java.lang.UnsatisfiedLinkError: org.jblas.NativeBlas.dcopy(I[DII[DII)V

s1tbx Problem Reports
#1

Hi everybody,
I am having this issue I can’t solve. I tried installing libgfortran3 and also the steps in https://forum.step.esa.int/t/error-in-applying-ers-orbit-informations/23195/12.

The log is:
java.lang.UnsatisfiedLinkError: org.jblas.NativeBlas.dcopy(I[DII[DII)V
at org.jblas.NativeBlas.dcopy(Native Method)
at org.jblas.ComplexDoubleMatrix.real(ComplexDoubleMatrix.java:917)
at org.jlinda.core.utils.SarUtils.intensity(SarUtils.java:152)
at org.jlinda.core.utils.SarUtils.magnitude(SarUtils.java:156)
at org.jlinda.core.coregistration.utils.CoregistrationUtils.crossCorrelateFFT(CoregistrationUtils.java:219)
at org.esa.s1tbx.insar.gpf.OffsetTrackingOp.getOffsets(OffsetTrackingOp.java:877)
Caused: org.esa.snap.core.gpf.OperatorException: org.jblas.NativeBlas.dcopy(I[DII[DII)V
at org.esa.snap.engine_utilities.gpf.OperatorUtils.catchOperatorException(OperatorUtils.java:432)
at org.esa.s1tbx.insar.gpf.OffsetTrackingOp.getOffsets(OffsetTrackingOp.java:892)
at org.esa.s1tbx.insar.gpf.OffsetTrackingOp.access$000(OffsetTrackingOp.java:72)
at org.esa.s1tbx.insar.gpf.OffsetTrackingOp$1.process(OffsetTrackingOp.java:578)
at org.esa.snap.core.util.ThreadRunnable.run(ThreadRunnable.java:23)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused: org.esa.snap.core.gpf.OperatorException: org.jblas.NativeBlas.dcopy(I[DII[DII)V
at org.esa.snap.engine_utilities.gpf.OperatorUtils.catchOperatorException(OperatorUtils.java:432)
at org.esa.s1tbx.insar.gpf.OffsetTrackingOp.computeSlaveGCPs(OffsetTrackingOp.java:596)
at org.esa.s1tbx.insar.gpf.OffsetTrackingOp.computeVelocity(OffsetTrackingOp.java:518)
at org.esa.s1tbx.insar.gpf.OffsetTrackingOp.computeTileStack(OffsetTrackingOp.java:413)
Caused: org.esa.snap.core.gpf.OperatorException: org.jblas.NativeBlas.dcopy(I[DII[DII)V
at org.esa.snap.engine_utilities.gpf.OperatorUtils.catchOperatorException(OperatorUtils.java:432)
at org.esa.s1tbx.insar.gpf.OffsetTrackingOp.computeTileStack(OffsetTrackingOp.java:508)
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(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)

Please help!
Thanks

#2

You should mention your platform and SNAP version. Someone with the same platform may have already found a solution. The problem comes from the jblas package. The gfortran version used by jblas has changed over time, so without more details we can’t be much help.

#3

Ok, sorry. Snap 8 (last update) and ubuntu 18.4.5
I just return to snap 7 and “offset tracking” works but have a problem applying the Orbit file. I can update Snap to 8 again.
Thanks!

#4

I fired up a VM with Mint 19, which is based on Ubuntu 18.04. Searching in
the “home” directory:

$ find .snap -name \*jblas\*.jar
~/.snap/system/modules/ext/org.jlinda.jlinda-nest/org-jblas/jblas.jar
~/.snap/system/modules/ext/org.jlinda.jlinda-core/org-jblas/jblas.jar

They are the same:

$ cmp $(find ~/.snap -name \*jblas\*.jar)
$ [no news is good news]

Extract the files to a scratch folder and look for libgfortan and libjblas:

$ mkdir tmp
$ cd tmp
$ ~/snap/jre/bin/jar -xf ~/.snap/system/modules/ext/org.jlinda.jlinda-nest/org-jblas/jblas.jar
$ ls
lib  META-INF  org
$ cd lib/static/Linux/amd64/
$ ls
libgfortran-4.so  libjblas_arch_flavor.so  libquadmath-0.so  sse3
$ ls sse3
libjblas.so

$ ldd sse3/libjblas.so
linux-vdso.so.1 (0x00007ffff744d000)
libgfortran.so.5 => /usr/lib/x86_64-linux-gnu/libgfortran.so.5 (0x00007f014ebc2000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f014e7d1000)
libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f014e591000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f014e1f3000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f014dfdb000)
/lib64/ld-linux-x86-64.so.2 (0x00007f01509ce000)

I don't see a reference to `libgfortran3`.  Do you have `/usr/lib/x86_64-linux-gnu/libgfortran.so.5`?  If not, you should be able to get it from an official Ubuntu package.
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