SNAP gpt warning

jmbcarreiras · October 10, 2024, 7:09am

I have java 8 installed and when running the following command line:

gpt S1_SLC_to_TC.xml -Pinput=“input filename” -Poutput=“output filename”

I get the following warnings:

OpenJDK 64-Bit Server VM warning: Option AggressiveOpts was deprecated in version 11.0 and will likely be removed in a future release.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.esa.snap.runtime.Engine (file:/C:/Dev/esa-snap/snap/modules/ext/org.esa.snap.snap-core/org-esa-snap/snap-runtime.jar) to method java.lang.ClassLoader.initializePath(java.lang.String)
WARNING: Please consider reporting this to the maintainers of org.esa.snap.runtime.Engine
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

That line of code applies the graph correctly, so there is no issue here.

Thank you
Joao

diana_harosa · October 10, 2024, 9:42am

What is your SNAP version?

jmbcarreiras · October 10, 2024, 9:43am

version 10

diana_harosa · October 10, 2024, 12:02pm

SNAP does not use the Java version installed on your system, as it includes its own Java runtime. For SNAP 10, Java 11 is used (see C:\Dev\esa-snap\jre for reference).
These warnings do not affect the proper functioning of SNAP.

JacobV · November 29, 2024, 1:20pm

Hello!

I think im having a similar issue, although mine causes a crash of SNAP 11. Im running a graph which works well on windows 10 but fails on Ubuntu 22.04 with

GPT exited with an error:

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.esa.snap.runtime.Engine (file:/home/javej/esa-snap/snap/modules/ext/org.esa.snap.snap-core/org-esa-snap/snap-runtime.jar) to method java.lang.ClassLoader.initializePath(java.lang.String)
WARNING: Please consider reporting this to the maintainers of org.esa.snap.runtime.Engine
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
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.
*** buffer overflow detected ***: terminated

I’ve just updated SNAP but the EngineVersion error persists. SNAP has 21 gigabytes of RAM available, so i dont think the issue lies there.

Any idea what the issue is?

Thanks
Jacob

diana_harosa · November 29, 2024, 1:46pm

Could you provide the graph you are using?

JacobV · November 29, 2024, 4:43pm

Yes, here it is.


<graph id="Graph">
  <version>1.0</version>
  <node id="Read">
    <operator>Read</operator>
    <sources/>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <useAdvancedOptions>false</useAdvancedOptions>
      <file>${inputSafeFile}</file>
      <copyMetadata>true</copyMetadata>
      <bandNames/>
      <pixelRegion>0,0,2147483647,2147483647</pixelRegion>
      <maskNames/>
    </parameters>
  </node>
  <node id="Apply-Orbit-File">
    <operator>Apply-Orbit-File</operator>
    <sources>
      <sourceProduct refid="Read"/>
    </sources>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <orbitType>Sentinel Precise (Auto Download)</orbitType>
      <polyDegree>3</polyDegree>
      <continueOnFail>false</continueOnFail>
    </parameters>
  </node>
  <node id="ThermalNoiseRemoval">
    <operator>ThermalNoiseRemoval</operator>
    <sources>
      <sourceProduct refid="Apply-Orbit-File"/>
    </sources>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <selectedPolarisations/>
      <removeThermalNoise>true</removeThermalNoise>
      <outputNoise>false</outputNoise>
      <reIntroduceThermalNoise>false</reIntroduceThermalNoise>
    </parameters>
  </node>
  <node id="Calibration">
    <operator>Calibration</operator>
    <sources>
      <sourceProduct refid="Remove-GRD-Border-Noise"/>
    </sources>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <sourceBands/>
      <auxFile>Latest Auxiliary File</auxFile>
      <externalAuxFile/>
      <outputImageInComplex>false</outputImageInComplex>
      <outputImageScaleInDb>false</outputImageScaleInDb>
      <createGammaBand>false</createGammaBand>
      <createBetaBand>false</createBetaBand>
      <selectedPolarisations/>
      <outputSigmaBand>true</outputSigmaBand>
      <outputGammaBand>false</outputGammaBand>
      <outputBetaBand>false</outputBetaBand>
    </parameters>
  </node>
  <node id="Remove-GRD-Border-Noise">
    <operator>Remove-GRD-Border-Noise</operator>
    <sources>
      <sourceProduct refid="ThermalNoiseRemoval"/>
    </sources>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <selectedPolarisations/>
      <borderLimit>500</borderLimit>
      <trimThreshold>0.5</trimThreshold>
    </parameters>
  </node>
  <node id="Terrain-Correction">
    <operator>Terrain-Correction</operator>
    <sources>
      <sourceProduct refid="Calibration"/>
    </sources>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <sourceBands/>
      <demName>SRTM 3Sec</demName>
      <externalDEMFile/>
      <externalDEMNoDataValue>0.0</externalDEMNoDataValue>
      <externalDEMApplyEGM>true</externalDEMApplyEGM>
      <demResamplingMethod>BILINEAR_INTERPOLATION</demResamplingMethod>
      <imgResamplingMethod>BILINEAR_INTERPOLATION</imgResamplingMethod>
      <pixelSpacingInMeter>0.0</pixelSpacingInMeter>
      <pixelSpacingInDegree>0.0</pixelSpacingInDegree>
      <mapProjection>GEOGCS[&quot;WGS84(DD)&quot;, &#xd;
  DATUM[&quot;WGS84&quot;, &#xd;
    SPHEROID[&quot;WGS84&quot;, 6378137.0, 298.257223563]], &#xd;
  PRIMEM[&quot;Greenwich&quot;, 0.0], &#xd;
  UNIT[&quot;degree&quot;, 0.017453292519943295], &#xd;
  AXIS[&quot;Geodetic longitude&quot;, EAST], &#xd;
  AXIS[&quot;Geodetic latitude&quot;, NORTH]]</mapProjection>
      <alignToStandardGrid>false</alignToStandardGrid>
      <standardGridOriginX>0.0</standardGridOriginX>
      <standardGridOriginY>0.0</standardGridOriginY>
      <nodataValueAtSea>false</nodataValueAtSea>
      <saveDEM>false</saveDEM>
      <saveLatLon>false</saveLatLon>
      <saveIncidenceAngleFromEllipsoid>true</saveIncidenceAngleFromEllipsoid>
      <saveLocalIncidenceAngle>false</saveLocalIncidenceAngle>
      <saveProjectedLocalIncidenceAngle>false</saveProjectedLocalIncidenceAngle>
      <saveSelectedSourceBand>true</saveSelectedSourceBand>
      <saveLayoverShadowMask>false</saveLayoverShadowMask>
      <outputComplex>false</outputComplex>
      <applyRadiometricNormalization>false</applyRadiometricNormalization>
      <saveSigmaNought>false</saveSigmaNought>
      <saveGammaNought>false</saveGammaNought>
      <saveBetaNought>false</saveBetaNought>
      <incidenceAngleForSigma0>Use projected local incidence angle from DEM</incidenceAngleForSigma0>
      <incidenceAngleForGamma0>Use projected local incidence angle from DEM</incidenceAngleForGamma0>
      <auxFile>Latest Auxiliary File</auxFile>
      <externalAuxFile/>
    </parameters>
  </node>
  <node id="Write">
    <operator>Write</operator>
    <sources>
      <sourceProduct refid="Terrain-Correction"/>
    </sources>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <file>${outputSafeFile}</file>
      <formatName>GeoTIFF-BigTIFF</formatName>
    </parameters>
  </node>
  <applicationData id="Presentation">
    <Description>Sentinel-1 GRD Sigma0 standard preprocessing graph</Description>
    <node id="Read">
            <displayPosition x="34.0" y="40.0"/>
    </node>
    <node id="Apply-Orbit-File">
      <displayPosition x="36.0" y="72.0"/>
    </node>
    <node id="ThermalNoiseRemoval">
      <displayPosition x="36.0" y="105.0"/>
    </node>
    <node id="Calibration">
      <displayPosition x="36.0" y="167.0"/>
    </node>
    <node id="Remove-GRD-Border-Noise">
      <displayPosition x="36.0" y="136.0"/>
    </node>
    <node id="Terrain-Correction">
      <displayPosition x="36.0" y="199.0"/>
    </node>
    <node id="Write">
            <displayPosition x="36.0" y="229.0"/>
    </node>
  </applicationData>
</graph>

I’m now also getting a similar error on windows 10, using SNAP 10. I suppose that means its probably my graph or my setup but it hasn’t failed this way before. The error I’m getting on windows 10 is as follows:

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.esa.snap.runtime.Engine (file:/C:/Users/b307579/AppData/Local/Programs/snap10/snap/modules/ext/org.esa.snap.snap-core/org-esa-snap/snap-runtime.jar) to method java.lang.ClassLoader.initializePath(java.lang.String)
WARNING: Please consider reporting this to the maintainers of org.esa.snap.runtime.Engine
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
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.
java.util.zip.ZipException: zip END header not found
at jdk.zipfs/jdk.nio.zipfs.ZipFileSystem.zerror(ZipFileSystem.java:1908)
at jdk.zipfs/jdk.nio.zipfs.ZipFileSystem.findEND(ZipFileSystem.java:1052)
at jdk.zipfs/jdk.nio.zipfs.ZipFileSystem.initCEN(ZipFileSystem.java:1061)
at jdk.zipfs/jdk.nio.zipfs.ZipFileSystem.(ZipFileSystem.java:135)
at jdk.zipfs/jdk.nio.zipfs.ZipFileSystemProvider.newFileSystem(ZipFileSystemProvider.java:136)
at java.base/java.nio.file.FileSystems.newFileSystem(FileSystems.java:406)
at org.esa.snap.engine_utilities.util.ZipFileSystemBuilder.newZipFileSystem(ZipFileSystemBuilder.java:17)
at org.esa.snap.engine_utilities.util.FileSystemUtils.isZipFile(FileSystemUtils.java:24)
at org.esa.snap.engine_utilities.dataio.VirtualDirEx.build(VirtualDirEx.java:95)
at eu.esa.opt.dataio.s2.filepatterns.S2NamingConventionUtils.transformToSentinel2VirtualPath(S2NamingConventionUtils.java:307)
at eu.esa.opt.dataio.s2.ortho.S2ProductCRSCache$S2ProductCRSCacheEntry.(S2ProductCRSCache.java:57)
at eu.esa.opt.dataio.s2.ortho.S2ProductCRSCache.ensureIsCached(S2ProductCRSCache.java:156)
at eu.esa.opt.dataio.s2.ortho.S2OrthoProductReaderPlugIn.getDecodeQualification(S2OrthoProductReaderPlugIn.java:101)
at org.esa.snap.core.dataio.ProductIO.getProductReaderForInput(ProductIO.java:289)
at org.esa.snap.core.gpf.common.ReadOp.initialize(ReadOp.java:175)
at org.esa.snap.core.gpf.internal.OperatorContext.initializeOperator(OperatorContext.java:528)
at org.esa.snap.core.gpf.internal.OperatorContext.getTargetProduct(OperatorContext.java:298)
at org.esa.snap.core.gpf.Operator.getTargetProduct(Operator.java:359)
at org.esa.snap.core.gpf.graph.NodeContext.initTargetProduct(NodeContext.java:77)
at org.esa.snap.core.gpf.graph.GraphContext.initNodeContext(GraphContext.java:199)
at org.esa.snap.core.gpf.graph.GraphContext.initNodeContext(GraphContext.java:182)
at org.esa.snap.core.gpf.graph.GraphContext.initNodeContext(GraphContext.java:182)
at org.esa.snap.core.gpf.graph.GraphContext.initNodeContext(GraphContext.java:182)
at org.esa.snap.core.gpf.graph.GraphContext.initNodeContext(GraphContext.java:182)
at org.esa.snap.core.gpf.graph.GraphContext.initNodeContext(GraphContext.java:182)
at org.esa.snap.core.gpf.graph.GraphContext.initNodeContext(GraphContext.java:182)
at org.esa.snap.core.gpf.graph.GraphContext.initOutput(GraphContext.java:166)
at org.esa.snap.core.gpf.graph.GraphContext.(GraphContext.java:85)
at org.esa.snap.core.gpf.graph.GraphContext.(GraphContext.java:58)
at org.esa.snap.core.gpf.graph.GraphProcessor.executeGraph(GraphProcessor.java:127)
at org.esa.snap.core.gpf.main.DefaultCommandLineContext.executeGraph(DefaultCommandLineContext.java:86)
at org.esa.snap.core.gpf.main.CommandLineTool.executeGraph(CommandLineTool.java:547)
at org.esa.snap.core.gpf.main.CommandLineTool.runGraph(CommandLineTool.java:391)
at org.esa.snap.core.gpf.main.CommandLineTool.runGraphOrOperator(CommandLineTool.java:287)
at org.esa.snap.core.gpf.main.CommandLineTool.run(CommandLineTool.java:188)
at org.esa.snap.core.gpf.main.CommandLineTool.run(CommandLineTool.java:121)
at org.esa.snap.core.gpf.main.GPT.run(GPT.java:60)
at org.esa.snap.core.gpf.main.GPT.main(GPT.java:37)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
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 java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:84)
at com.exe4j.runtime.WinLauncher.main(WinLauncher.java:94)
at com.install4j.runtime.launcher.WinLauncher.main(WinLauncher.java:25)