC__1SDV_20190103T170041_20190103T170108_025316_02CD10_2226 to output.dim
Writing...
..12%..22%.....38%36%34%.....50%....60%....70%....80%....90%.... done.
INFO: org.esa.snap.core.gpf.common.WriteOp: End writing product output to output.dim
INFO: org.esa.snap.core.gpf.common.WriteOp: Time:  1.832 s total,  1.220 ms per line, 0.000053 ms per pixel

# /usr/local/snap/bin/gpt -x -J-Xmx9000m Back-Geocoding output.dim
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: org.hsqldb.persist.Logger: dataFileCache open start
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x0000000000002076, pid=216, tid=0x00007f3bca8feb20
#
# JRE version: OpenJDK Runtime Environment (8.0_232-b09) (build 1.8.0_232-b09)
# Java VM: OpenJDK 64-Bit Server VM (25.232-b09 mixed mode linux-amd64 compressed oops)
# Derivative: IcedTea 3.14.0
# Distribution: Custom build (Tue Mar  3 13:24:22 UTC 2020)
# Problematic frame:
# C  0x0000000000002076
#
# Core dump written. Default location: /data/core or core.216
#
# An error report file with more information is saved as:
# /data/hs_err_pid216.log
#
# If you would like to submit a bug report, please include
# instructions on how to reproduce the bug and visit:
#   https://icedtea.classpath.org/bugzilla
#
Aborted (core dumped)

Please find the error report file : here

Vincent

[neteler]

Hi Vincent, we are a bit at a loss here. Perhaps it is an Alpine related library issue, perhaps a SNAP 8 issue.

Maybe worth discussing in the SNAP forum? https://forum.step.esa.int/

[vincentvaroquauxads]

Hi Markus,
Sorry for the late answer.
The discussion can continue on the SNAP forum : https://forum.step.esa.int/t/snap-8-backgeocoding-in-alpine-linux-docker/27832

Vincent

[neteler]

@vincentvaroquaux
I have created a new Docker file based on Ubuntu:
https://hub.docker.com/r/mundialis/esa-snap/tags?page=1&ordering=last_updated

docker pull mundialis/esa-snap:ubuntu

Perhaps you want to give it a try and check if the desired functionality is working as expected.

[neteler]

In addition the Alpine Docker image has been updated with the libgfortran package now added.

[neteler]

Update: we have now SNAP 9.0 included. Please try again.

[mmacata]

If there are any further problems, please open a new ticket.