Snap2stamps error

[suribabu]

Try this below one:

Snap2stamps error

Try to change <useSuppliedShifts>false</useSuppliedShifts> to <useSuppliedRangeShift>false</useSuppliedRangeShift> <useSuppliedAzimuthShift>false</useSuppliedAzimuthShift> in coreg_ifg_computation.xml file This option is changed to two attributes in range and azimute for snap V.7

[mirza.waqar]

I already did this but still getting the same error.

[suribabu]

Have you changed in both the corgistration files in graphs folder?

[mirza.waqar]

yes I changed in both coregistration files. However I was getting same erro. Now I installed SNAP 6.0 and my process is working fine without any error. Thank you for your prompt reply.

[ionutciocirlie]

Hello everyone,

I’m working on a PSI project and I followed all the data preparation steps from the RUS training webinar.

Currently I’m facing the same problem with the mt_prep_snap function - 'Segmentation fault (core dumped).

• I need to mention that I already installed GCC 7!
• I checked all the interferograms
  The first image is the master one.
  
  
  
  
  

I don’t really know what to try anymore, I tried all the things that I read here.
PS: UBUNTU 22.04.1 running on VM.
Thank you!

[suribabu]

Try this below one.

Segmentation Fault (core dumped) error during mt_prep_snap

@JeroBande is right, the problem is the compiler version. StaMPS has to be compiled with gcc-7 (gcc-9 was installed in my case and used for the compilation of StaMPS which led to incorrectly compiled scripts) So this is what it solved the problem in my case (partially copied from here). I cannot grant that it will solve all problems, but changing the compiler makes a difference. If you get stuck at one of these steps, please try to continue searching the web, because I have no clue how to troub…

[ionutciocirlie]

Hello and thank you!

I already did it, I check it and the installed version is GCC 7.

[suribabu]

One more thing, it is better to use the older version of ubuntu like 18.04 LTS or 20.04 LTS. I’m using ubuntu 18.04 LTS StaMPS running without any error.

[ionutciocirlie]

I will reinstall an older version of Ubuntu and try it again! I will update you!

[ionutciocirlie]

Hello guys, I reinstalled Ubuntu 18.x from Ubtunu 22.x and the erros are gone! The process has been completed without any error.

Unfortunatelly I’m facing a problem with the TRAIN toolbox, in the MATBAL I’m getting “aps_linear not found” when I’m trying to run “help aps_linear”.

The APS _CONFIG.sh was edited like this:

What I don’t understad is where I can find the “get_modis.py”, I don’t have a python_pakages folder, in the TRAIN, but I created it myself and create the python file from the github.

[suribabu]

TRAIN is another software, we have to install separately, then it will work in StaMPS (as per my knowledge).

[Shadi1]

I have got a this problem during the coregisteration and interferogram creation step. The result ifg and coreg folders are empty. and the following message repeats for every slave image. What can I do if you could help me ?

shadi@shadi-Inspiron-7577:/media/shadi/My Passport/RadarData/Ataqa/P58_F92/project_93/bin$ python2 coreg_ifg_topsar.py project.conf
/media/shadi/My Passport/RadarData/Ataqa/P58_F92/project_93
/media/shadi/My Passport/RadarData/Ataqa/P58_F92/project_93/graphs
IW3
/media/shadi/My Passport/RadarData/Ataqa/P58_F92/project_93/master/S1A_IW_SLC__1SDV_20161209T155620_20161209T155647_014305_017282_64CF_Orb.dim
/home/shadi/esa_snap/bin/gpt
/media/shadi/My Passport/RadarData/Ataqa/P58_F92/project_93/graphs/coreg_ifg_computation_subset.xml

#####################################################################

Coregistration and Interferogram computation started:

#####################################################################

/media/shadi/My Passport/RadarData/Ataqa/P58_F92/project_93/split/20161203/20161203_IW3.dim
[1] Processing slave file :20161203_IW3.dim

SNAP STDOUT: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.
Executing processing graph
INFO: org.hsqldb.persist.Logger: dataFileCache open start
– org.jblas ERROR Couldn’t load copied link file: java.lang.UnsatisfiedLinkError: /tmp/jblas7029820464248639480/libjblas.so: libgfortran.so.5: cannot open shared object file: No such file or directory.

WARNING: org.esa.s1tbx.insar.gpf.coregistration.CreateStackOp: Unable to calculate baselines. org.jblas.NativeBlas.dgemm(CCIIID[DII[DIID[DII)V
org.jblas.NativeBlas.dgemm(CCIIID[DII[DIID[DII)V
done.

Error: [NodeId: Interferogram] org.jblas.NativeBlas.dgemm(CCIIID[DII[DIID[DII)V
– org.jblas INFO Deleting /tmp/jblas7029820464248639480/libgfortran-4.so
– org.jblas INFO Deleting /tmp/jblas7029820464248639480/libquadmath-0.so
– org.jblas INFO Deleting /tmp/jblas7029820464248639480/libjblas_arch_flavor.so
– org.jblas INFO Deleting /tmp/jblas7029820464248639480/libjblas.so
– org.jblas INFO Deleting /tmp/jblas7029820464248639480

[1] Finished process in 9.69786715508 seconds.

#####################################################################

/media/shadi/My Passport/RadarData/Ataqa/P58_F92/project_93/split/20160531/20160531_IW3.dim
[2] Processing slave file :20160531_IW3.dim

SNAP STDOUT: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.
Executing processing graph
INFO: org.hsqldb.persist.Logger: dataFileCache open start
– org.jblas ERROR Couldn’t load copied link file: java.lang.UnsatisfiedLinkError: /tmp/jblas7406801691280682804/libjblas.so: libgfortran.so.5: cannot open shared object file: No such file or directory.

WARNING: org.esa.s1tbx.insar.gpf.coregistration.CreateStackOp: Unable to calculate baselines. org.jblas.NativeBlas.dgemm(CCIIID[DII[DIID[DII)V
org.jblas.NativeBlas.dgemm(CCIIID[DII[DIID[DII)V
done.

Error: [NodeId: Interferogram] org.jblas.NativeBlas.dgemm(CCIIID[DII[DIID[DII)V
– org.jblas INFO Deleting /tmp/jblas7406801691280682804/libgfortran-4.so
– org.jblas INFO Deleting /tmp/jblas7406801691280682804/libquadmath-0.so
– org.jblas INFO Deleting /tmp/jblas7406801691280682804/libjblas_arch_flavor.so
– org.jblas INFO Deleting /tmp/jblas7406801691280682804/libjblas.so
– org.jblas INFO Deleting /tmp/jblas7406801691280682804

[2] Finished process in 3.67021203041 seconds.

Here’s what’s inside the project.conf file

[suribabu]

sudo apt-get update

sudo apt install libgfortran5

[Shadi1]

Any tips how to create this get_modis.py file ?

I cannot find it inside the TRAIN folder either. There’s no such folder named python packages in my entire linux system

[Shadi1]

This problem was solved previously but now I am getting this new error during coregisteration and the following sub-steps while operating of descending images.

/home/shadi/descending_2017_2018/Frame495/split/20171001/20171001_IW1.dim
[3] Processing slave file :20171001_IW1.dim

SNAP STDOUT: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.
Executing processing graph
INFO: org.hsqldb.persist.Logger: dataFileCache open start
INFO: org.esa.s1tbx.sentinel1.gpf.SpectralDiversityOp: Shifts written to file: /home/shadi/.snap/var/log/IW1_range_shifts.json
INFO: org.esa.s1tbx.sentinel1.gpf.SpectralDiversityOp: Estimating azimuth offset for blocks in overlap: 1/2
INFO: org.esa.s1tbx.sentinel1.gpf.SpectralDiversityOp: Estimating azimuth offset for blocks in overlap: 2/2
WARNING: org.esa.s1tbx.sentinel1.gpf.SpectralDiversityOp: NetworkESD (azimuth shift): arc = IW1_VV_mst_30Nov2017_IW1_VV_slv1_01Oct2017 overlap area = 1, weight for this overlap is 0.0
INFO: org.esa.s1tbx.sentinel1.gpf.SpectralDiversityOp: Shifts written to file: /home/shadi/.snap/var/log/IW1_azimuth_shifts.json
…10%…20%…30%…40%…50%…60%.java.lang.NullPointerException
java.lang.NullPointerException
90% done.
org.esa.snap.core.gpf.OperatorException: Cannot construct DataBuffer.
at org.esa.snap.core.gpf.graph.GraphProcessor$GPFImagingListener.errorOccurred(GraphProcessor.java:389)
at com.sun.media.jai.util.SunTileScheduler.sendExceptionToListener(SunTileScheduler.java:1646)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:921)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PlanarImage.cobbleFloat(PlanarImage.java:3254)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2181)
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.s1tbx.sentinel1.gpf.SpectralDiversityOp.performRangeAzimuthShift(SpectralDiversityOp.java:2284)
at org.esa.s1tbx.sentinel1.gpf.SpectralDiversityOp.computeTileStack(SpectralDiversityOp.java:821)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeRect(OperatorImageTileStack.java:122)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeTile(OperatorImageTileStack.java:86)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PlanarImage.cobbleFloat(PlanarImage.java:3254)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2181)
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.s1tbx.sentinel1.gpf.TOPSARDeburstOp.computeTileInOneSwathFloat(TOPSARDeburstOp.java:904)
at org.esa.s1tbx.sentinel1.gpf.TOPSARDeburstOp.computeTileStack(TOPSARDeburstOp.java:811)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeRect(OperatorImageTileStack.java:122)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeTile(OperatorImageTileStack.java:86)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PlanarImage.cobbleShort(PlanarImage.java:2951)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2172)
at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
at org.esa.snap.core.datamodel.Band.readRasterData(Band.java:309)
at org.esa.snap.core.dataio.ProductSubsetBuilder.readBandRasterDataRegion(ProductSubsetBuilder.java:393)
at org.esa.snap.core.dataio.ProductSubsetBuilder.readBandRasterDataImpl(ProductSubsetBuilder.java:330)
at org.esa.snap.core.dataio.AbstractProductReader.readBandRasterData(AbstractProductReader.java:277)
at org.esa.snap.core.gpf.common.SubsetOp.computeTile(SubsetOp.java:295)
at org.esa.snap.core.gpf.internal.OperatorImage.computeRect(OperatorImage.java:82)
at javax.media.jai.SourcelessOpImage.computeTile(SourcelessOpImage.java:137)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2085)
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.OperatorImageTileStack.computeRect(OperatorImageTileStack.java:116)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeTile(OperatorImageTileStack.java:86)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at com.sun.media.jai.util.RequestJob.compute(SunTileScheduler.java:247)
at com.sun.media.jai.util.WorkerThread.run(SunTileScheduler.java:468)
Caused by: java.lang.RuntimeException: Cannot construct DataBuffer.
at com.sun.media.jai.util.DataBufferUtils.constructDataBuffer(DataBufferUtils.java:132)
at com.sun.media.jai.util.DataBufferUtils.createDataBufferFloat(DataBufferUtils.java:214)
at javax.media.jai.ComponentSampleModelJAI.createDataBuffer(ComponentSampleModelJAI.java:271)
at javax.media.jai.RasterFactory.createWritableRaster(RasterFactory.java:691)
at javax.media.jai.PlanarImage.createWritableRaster(PlanarImage.java:1982)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.createWritableRaster(OperatorImageTileStack.java:181)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.getWritableRaster(OperatorImageTileStack.java:171)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.getWritableRaster(OperatorImageTileStack.java:153)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeRect(OperatorImageTileStack.java:111)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeTile(OperatorImageTileStack.java:86)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
… 47 more

Error: Cannot construct DataBuffer.
– org.jblas INFO Deleting /tmp/jblas7116186565449515897/libgfortran-4.so
– org.jblas INFO Deleting /tmp/jblas7116186565449515897/libquadmath-0.so
– org.jblas INFO Deleting /tmp/jblas7116186565449515897/libjblas_arch_flavor.so
– org.jblas INFO Deleting /tmp/jblas7116186565449515897/libjblas.so
– org.jblas INFO Deleting /tmp/jblas7116186565449515897

[3] Finished process in 168.885437965 seconds.

[mdelgado]

Could it be due to memory? RAM? or Java Xmx parameter?

[Shadi1]

@mdelgado

Could it be due to memory? RAM?

Yes, I have located where the problem was. My computer is a little too weak to handle such intensive processing. Even though I have set

COMPUTING RESOURCES TO EMPLOY

CPU=8
CACHE=12G

Those project configuration settings were not applied for some reason neither when cache=12G nor cache=8G , so I changed the cache option in SNAP itelf but automatically computing the system’s cache size and here’s what I got

Some interferograms were successfully created while others weren’t. So, I took a further step and reduced the AOI to be subset and now all the slaves have been successfully used to create interferograms. This snap-to-stamps processing is just too demanding. I thought the process would take too long but never thought it would crash or cause errors if the system couldn’t handle it

[Shadi1]

There’s something really strange though. All the interferograms look like this

[mdelgado]

Please check if the secondary images overlap the entire reference AOI

[Edwardo]

Hello everyone, I just did the corregistration and interferogram formation but it gives me this warning message: WARNING: org.jlinda.core.Baseline: Max. error bperp modeling at 3D datapoints: 25.741510197840086m. this warning only appear in one pair of images from the stack, is this normal? or has a solution?. Any help is useful.