GRD processing issues with docker image

[jonas-eberle]

Hi Andreas,

I have some issues when starting the processing using the docker image.

The import works fine for single file processing, but not for batch processing. Batch processing seems to use SNAP for import, this might be the reason for failing.

GRD to both, RTC and GTC:
log_import for single file processing:

Colums total: 26530
Colums cut left side: 644
Colums cut right side: 993
Amount of columns kept: 25537
Write valid columns of image to disk
time elapsed: 7.60805797577

log_cal_ml / log_tc_db / log_ls_mask:

INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters
SEVERE: org.esa.s2tbx.dataio.gdal.activator.GDALPlugInActivator: The environment variable LD_LIBRARY_PATH does not contain the current folder '.'. Its value is '/usr/lib/R/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/default-java/jre/lib/amd64/server'.
java.lang.IllegalArgumentException: The environment variable LD_LIBRARY_PATH does not contain the current folder '.'. Its value is '/usr/lib/R/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/default-java/jre/lib/amd64/server'.
at org.esa.s2tbx.dataio.gdal.activator.GDALDistributionInstaller.processInstalledLinuxDistribution(GDALDistributionInstaller.java:131)
at org.esa.s2tbx.dataio.gdal.activator.GDALDistributionInstaller.install(GDALDistributionInstaller.java:82)
at org.esa.s2tbx.dataio.gdal.activator.GDALPlugInActivator.start(GDALPlugInActivator.java:22)
at org.esa.snap.runtime.Engine.informActivators(Engine.java:222)
at org.esa.snap.runtime.Engine.lambda$start$0(Engine.java:121)
at org.esa.snap.runtime.Engine.runClientCode(Engine.java:189)
at org.esa.snap.runtime.Engine.start(Engine.java:121)
at org.esa.snap.runtime.Engine.start(Engine.java:90)
at org.esa.snap.runtime.Launcher.run(Launcher.java:51)
at org.esa.snap.runtime.Launcher.main(Launcher.java:31)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:62)
at com.install4j.runtime.launcher.UnixLauncher.main(UnixLauncher.java:57)

java.lang.NumberFormatException: For input string: "-Pinput=/root/test1/DATA/015A/20170716-015A/TMP/S1B_IW_GRDH_1SDV_20170716T171413_20170716T171438_006516_00B74F_AADC_speckle.dim"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:580)
at java.lang.Integer.parseInt(Integer.java:615)
at org.esa.snap.core.gpf.main.CommandLineArgs.parseOptionArgumentInt(CommandLineArgs.java:271)
at org.esa.snap.core.gpf.main.CommandLineArgs.parseArgs(CommandLineArgs.java:136)
at org.esa.snap.core.gpf.main.CommandLineArgs.parseArgs(CommandLineArgs.java:70)
at org.esa.snap.core.gpf.main.CommandLineTool.run(CommandLineTool.java:112)
at org.esa.snap.core.gpf.main.GPT.run(GPT.java:54)
at org.esa.snap.core.gpf.main.GPT.main(GPT.java:34)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.esa.snap.runtime.Launcher.lambda$run$0(Launcher.java:55)
at org.esa.snap.runtime.Engine.runClientCode(Engine.java:189)
at org.esa.snap.runtime.Launcher.run(Launcher.java:51)
at org.esa.snap.runtime.Launcher.main(Launcher.java:31)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:62)
at com.install4j.runtime.launcher.UnixLauncher.main(UnixLauncher.java:57)

Error: For input string: "-Pinput=/root/test1/DATA/015A/20170716-015A/TMP/S1B_IW_GRDH_1SDV_20170716T171413_20170716T171438_006516_00B74F_AADC_speckle.dim"

---

By the way the log info says successfully processed file:

Importing S1 GRD data file, applying the precise orbit file and removing thermal noise ... done (0 minutes and 28 seconds elapsed)
Removing GRD Border Noise ... done (0 minutes and 16 seconds elapsed)
Applying the Lee Sigma Speckle Filter ... done (3 minutes and 7 seconds elapsed)
Calibrating to Gamma0 (based on ellipsoid earth model) and multi-look by a factor of 3 ... done (0 minutes and 5 seconds elapsed)
Creating a layover/shadow mask ... done (0 minutes and 4 seconds elapsed)
Applying the geometric terrain correction and transform backscatter to decibel scale ... done (0 minutes and 4 seconds elapsed)
Creating final output file ... done (0 minutes and 0 seconds elapsed)
Mask out layover/shadow areas ... done (0 minutes and 0 seconds elapsed)
Create a kmz file for Google Earth Visualization ... done (0 minutes and 0 seconds elapsed)

Info: Succesfully processed file: S1B_IW_GRDH_1SDV_20170716T171413_20170716T171438_006516_00B74F_AADC_speckle.dim to a geometrically terrain corrected product.

Creating final output file (Band 1: VV, Band 2: VH, Band 3 VV/VH ratio) ... done (0 minutes and 0 seconds elapsed)
Processing failed for some reason.

[BuddyVolly]

Hi Jonas,

unfortunately the SNAP error messages are not quite helpful. However you can ignore the INFO and SEVERE messages. Those should not affect the processing. Also note that error handling has to be improved for the toolkit.

Just for clarification, what are the specifications of your machine? Do you have enough RAM and/or disk space? As far as I can see from the log info posted below, the problem is within the calibration step that should take longer than 5 seconds.