Error in SAR image corregistration: Error: [Nodeld: CreateStack] org.jblas.NativeBlas.dgemm(CCIIID[DII[DIID[DII)V)

Hi adriaan,

I don’t know if we can resolve this.
It seems that this issue is caused by the usage of the jblas and this wasn’t updated since a while. Probably it would be best to replace jblas by another library, but I don’t know if this can easily be achieved.

Because this is an s1tbx issue, I think @lveci needs to investigate this.

Hi,

I have installed SNAP 8 in Ubuntu 18.04 and when I try to perform the co registration of a SAOCOM pair I get the same error [Error: [Nodeld: CreateStack] org.jblas.NativeBlas.dgemm(CCIIID[DII[DIID[DII)V)"] despite I have installed libgfortran as is mentioned in this comment

This problem not appear in a computer with Windows OS.

Thanks

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I’m having the same issue, the only difference being I’m using Sentinel-1 data.
sudo apt install libgfortran3 appears not to have made any difference.

Not present in SNAP 7 - I am just sticking to this version

@lveci Did you have a solution to this problem? I there was a workaround for 7 does that not work for 8?

jblas should probalby be replaced but testing is needed to ensure it does not create some numerical side-effects.

Hi,
apparently, I have the same problem. Ubuntu 18.04, the latest version of SNAP (8.0) installed, and the latest version of libgfortran3 already pre-installed (I had the same issue with SNAP 7.0), but this time, it is not working, any new suggestion?
Thanks

Me and 12 other class attendees using Ubuntu 18.04 all have the reported problem in SNAP 8.0.
Neither installing libgfortran3 or jblas libraries helped to fix the issue.
For now we downgraded to SNAP 7 and it all works.

@lveci Sentinel-1 in versions 8.0.[0-2] results in [Error: [Nodeld: Back-Geocoding] org.jblas.NativeBlas.dgemm(CCIIID[DII[DIID[DII)V)"]
FYI: a slightly older prerelease version of 8 that I built on CentOS 7 does not have this error.

Dear SNAP developers,

It appears that me and other colleagues still have this issue (org.jblas.NativeBlas.dgemm(CCIIID[DII[DIID[DII)V)). The proposed solution

does not work since libgfortran3is already installed. Reinstalation does not seem to circumvent the issue.

Also note that this error appeared in SNAP 8. I’m using Linux Mint (based on Ubuntu, based on Fortran), last version. The version 6 and 7 are working fine.

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I also had this problem, lately. When I updated from Ubuntu 18 to the latest version (20), it was gone. So in my case it was somehow related to the operating system or a missing library. I only tested SNAP 8 though.

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sudo apt-get update

sudo apt install libgfortran5

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I encountered this error and installing libgfortran5 fixed the error for me as mentioned by @nachin6789.
I am using SNAP 8 on Ubuntu 20.04 LTS

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Works like a charm. Thank you very much.
Q.

Hi,

I have installed SNAP 8 in Ubuntu 18.04 and when I try to perform the python coreg_ifg_topsar py project.conf for 118 images,I get the same error :roll_eyes:
application/pi/SAMIRA/subsidence//split/20190424/20190424_IW2.dim

[2] Processing slave file :20190424_IW2.dim

SNAP STDOUT:INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters

INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: GDAL 2.4.1 found on system. JNI driver will be used.

INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Installed GDAL 2.4.1 set to be used by SNAP.

Native library load failed.

java.lang.UnsatisfiedLinkError: /application/pi/.snap/auxdata/gdal/gdal-2-4-X-jni/libgdalalljni.so: libgdal.so.20: cannot open shared object file: No such file or directory

SEVERE: org.esa.s2tbx.dataio.gdal.GDALLoader: Failed to initialize GDAL native drivers. GDAL readers and writers were disabled.java.lang.reflect.InvocationTargetException

INFO: org.esa.snap.core.util.EngineVersionCheckActivator: Please check regularly for new updates for the best SNAP experience.

INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Installed GDAL 2.4.1 set to be used by SNAP.

Executing processing graph

INFO: org.hsqldb.persist.Logger: dataFileCache open start

done.

java.lang.NullPointerException

at org.esa.s1tbx.sentinel1.gpf.SpectralDiversityOp.initialize(SpectralDiversityOp.java:309)

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:385)

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.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:118)

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: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:84)

at com.install4j.runtime.launcher.UnixLauncher.start(UnixLauncher.java:66)

at install4j.org.esa.snap.runtime.Launcher_gpt.main(Unknown Source)

Error: java.lang.NullPointerException

– org.jblas INFO Deleting /tmp/jblas4565772489320838501/libquadmath-0.so

– org.jblas INFO Deleting /tmp/jblas4565772489320838501/libgfortran-4.so

– org.jblas INFO Deleting /tmp/jblas4565772489320838501/libjblas_arch_flavor.so

– org.jblas INFO Deleting /tmp/jblas4565772489320838501/libjblas.so

– org.jblas INFO Deleting /tmp/jblas4565772489320838501

[2] Finished process in 9.16844797134 seconds.

I encountered this error and installed libgfortran5 ,but it not fix now.
Anyone have an idea?

This issue does nothing have to do with the libgfortran5.
There must be another problem.
But I can’t see.
At the code location where the exception occurs only the esdEstimator parameter can be null. But this is actually prevented by the parameter framework. One of the values Average or Periodogram must be used.

Maybe there is an issue in the coreg_ifg_topsar python script.

thanks your good response,I have attached the scripts for you, please look at this and guide me,
Sincerecly,
coreg_ifg_computation.xml (5.9 KB) coreg_ifg_topsar.py (4.9 KB) project.conf (712 Bytes)

Same issue while doing TOPS coregistration. Fixed the error following @nachin6789 suggestion.

Using SNAP 8 on Linux Mint 19.1 Tessa

i’m using red hat enterprise linux workstation release 7.9
Linux 3.10.0-1127.13.1.el7.x86_64 x86_64
Snap version is 8

i’m getting this error while running coreg_ifg_topsar script

i tried installing libgfortran5 with yum but didn’t work

please help

@marpet, can you please help us with the SNAP 8 dependencies needed in Red Hat OS?
Thanks!

I have not much experience with this. It is an issue of S1TBX.
[SITBX-603] Create Stack Error in graph: [NodeId: 2-CreateStack] - JIRA (atlassian.net)
[SITBX-769] Investigate if we can replace jblas - JIRA (atlassian.net)

Maybe @jun_lu or @lveci can comment on this.

The fix which was working on centos might help:

1 Like