WARN serverStartup - Nc4Iosp: NetCDF-4 C library not present

[nena.v]

We are running a GPT script on a PC and getting the error below. It runs fine on several other computers. Can someone advise on what might be causing this, and how to fix it?

WARNING: org.esa.s1tbx.sar.gpf.orbits.ApplyOrbitFileOp: Using Sentinel Restituted C:\Users\NAME.snap\auxdata\Orbits\Sentinel-1\RESORB\S1B\2021\09\S1B_OPER_AUX_RESORB_OPOD_20210918T052737_V20210918T011603_20210918T043333.EOF instead
.10215 [main] WARN serverStartup - Nc4Iosp: NetCDF-4 C library not present (jna_path=‘C:\Users\NAME.snap\auxdata\netcdf_natives\8.0.7\amd64’, libname=‘netcdf’).
java.lang.NoSuchMethodError: com.sun.jna.Native.load(Ljava/lang/String;Ljava/lang/Class;)Lcom/sun/jna/Library;
at ucar.nc2.jni.netcdf.Nc4Iosp.load(Nc4Iosp.java:124)
at ucar.nc2.jni.netcdf.Nc4Iosp.isClibraryPresent(Nc4Iosp.java:166)
at ucar.nc2.jni.netcdf.Nc4Iosp.create(Nc4Iosp.java:2369)
at ucar.nc2.NetcdfFileWriter.create(NetcdfFileWriter.java:902)
at org.esa.snap.dataio.netcdf.nc.NFileWriteable.create(NFileWriteable.java:111)
at org.esa.snap.dataio.netcdf.NetCdfWriteProfile.writeProduct(NetCdfWriteProfile.java:52)
at org.esa.snap.dataio.netcdf.DefaultNetCdfWriter.writeProductNodesImpl(DefaultNetCdfWriter.java:65)
at org.esa.snap.core.dataio.AbstractProductWriter.writeProductNodes(AbstractProductWriter.java:111)
at org.esa.snap.core.gpf.common.WriteOp.doExecute(WriteOp.java:315)
at org.esa.snap.core.gpf.internal.OperatorContext.executeOperator(OperatorContext.java:1300)
at org.esa.snap.core.gpf.Operator.execute(Operator.java:153)
at org.esa.snap.core.gpf.graph.GraphProcessor.executeGraph(GraphProcessor.java:189)
at org.esa.snap.core.gpf.graph.GraphProcessor.executeGraph(GraphProcessor.java:119)
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 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.exe4j.runtime.WinLauncher.main(WinLauncher.java:94)
at com.install4j.runtime.launcher.WinLauncher.main(WinLauncher.java:25)
10216 [main] INFO serverStartup - Nc4Iosp: set log level: old=-1 new=0
90% done.
java.lang.UnsupportedOperationException: Couldn’t load NetCDF C library (see log for details).
at ucar.nc2.jni.netcdf.Nc4Iosp.create(Nc4Iosp.java:2370)
at ucar.nc2.NetcdfFileWriter.create(NetcdfFileWriter.java:902)
at org.esa.snap.dataio.netcdf.nc.NFileWriteable.create(NFileWriteable.java:111)
at org.esa.snap.dataio.netcdf.NetCdfWriteProfile.writeProduct(NetCdfWriteProfile.java:52)
at org.esa.snap.dataio.netcdf.DefaultNetCdfWriter.writeProductNodesImpl(DefaultNetCdfWriter.java:65)
at org.esa.snap.core.dataio.AbstractProductWriter.writeProductNodes(AbstractProductWriter.java:111)
at org.esa.snap.core.gpf.common.WriteOp.doExecute(WriteOp.java:315)
at org.esa.snap.core.gpf.internal.OperatorContext.executeOperator(OperatorContext.java:1300)
at org.esa.snap.core.gpf.Operator.execute(Operator.java:153)
at org.esa.snap.core.gpf.graph.GraphProcessor.executeGraph(GraphProcessor.java:189)
at org.esa.snap.core.gpf.graph.GraphProcessor.executeGraph(GraphProcessor.java:119)
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 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.exe4j.runtime.WinLauncher.main(WinLauncher.java:94)
at com.install4j.runtime.launcher.WinLauncher.main(WinLauncher.java:25)

Error: Couldn’t load NetCDF C library (see log for details).
Picked up JAVA_TOOL_OPTIONS: -Djava.vendor=“SUN Microsystems Inc”

This error also keeps showing up:

WARNING: org.esa.snap.core.util.ServiceLoader: org.esa.snap.core.gpf.OperatorSpi: Provider org.esa.sen2coral.algorithms.RadiometricNormalisationPIFsOp$Spi could not be instantiated
java.lang.NoClassDefFoundError: com/vividsolutions/jts/geom/Geometry
at java.lang.Class.getDeclaredFields0(Native Method)
at java.lang.Class.privateGetDeclaredFields(Class.java:2583)
at java.lang.Class.getDeclaredFields(Class.java:1916)
at org.esa.snap.core.gpf.descriptor.AnnotationOperatorDescriptorBody.processAnnotationsRec(AnnotationOperatorDescriptorBody.java:78)
at org.esa.snap.core.gpf.descriptor.AnnotationOperatorDescriptorBody.processAnnotations(AnnotationOperatorDescriptorBody.java:68)
at org.esa.snap.core.gpf.descriptor.AnnotationOperatorDescriptorBody.(AnnotationOperatorDescriptorBody.java:34)
at org.esa.snap.core.gpf.descriptor.AnnotationOperatorDescriptor.(AnnotationOperatorDescriptor.java:20)
at org.esa.snap.core.gpf.OperatorSpi.(OperatorSpi.java:115)
at org.esa.snap.core.gpf.OperatorSpi.(OperatorSpi.java:99)
at org.esa.sen2coral.algorithms.RadiometricNormalisationPIFsOp$Spi.(RadiometricNormalisationPIFsOp.java:419)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at java.lang.Class.newInstance(Class.java:442)
at java.util.ServiceLoader$LazyIterator.nextService(ServiceLoader.java:380)
at java.util.ServiceLoader$LazyIterator.next(ServiceLoader.java:404)
at java.util.ServiceLoader$1.next(ServiceLoader.java:480)
at org.esa.snap.core.util.ServiceLoader.loadServices(ServiceLoader.java:40)
at org.esa.snap.core.gpf.internal.OperatorSpiRegistryImpl.loadOperatorSpis(OperatorSpiRegistryImpl.java:77)
at org.esa.snap.core.gpf.GPF.(GPF.java:105)
at org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterActivator.start(ToolAdapterActivator.java:19)
at org.esa.snap.runtime.Engine.informActivators(Engine.java:222)
at org.esa.snap.runtime.Engine.lambda$start$0(Engine.java:121)
at org.esa.snap.runtime.Engine.runClientCode(Engine.java:189)
at org.esa.snap.runtime.Engine.start(Engine.java:121)
at org.esa.snap.runtime.Engine.start(Engine.java:90)
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.exe4j.runtime.WinLauncher.main(WinLauncher.java:94)
at com.install4j.runtime.launcher.WinLauncher.main(WinLauncher.java:25)
Caused by: java.lang.ClassNotFoundException: com.vividsolutions.jts.geom.Geometry
at java.net.URLClassLoader.findClass(URLClassLoader.java:382)
at java.lang.ClassLoader.loadClass(ClassLoader.java:419)
at java.lang.ClassLoader.loadClass(ClassLoader.java:352)
… 36 more

[marpet]

This is strange.
The message means that the method is on available in the library. But the location (C:\Users\NAME.snap\auxdata\netcdf_natives\8.0.7\amd64) where it is loaded from is correct.
There could be several reasons. For example that during the download of the 8.0.7 update something went wrong. Not very likely but could be.
You could try several things.
Delete the folder C:\Users\NAME.snap\auxdata\netcdf_natives\8.0.7
Then try you gpt again. the library should be extracted again. Maybe now it works.
If not you probably have also a 8.0.4 or 8.0.5 or 8.0.6 folder in the netcdf_natives directory. Make a copy of it and rename it to 8.0.7. Then try again.
If this also does not help then uninstall SNAP and install it again. During installation mark the checkbox to remove all data.

[nena.v]

We will try this.
Maybe helpful to note that this is the same computer where we’re still having issues like this:

Update SNAP from 8.0.0 to latest version website unavailable

This week we installed SNAP 8.0.0 on a network computer, and we are now trying to update it to the latest version (I believe it’s 8.0.5?). However, when we try to update, both from the prompt in the SNAP GUI and from the command line, we are getting this error: Not all of the plugins have been successfully downloaded. The server may be unavailable at the moment. Try again later. We have installed and updated SNAP previously on virtual servers without issue. Is there currently a temporary iss…

[gnwiii]

If you are working with a system with an unreliable internet connection, or have many systems to update (e.g., computer lab), you may find it better to first download the updates and then apply them: .nbm files for offline install.