Several exceptions occur when processing MSI L1C with IdePix

[heptaflar]

I tried to process several MSI products with IdePix (no computation of mountain or cloud shadow). In every case an exception occurred. I used S2TBX Version 8.0.4 and MSI IdePix 8.0.2. Stack traces of exceptions thrown are copied below.

One exception:

java.lang.RuntimeException: Waiting thread received a null tile.
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(Unknown Source)
at javax.media.jai.OpImage.getTile(Unknown Source)
at javax.media.jai.PlanarImage.cobbleInt(Unknown Source)
at javax.media.jai.PlanarImage.getData(Unknown Source)
at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:449)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:435)
at org.esa.snap.core.gpf.Operator.getSourceTile(Operator.java:459)
at org.esa.snap.idepix.s2msi.operators.S2IdepixCloudBufferOp.computeTile(S2IdepixCloudBufferOp.java:81)
at org.esa.snap.core.gpf.internal.OperatorImage.computeRect(OperatorImage.java:82)
at javax.media.jai.SourcelessOpImage.computeTile(Unknown Source)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(Unknown Source)
at javax.media.jai.OpImage.getTile(Unknown Source)
at javax.media.jai.PlanarImage.getData(Unknown Source)
at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:449)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:435)
at org.esa.snap.core.gpf.internal.OperatorImage.computeRect(OperatorImage.java:75)
[catch] at javax.media.jai.SourcelessOpImage.computeTile(Unknown Source)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(Unknown Source)
at javax.media.jai.OpImage.getTile(Unknown Source)
at com.sun.media.jai.util.RequestJob.compute(Unknown Source)
at com.sun.media.jai.util.WorkerThread.run(Unknown Source)

Another exception:

java.lang.IllegalArgumentException: The specified region, if not null, must intersect with the image`s bounds.
at javax.media.jai.PlanarImage.getData(Unknown Source)
at javax.media.jai.RenderedOp.getData(Unknown Source)
at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:449)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:435)
at org.esa.snap.core.gpf.Operator.getSourceTile(Operator.java:459)
at org.esa.snap.idepix.s2msi.S2IdepixClassificationOp.computeTileStack(S2IdepixClassificationOp.java:233)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeRect(OperatorImageTileStack.java:122)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeTile(OperatorImageTileStack.java:86)
Caused: org.esa.snap.core.gpf.OperatorException: The specified region, if not null, must intersect with the image`s bounds.
at org.esa.snap.core.gpf.internal.OperatorExecutor$GPFImagingListener.errorOccurred(OperatorExecutor.java:381)
at com.sun.media.jai.util.SunTileScheduler.sendExceptionToListener(Unknown Source)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(Unknown Source)
at javax.media.jai.OpImage.getTile(Unknown Source)
at javax.media.jai.PlanarImage.cobbleInt(Unknown Source)
at javax.media.jai.PlanarImage.getData(Unknown Source)
at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:449)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:435)
at org.esa.snap.core.gpf.Operator.getSourceTile(Operator.java:459)
at org.esa.snap.idepix.s2msi.operators.S2IdepixCloudBufferOp.computeTile(S2IdepixCloudBufferOp.java:81)
at org.esa.snap.core.gpf.internal.OperatorImage.computeRect(OperatorImage.java:82)
at javax.media.jai.SourcelessOpImage.computeTile(Unknown Source)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(Unknown Source)
at javax.media.jai.OpImage.getTile(Unknown Source)
at javax.media.jai.PlanarImage.getData(Unknown Source)
at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:449)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:435)
at org.esa.snap.core.gpf.internal.OperatorImage.computeRect(OperatorImage.java:75)
at javax.media.jai.SourcelessOpImage.computeTile(Unknown Source)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(Unknown Source)
at javax.media.jai.OpImage.getTile(Unknown Source)
at com.sun.media.jai.util.RequestJob.compute(Unknown Source)
[catch] at com.sun.media.jai.util.WorkerThread.run(Unknown Source)

[marpet]

When resampling beforehand it works. Actually S2 resamples the data on its own.
It could be that the reader for S2 data has changed in 8.04 of S2TBX update. And this is causing an issue.

[marpet]

S2 Idepix does not resample by default. But should warn that the product is not resampled.
S2 Resampling must be used, not the general Resampling.

[tiagoams]

I think I am getting the same error when running IdePix, after running "S2 resampling" to 10m.

SNAP Error during IdePix
OperatorException
Waiting Thread received a null tile

This is the image:
S2A_MSIL1C_20180607T085601_N0206_R007_T35SMD_20180607T110513

Snap 8.04 on Linux

Is there a workaround at this stage? Maybe regress the version of snap or the toolbox...

java.lang.RuntimeException: Waiting thread received a null tile.
	at com.sun.media.jai.util.SunTileScheduler.scheduleTile(Unknown Source)
	at javax.media.jai.OpImage.getTile(Unknown Source)
	at javax.media.jai.PlanarImage.getData(Unknown Source)
	at javax.media.jai.PlanarImage.getExtendedData(Unknown Source)
	at javax.media.jai.ScaleOpImage.computeTile(Unknown Source)
Caused: org.esa.snap.core.gpf.OperatorException: Waiting thread received a null tile.
	at org.esa.snap.core.gpf.internal.OperatorExecutor$GPFImagingListener.errorOccurred(OperatorExecutor.java:381)
	at com.sun.media.jai.util.SunTileScheduler.sendExceptionToListener(Unknown Source)
	at com.sun.media.jai.util.SunTileScheduler.scheduleTile(Unknown Source)
	at javax.media.jai.OpImage.getTile(Unknown Source)
	at javax.media.jai.PlanarImage.copyData(Unknown Source)
	at javax.media.jai.PlanarImage.copyExtendedData(Unknown Source)
	at com.sun.media.jai.opimage.BorderOpImage.computeTile(Unknown Source)
	at com.sun.media.jai.util.SunTileScheduler.scheduleTile(Unknown Source)
	at javax.media.jai.OpImage.getTile(Unknown Source)
	at com.sun.media.jai.opimage.CropOpImage.getTile(Unknown Source)
	at javax.media.jai.PlanarImage.getData(Unknown Source)
	at javax.media.jai.RenderedOp.getData(Unknown Source)
	at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
	at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:449)
	at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:435)
	at org.esa.snap.core.gpf.Operator.getSourceTile(Operator.java:459)
	at org.esa.snap.idepix.s2msi.S2IdepixPostProcessOp.computeTile(S2IdepixPostProcessOp.java:174)
	at org.esa.snap.core.gpf.internal.OperatorImage.computeRect(OperatorImage.java:82)
	at javax.media.jai.SourcelessOpImage.computeTile(Unknown Source)
	at com.sun.media.jai.util.SunTileScheduler.scheduleTile(Unknown Source)
	at javax.media.jai.OpImage.getTile(Unknown Source)
	at javax.media.jai.PlanarImage.getData(Unknown Source)
	at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
	at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:449)
	at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:435)
	at org.esa.snap.core.gpf.internal.OperatorImage.computeRect(OperatorImage.java:75)
	at javax.media.jai.SourcelessOpImage.computeTile(Unknown Source)
	at com.sun.media.jai.util.SunTileScheduler.scheduleTile(Unknown Source)
	at javax.media.jai.OpImage.getTile(Unknown Source)
	at com.sun.media.jai.util.RequestJob.compute(Unknown Source)
[catch] at com.sun.media.jai.util.WorkerThread.run(Unknown Source)

[marpet]

Hello tiagoams, thanks for your report.
Can you provide more information? For example, the configuration you have used.
You can get the parametrization of the operator from the File menu of the operator.
You say you are using Linux. How much RAM does the system have? Is it a VM?
An update might help to. you are using SNAP 8.0.4. Meanwhile 8.0.9 is available.
Which version of S2 IdePix are you using? Is it already 8.0.2?

[tiagoams]

IdePix S2 parameterization for ocean:

<parameters>
    <copyToaReflectances>true</copyToaReflectances>
    <copyFeatureValues>false</copyFeatureValues>
    <computeMountainShadow>false</computeMountainShadow>
    <computeCloudShadow>true</computeCloudShadow>
    <computeCloudBuffer>true</computeCloudBuffer>
    <computeCloudBufferForCloudAmbiguous>true</computeCloudBufferForCloudAmbiguous>
    <cloudBufferWidth>2</cloudBufferWidth>
    <demName>SRTM 3Sec</demName>
</parameters>

Snap Engine Kit Module: Version: 8.0.8
IdePix S2-MSI Version: 8.0.2

Azure Ubuntu 20.04 VM with 32GB RAM, 4 cores

(base) tams00@corp.cefas.co.uk:~/tempimages$ /mnt/software/snap/bin/snap --list --modules
Code Name                                          Version  State           
-------------------------------------------------- -------- ----------------
org.csa.rstb.rstb.op.polarimetric.tools            8.0.5    Available       
org.esa.s2tbx.s2tbx.s2msi.reader                   8.0.4    Upgrade to 8.0.5
org.esa.snap.snap.temporal.percentile              8.0.8    Upgrade to 8.0.9
org.netbeans.swing.plaf                            1.41.1   Enabled         
org.netbeans.modules.extexecution                  1.48.1   Enabled         
org.esa.snap.snap.unmix.ui                         8.0.8    Upgrade to 8.0.9
org.netbeans.modules.options.api                   1.45.1   Enabled         
org.esa.snap.snap.pgx.reader                       8.0.8    Upgrade to 8.0.9
org.esa.snap.snap.remote.products.repository       8.0.8    Upgrade to 8.0.9
org.esa.snap.snap.dastool                          1.0.1    Available       
org.openide.modules                                7.48.1   Enabled         
org.esa.s2tbx.s2tbx.forest.cover.change            8.0.4    Upgrade to 8.0.5
org.esa.snap.snap.smart.configurator.ui            8.0.8    Upgrade to 8.0.9
org.esa.s3tbx.s3tbx.landsat.reader                 8.0.4    Enabled         
org.esa.sen2coral.sen2coral.kit                    1.0.0    Available       
org.openide.util.lookup                            8.33.1   Enabled         
org.netbeans.modules.masterfs.nio2                 1.15.1   Enabled         
org.esa.s2tbx.s2tbx.alosAV2.reader                 8.0.4    Upgrade to 8.0.5
org.esa.s3tbx.s3tbx.sentinel3.reader               8.0.4    Enabled         
org.esa.chris.chris.noise.reduction                3.0.0    Available       
org.esa.snap.snap.python                           8.0.8    Upgrade to 8.0.9
org.esa.s2tbx.s2tbx.worldview2esa.reader           8.0.4    Upgrade to 8.0.5
org.esa.s1tbx.s1tbx.kit                            8.0.5    Enabled         
org.netbeans.api.annotations.common                1.27.1   Enabled         
org.esa.s2tbx.s2tbx.gdal.reader                    8.0.4    Upgrade to 8.0.5
org.esa.snap.snap.remote.execution.ui              8.0.8    Upgrade to 8.0.9
org.esa.snap.snap.zarr                             0.3      Available       
org.esa.snap.globcover.worldmap                    8.0.8    Upgrade to 8.0.9
org.netbeans.core.output2                          1.41.1   Enabled         
org.esa.snap.snap.branding                         8.0.8    Upgrade to 8.0.9
org.esa.snap.snap.core                             8.0.8    Upgrade to 8.0.9
org.netbeans.core.netigso                          1.31.1   Enabled         
org.esa.s3tbx.s3tbx.spot.vgt.reader                8.0.4    Enabled         
org.netbeans.libs.jna.platform                     1.14.1   Enabled         
org.esa.s3tbx.s3tbx.sentinel3.reader.ui            8.0.4    Enabled         
org.esa.snap.snap.smart.configurator               8.0.8    Upgrade to 8.0.9
org.esa.s2tbx.s2tbx.otb.adapters.kit               7.0.0    Available       
org.esa.s2tbx.s2tbx.land.cover                     8.0.4    Upgrade to 8.0.5
org.openide.execution                              9.3.1    Enabled         
org.esa.snap.snap.statistics                       8.0.8    Upgrade to 8.0.9
org.esa.s1tbx.s1tbx.commons                        8.0.5    Enabled         
org.esa.s3tbx.s3tbx.mphchl                         8.0.4    Enabled         
org.esa.s3tbx.s3tbx.meris.l2auxdata                8.0.4    Enabled         
org.esa.snap.idepix.probav                         8.0.0    Available       
org.csa.rstb.rstb.op.calibration                   8.0.5    Available       
org.esa.snap.ceres.ui                              8.0.8    Upgrade to 8.0.9
org.netbeans.spi.quicksearch                       1.27.1   Enabled         
org.openide.windows                                6.75.1   Enabled         
org.esa.s3tbx.s3tbx.o2a.harmonisation              8.0.4    Enabled         
org.netbeans.modules.sampler                       1.14.1   Enabled         
org.netbeans.modules.autoupdate.ui                 1.45.1   Enabled         
org.csa.rstb.rstb.op.soil.moisture                 8.0.5    Available       
org.esa.s3tbx.s3tbx.aatsr.sst.ui                   8.0.4    Enabled         
org.esa.snap.snap.collocation                      8.0.8    Upgrade to 8.0.9
org.esa.s3tbx.s3tbx.olci.radiometry                8.0.4    Enabled         
org.esa.s2tbx.s2tbx.radiometric.indices.ui         8.0.4    Upgrade to 8.0.5
org.esa.snap.snap.gpf.ui                           8.0.8    Upgrade to 8.0.9
org.netbeans.modules.templates                     1.7.1    Enabled         
org.esa.snap.ceres.core                            8.0.8    Upgrade to 8.0.9
org.esa.snap.snap.raster                           8.0.8    Upgrade to 8.0.9
org.esa.snap.netbeans.tile                         1.0      Enabled         
org.esa.s3tbx.s3tbx.slstr.regrid                   8.0.4    Enabled         
org.openide.util.enumerations                      6.33.1   Installed       
org.esa.snap.snap.csv.dataio                       8.0.8    Upgrade to 8.0.9
org.netbeans.modules.extbrowser                    1.53.1   Enabled         
org.openide.actions                                6.39.1   Enabled         
org.openide.compat                                 6.39.1   Installed       
org.esa.s2tbx.Pansharpening.bayes                  7.0.0    Available       
org.esa.snap.snap.pixel.extraction                 8.0.8    Upgrade to 8.0.9
org.esa.snap.seadas.seadas.reader.ui               1.9.4    Enabled         
org.esa.s1tbx.s1tbx.op.analysis.ui                 8.0.5    Enabled         
org.openide.loaders                                7.66.1   Enabled         
org.esa.s2tbx.s2tbx.gdal.reader.ui                 8.0.0.0  Available       
org.openide.nodes                                  7.45.1   Enabled         
org.esa.chris.chris.atmospheric.correction         3.0.0    Available       
org.netbeans.modules.keyring.fallback              1.8.1    Enabled         
org.esa.snap.snap.binning                          8.0.8    Upgrade to 8.0.9
org.netbeans.swing.outline                         1.34.1   Enabled         
org.esa.chris.chris.cloud.screening                3.0.0    Available       
org.esa.s1tbx.s1tbx.op.feature.extraction          8.0.5    Enabled         
org.openide.io                                     1.49.1   Enabled         
org.esa.s3tbx.s3tbx.merisl3.reader                 8.0.4    Enabled         
org.esa.snap.snap.pixel.extraction.ui              8.0.8    Upgrade to 8.0.9
org.jlinda.jlinda.nest                             8.0.5    Enabled         
org.esa.s3tbx.s3tbx.fub.wew.ui                     8.0.4    Enabled         
org.esa.s2tbx.s2tbx.spot.reader                    8.0.4    Upgrade to 8.0.5
org.esa.s2tbx.s2tbx.radiometric.indices            8.0.4    Upgrade to 8.0.5
net.java.html.geo                                  1.3.0    Installed       
org.esa.snap.snap.gpf                              8.0.8    Upgrade to 8.0.9
org.esa.snap.snap.land.cover.ui                    8.0.8    Upgrade to 8.0.9
org.netbeans.libs.asm                              5.3.1    Enabled         
org.esa.s2tbx.s2tbx.muscate.reader                 8.0.4    Upgrade to 8.0.5
org.esa.snap.snap.bigtiff                          8.0.8    Upgrade to 8.0.9
org.esa.snap.snap.tango                            8.0.8    Upgrade to 8.0.9
org.esa.s2tbx.s2tbx.grm.ui                         8.0.4    Upgrade to 8.0.5
org.esa.s3tbx.s3tbx.meris.smac                     8.0.4    Enabled         
org.esa.smostbx.smos.tools                         5.8.1    Available       
org.netbeans.modules.masterfs.linux                1.13.1   Enabled         
org.netbeans.modules.favorites                     1.46.1   Enabled         
eu.s2gm.s2gm.snap.plugins                          1.2.3    Available       
org.esa.s1tbx.s1tbx.op.sar.processing              8.0.5    Enabled         
org.esa.snap.iCOR.sentinel2.sta                    3.0.0    Enabled         
org.esa.snap.snap.rut                              2.0      Available       
org.esa.snap.snap.arcbingrid.reader                8.0.8    Upgrade to 8.0.9
org.netbeans.modules.options.keymap                1.37.1   Enabled         
org.netbeans.modules.queries                       1.43.1   Enabled         
org.esa.snap.snap.envisat.reader                   8.0.8    Upgrade to 8.0.9
org.esa.sen2coral.sen2coral.algorithms             1.0.0    Available       
org.esa.snap.idepix.modis                          8.0.0    Enabled         
org.esa.s3tbx.s3tbx.insitu.client.ui               8.0.4    Enabled         
org.vito.probavbox.probavbox.kit                   2.2.0    Available       
org.esa.s2tbx.s2tbx.rapideye.reader                8.0.4    Upgrade to 8.0.5
org.netbeans.modules.editor.mimelookup             1.40.1   Enabled         
org.esa.smostbx.smos.gui                           5.8.1    Available       
org.esa.s2tbx.sen2three                            6.0.0    Available       
org.esa.snap.snap.worldwind                        8.0.8    Upgrade to 8.0.9
org.esa.s1tbx.s1tbx.rcp                            8.0.5    Enabled         
org.esa.snap.ceres.glayer                          8.0.8    Upgrade to 8.0.9
org.esa.snap.snap.jython                           8.0.0    Enabled         
org.esa.s3tbx.s3tbx.arc.ui                         8.0.4    Enabled         
org.esa.s2tbx.s2tbx.gdal.writer                    8.0.4    Upgrade to 8.0.5
org.csa.rstb.rstb.op.soil.moisture.ui              8.0.5    Available       
org.netbeans.libs.felix                            2.15.1   Enabled         
org.esa.s2tbx.Segmentation.cc                      7.0.0    Available       
org.esa.snap.snap.pconvert                         8.0.8    Upgrade to 8.0.9
org.csa.rstb.rstb.op.classification.ui             8.0.5    Available       
org.esa.snap.snap.geotiff                          8.0.8    Upgrade to 8.0.9
org.netbeans.modules.progress.ui                   1.33.1   Enabled         
org.esa.snap.snap.virtual.file.system.ui           8.0.8    Upgrade to 8.0.9
org.netbeans.modules.masterfs.ui                   2.3.1.2  Enabled         
org.esa.snap.snap.rcp                              8.0.8    Upgrade to 8.0.9
org.esa.s3tbx.s3tbx.atsr.reader                    8.0.4    Enabled         
org.esa.chris.chris.atmospheric.correction.lut     3.0.0    Available       
org.netbeans.core.multiview                        1.44.1   Installed       
org.esa.s1tbx.s1tbx.op.insar                       8.0.5    Enabled         
org.esa.sen2coral.sen2coral.inversion.ui           1.0.0    Available       
net.java.html.boot.fx                              1.3.0    Installed       
org.netbeans.api.visual                            2.47.1   Installed       
org.esa.snap.snap.classification                   8.0.8    Upgrade to 8.0.9
org.netbeans.modules.keyring.impl                  1.24.1   Enabled         
org.openide.options                                6.37.1   Installed       
org.openide.explorer                               6.62.1   Enabled         
org.esa.s2tbx.Pansharpening.rcs                    7.0.0    Available       
org.openide.filesystems.compat8                    9.9.1    Enabled         
org.esa.snap.snap.cluster.analysis                 8.0.8    Upgrade to 8.0.9
org.esa.s2tbx.s2tbx.gdal.writer.ui                 8.0.4    Upgrade to 8.0.5
org.esa.snap.snap.classification.ui                8.0.8    Upgrade to 8.0.9
org.esa.chris.chris.toa.reflectance.computation    3.0.0    Available       
org.esa.s1tbx.s1tbx.op.calibration.ui              8.0.5    Enabled         
org.netbeans.core.osgi                             1.22.1   Installed       
org.esa.snap.snap.getasse30.dem                    8.0.8    Upgrade to 8.0.9
org.netbeans.modules.netbinox                      1.41.1   Installed       
org.esa.snap.snap.product.library                  8.0.3    Enabled         
org.esa.s2tbx.s2tbx.ikonos.reader                  8.0.4    Upgrade to 8.0.5
org.esa.s3tbx.s3tbx.c2rcc                          8.0.4    Enabled         
org.netbeans.core.ui                               1.45.1   Enabled         
org.netbeans.core.startup.base                     1.62.1.1 Enabled         
org.esa.snap.snap.watermask.ui                     8.0.8    Upgrade to 8.0.9
org.esa.snap.snap.virtual.file.system              8.0.8    Upgrade to 8.0.9
org.esa.snap.idepix.spotvgt                        8.0.0    Available       
org.netbeans.modules.core.kit                      1.30.1   Enabled         
org.esa.snap.idepix.landsat8                       8.0.0    Enabled         
org.esa.s2tbx.s2tbx.worldview2.reader              8.0.4    Upgrade to 8.0.5
org.csa.rstb.rstb.kit                              8.0.5    Available       
org.esa.s2tbx.s2tbx.biophysical                    8.0.4    Upgrade to 8.0.5
org.esa.sen2coral.sen2coral.inversion              1.0.0    Available       
org.esa.smostbx.smos.reader                        5.8.1    Available       
org.netbeans.libs.junit4                           1.17.1   Installed       
org.esa.s3tbx.s3tbx.meris.brr                      8.0.4    Enabled         
org.esa.s1tbx.s1tbx.op.utilities.ui                8.0.5    Enabled         
org.esa.snap.snap.sta                              8.0.8    Upgrade to 8.0.9
org.esa.s1tbx.s1tbx.cloud                          8.0.5    Enabled         
org.esa.snap.idepix.viirs                          8.0.0    Enabled         
org.netbeans.modules.autoupdate.services           1.52.1   Enabled         
org.esa.snap.seadas.seadas.reader                  1.9.4    Enabled         
org.esa.snap.iCOR.sentinel3.sta                    3.0.0    Enabled         
org.esa.snap.snap.watermask                        8.0.8    Upgrade to 8.0.9
org.esa.s1tbx.s1tbx.op.ocean.ui                    8.0.5    Enabled         
org.esa.smostbx.smos.kit                           5.8.1    Available       
org.esa.snap.snap.collocation.ui                   8.0.8    Upgrade to 8.0.9
org.esa.snap.snap.dem                              8.0.8    Upgrade to 8.0.9
org.netbeans.core.network                          1.10.1   Enabled         
org.esa.snap.idepix.olci                           8.0.1    Enabled         
org.esa.snap.snap.envi.reader                      8.0.8    Upgrade to 8.0.9
org.esa.snap.lib.openjpeg                          8.0.8    Upgrade to 8.0.9
org.netbeans.api.search                            1.21.1   Installed       
org.openide.filesystems.nb                         9.9.1    Enabled         
org.netbeans.modules.keyring                       1.24.1   Enabled         
org.netbeans.core.windows                          2.81.1   Enabled         
org.netbeans.api.templates                         1.7.1    Enabled         
org.esa.snap.snap.netcdf                           8.0.8    Upgrade to 8.0.9
org.esa.s3tbx.s3tbx.arc                            8.0.4    Enabled         
org.esa.chris.chris.geometric.correction           3.0.0    Available       
org.esa.s3tbx.s3tbx.alos.reader                    8.0.4    Enabled         
org.netbeans.modules.autoupdate.cli                1.13.1   Enabled         
org.esa.s1tbx.s1tbx.io.ephemeris                   8.0.5    Enabled         
org.esa.s2tbx.s2tbx.spectral.angle.mapper          8.0.4    Upgrade to 8.0.5
org.netbeans.modules.uihandler                     2.35.1   Installed       
org.esa.snap.snap.virtual.file.system.preferences. 8.0.8    Upgrade to 8.0.9
org.esa.s1tbx.s1tbx.op.utilities                   8.0.5    Enabled         
org.esa.s2tbx.s2tbx.s2msi.reader.ui                8.0.4    Upgrade to 8.0.5
org.esa.s2tbx.s2tbx.coregistration.ui              8.0.4    Upgrade to 8.0.5
org.netbeans.modules.templatesui                   1.3.1    Installed       
org.esa.s3tbx.s3tbx.fub.wew                        8.0.4    Enabled         
org.esa.snap.snap.binning.ui                       8.0.8    Upgrade to 8.0.9
org.esa.s3tbx.s3tbx.owt.classification             8.0.4    Enabled         
org.esa.s2tbx.lib.gdal                             8.0.4    Upgrade to 8.0.5
org.esa.s2tbx.sen2cor280                           7.0.0    Enabled         
org.esa.snap.idepix.seawifs                        8.0.0    Enabled         
org.esa.snap.netbeans.docwin                       1.0.2.0  Enabled         
org.esa.s2tbx.MultivariateAlterationDetector       7.0.0    Available       
org.netbeans.bootstrap                             2.76.1   Enabled         
org.vito.probavbox.probavbox.reader                2.2.0    Available       
org.netbeans.modules.print                         7.26.1   Enabled         
org.jlinda.jlinda.core                             8.0.5    Enabled         
org.esa.s2tbx.s2tbx.kompsat2.reader                8.0.4    Upgrade to 8.0.5
org.openide.util                                   9.7.1    Enabled         
org.netbeans.modules.spi.actions                   1.28.1   Installed       
org.esa.s1tbx.s1tbx.op.feature.extraction.ui       8.0.5    Enabled         
com.airbus.snap.snap.novasar.reader                1.2.1    Available       
org.esa.snap.iCOR.landsat8.sta                     3.0.0    Enabled         
org.esa.s3tbx.s3tbx.avhrr.reader                   8.0.4    Enabled         
org.esa.snap.ceres.jai                             8.0.8    Upgrade to 8.0.9
org.esa.s2tbx.s2tbx.s2msi.mci.ui                   8.0.4    Upgrade to 8.0.5
org.esa.snap.core.gpf.operators.tooladapter.snaphu 8.0.0    Available       
org.esa.s2tbx.s2tbx.coregistration                 8.0.4    Upgrade to 8.0.5
org.esa.s2tbx.s2tbx.reflectance.to.radiance        8.0.4    Upgrade to 8.0.5
org.jlinda.jlinda.nest.ui                          8.0.5    Enabled         
org.esa.snap.idepix.meris                          8.0.1    Enabled         
org.netbeans.core.io.ui                            1.30.1   Enabled         
org.netbeans.html.xhr4j                            1.3.0    Installed       
org.netbeans.api.progress.compat8                  1.47.1   Installed       
org.openide.dialogs                                7.42.1   Enabled         
org.esa.snap.blue.marble.worldmap                  8.0.8    Upgrade to 8.0.9
org.esa.snap.snap.hdf5.writer                      8.0.8    Upgrade to 8.0.9
org.esa.snap.snap.land.cover                       8.0.8    Upgrade to 8.0.9
org.openide.awt                                    7.67.1   Enabled         
org.esa.s3tbx.s3tbx.modis.reader                   8.0.4    Enabled         
org.netbeans.api.io                                1.3.1    Enabled         
org.netbeans.api.intent                            1.2.1    Enabled         
org.esa.s3tbx.s3tbx.rad2refl                       8.0.4    Enabled         
com.iceye.esa.snap.iceye.slc.reader                8.0.5    Enabled         
org.csa.rstb.rstb.op.polarimetric.tools.ui         8.0.5    Available       
org.csa.rstb.rstb.op.classification                8.0.5    Available       
org.esa.s2tbx.s2tbx.alosPRI.reader                 8.0.4    Upgrade to 8.0.5
org.esa.s2tbx.Pansharpening.lmvm                   7.0.0    Available       
org.netbeans.api.progress.nb                       1.47.1   Enabled         
org.esa.s1tbx.s1tbx.io.ephemeris.ui                8.0.5    Enabled         
org.esa.s2tbx.s2tbx.pleiades.reader                8.0.4    Upgrade to 8.0.5
org.esa.s3tbx.s3tbx.slstr.pdu.stitching.ui         8.0.4    Enabled         
org.esa.s2tbx.s2tbx.preferences.ui                 8.0.4    Upgrade to 8.0.5
org.esa.chris.chris.util                           3.0.0    Available       
org.esa.s3tbx.s3tbx.flhmci                         8.0.4    Enabled         
org.esa.s2tbx.s2tbx.forest.cover.change.ui         8.0.4    Upgrade to 8.0.5
org.esa.snap.snap.product.library.v2               8.0.8    Upgrade to 8.0.9
org.netbeans.api.progress                          1.47.1   Enabled         
net.java.html.sound                                1.3.0    Installed       
ncsa.hdf.lib.hdf                                   2.7.1    Enabled         
org.esa.s2tbx.s2tbx.commons                        8.0.4    Upgrade to 8.0.5
org.openide.util.ui                                9.6.1    Enabled         
org.esa.s2tbx.s2tbx.cache                          8.0.4    Upgrade to 8.0.5
org.esa.s3tbx.s3tbx.aatsr.sst                      8.0.4    Enabled         
org.netbeans.libs.javafx                           2.7.1    Installed       
org.openide.text                                   6.67.1   Enabled         
org.esa.snap.snap.help                             8.0.8    Upgrade to 8.0.9
org.esa.smostbx.smos.ee2netcdf.ui                  5.8.1    Available       
org.esa.s3tbx.s3tbx.meris.ops                      8.0.4    Enabled         
org.netbeans.libs.osgi                             1.21.1   Enabled         
org.esa.snap.snap.ui                               8.0.8    Upgrade to 8.0.9
org.esa.snap.idepix.s2msi                          8.0.2    Enabled         
org.esa.s2tbx.s2tbx.s2msi.resampler                8.0.4    Upgrade to 8.0.5
org.esa.s2tbx.s2tbx.spectral.angle.mapper.ui       8.0.4    Upgrade to 8.0.5
org.esa.s2tbx.Segmentation.meanshift               7.0.0    Available       
org.esa.snap.snap.product.library.ui.v2            8.0.8    Upgrade to 8.0.9
org.esa.s3tbx.s3tbx.flhmci.ui                      8.0.4    Enabled         
net.java.html.json                                 1.3.0    Installed       
org.netbeans.core.startup                          1.62.1.1 Enabled         
org.esa.s3tbx.s3tbx.meris.radiometry               8.0.4    Enabled         
org.esa.smostbx.smos.dgg                           5.8.1    Available       
org.netbeans.core.execution                        1.41.1   Enabled         
org.esa.s3tbx.s3tbx.kit                            8.0.4    Enabled         
org.esa.s3tbx.s3tbx.meris.radiometry.ui            8.0.4    Enabled         
org.esa.smostbx.smos.lsmask                        5.8.1    Available       
org.esa.s1tbx.s1tbx.op.sar.processing.ui           8.0.5    Enabled         
org.esa.snap.ceres.binio                           8.0.8    Upgrade to 8.0.9
org.netbeans.core                                  3.51.1   Enabled         
org.netbeans.modules.sendopts                      2.35.1   Enabled         
org.esa.snap.ceres.binding                         8.0.8    Upgrade to 8.0.9
org.esa.snap.snap.raster.ui                        8.0.8    Upgrade to 8.0.9
org.jdesktop.layout                                1.33.1   Installed       
net.java.html.boot                                 1.3.0    Installed       
net.java.html.boot.script                          1.3.0    Installed       
org.esa.snap.snap.engine.kit                       8.0.8    Upgrade to 8.0.9
org.esa.snap.snap.product.library.ui               8.0.3    Available       
org.esa.snap.snap.sta.ui                           8.0.8    Upgrade to 8.0.9
org.esa.s2tbx.s2tbx.reflectance.to.radiance.ui     8.0.4    Upgrade to 8.0.5
org.csa.rstb.rstb.io                               8.0.5    Available       
org.netbeans.core.nativeaccess                     1.31.1   Enabled         
org.esa.snap.snap.jp2.reader                       8.0.8    Upgrade to 8.0.9
org.esa.snap.idepix.core                           8.0.1    Enabled         
org.esa.chris.chris.kit                            3.0.0    Available       
org.esa.snap.snap.engine.utilities                 8.0.8    Upgrade to 8.0.9
org.esa.s3tbx.s3tbx.ppe.operator                   8.0.4    Enabled         
org.esa.snap.snap.dem.ui                           8.0.8    Upgrade to 8.0.9
org.esa.s2tbx.s2tbx.deimos.reader                  8.0.4    Upgrade to 8.0.5
org.esa.s1tbx.s1tbx.op.sentinel1.ui                8.0.5    Enabled         
org.netbeans.modules.settings                      1.49.1   Enabled         
org.esa.s2tbx.sen2cor255                           7.0.0    Enabled         
org.esa.snap.ceres.metadata                        8.0.8    Upgrade to 8.0.9
org.esa.s2tbx.s2tbx.spot6.reader                   8.0.4    Upgrade to 8.0.5
org.netbeans.modules.masterfs                      2.55.1.2 Enabled         
org.esa.s1tbx.s1tbx.op.sentinel1                   8.0.5    Enabled         
org.netbeans.lib.uihandler                         1.45.1   Installed       
org.esa.s2tbx.SFSTextureExtraction                 7.0.0    Available       
org.esa.s3tbx.s3tbx.l1csyn.op                      3.0      Available       
org.esa.sen2coral.sen2coral.algorithms.ui          1.0.0    Available       
org.esa.s2tbx.Segmentation.watershed               7.0.0    Available       
net.java.html                                      1.3.0    Installed       
org.esa.s1tbx.s1tbx.op.insar.ui                    8.0.5    Enabled         
org.esa.s2tbx.s2tbx.cache.ui                       8.0.4    Upgrade to 8.0.5
org.esa.smostbx.smos.ee2netcdf                     5.8.1    Available       
org.esa.s3tbx.s3tbx.slstr.pdu.stitching            8.0.4    Enabled         
org.netbeans.core.multitabs                        1.12.1.1 Enabled         
org.esa.s2tbx.s2tbx.sta.adapters.help              8.0.4    Upgrade to 8.0.5
org.netbeans.modules.editor.mimelookup.impl        1.32.1   Enabled         
org.esa.s3tbx.s3tbx.meris.sdr                      8.0.4    Enabled         
org.openide.filesystems                            9.10.1   Enabled         
org.esa.snap.snap.graph.builder                    8.0.8    Upgrade to 8.0.9
org.esa.s2tbx.s2tbx.kit                            8.0.4    Upgrade to 8.0.5
org.esa.s2tbx.Segmentation.mprofiles               7.0.0    Available       
org.netbeans.modules.extexecution.base             1.4.1    Enabled         
org.esa.s1tbx.s1tbx.io                             8.0.5    Enabled         
org.netbeans.api.htmlui                            1.5.1    Installed       
org.esa.s3tbx.s3tbx.rad2refl.ui                    8.0.4    Enabled         
org.esa.s2tbx.lib.gdal.preferences.ui              8.0.4    Upgrade to 8.0.5
org.esa.s2tbx.s2tbx.s2msi.mci                      8.0.4    Upgrade to 8.0.5
org.netbeans.swing.tabcontrol                      1.56.1   Enabled         
org.netbeans.libs.jna                              1.44.1   Enabled         
org.esa.snap.snap.unmix                            8.0.8    Upgrade to 8.0.9
org.netbeans.html.ko4j                             1.3.0    Installed       
org.esa.s2tbx.s2tbx.grm                            8.0.4    Upgrade to 8.0.5
org.esa.snap.snap.remote.execution                 8.0.8    Upgrade to 8.0.9
org.esa.snap.snap.ndvi                             8.0.8    Upgrade to 8.0.9
org.esa.s2tbx.s2tbx.jp2.writer                     8.0.4    Upgrade to 8.0.5
org.netbeans.modules.javahelp                      2.41.1   Enabled         
org.esa.s3tbx.s3tbx.meris.cloud                    8.0.4    Enabled         
org.openide.execution.compat8                      9.2.1    Installed       
org.esa.s3tbx.s3tbx.fu.operator                    8.0.4    Enabled         
org.esa.s1tbx.s1tbx.op.calibration                 8.0.5    Enabled         
org.netbeans.libs.jsr223                           1.35.1   Installed       
org.esa.chris.chris.reader                         3.0.0    Available       
-------------------------------------------------- -------- ----------------

[marpet]

Thanks for the updated information. With this configuration it should be possible to run idepix.
However, on VMs we have seen more issues and poorer performance as on equally equipped hardware.
So, this might be a problem.

What might cause a problem if the RAM of the VM has been increased after SNAP has been installed.
You can check how much memory SNAP can use by calling gpt --diag on the command line
This will give you information like this:

...
Java version: 1.8.0_242
Processors: 12
Max memory: 9.8 GB
Cache size: 1024.0 MB
Tile parallelism: 12
...

The max memory value should be at ~24GB for your system.
If it is not, you can change the memory setting:
Change Memory Settings

I'm not sure if you have stored the result of the S2 resampling to disk and started with IdePix from the saved file. THis should also help to get the data processed.

One tip for the S2 resampling. Add a subset operation before writing the result and exclude all the view_zenith_B## and view azimuth_B##. IdePix uses only the view_zneith_mean and view_azimuth_mean.
This reduces a lot the disk space and improves the performance.

[tiagoams]

Thanks for the suggestions.
It all seems as expected on this VM, with 19GB free. I am also writting the resampled image to a BEAM file. I will try excluding view_xxx and increase cache to 2GB.

$ gpt --diag
...
Java version: 1.8.0_242
Processors: 4
Max memory: 18.7 GB
Cache size: 1024.0 MB
Tile parallelism: 4
Tile size: 512 x 512 pixels
...
$ free -h
              total        used        free      shared  buff/cache   available
Mem:           31Gi       1.6Gi        19Gi        11Mi        10Gi        29Gi
Swap:         1.0Gi        63Mi       960Mi