I’m now trying to use the compiled version via GPT following @Marco_EOM instructions here: How to setup GPT commandline from source code? - #7 by marpet
However, it complains that it can’t find the HDF5 library. I tried to include it with command line options like this, but it still doesn’t find it:
cat /snap_source/compiled/bin/gpt.sh
#!/bin/sh
java -cp "../modules/*:../lib/*:../modules/lib/*" -Dsnap.mainClass=org.esa.snap.core.gpf.main.GPT -Dsnap.home="../" -Xmx20G org.esa.snap.runtime.Launcher -Dncsa.hdf.hdflib.HDFLibrary.hdflib=/mnt/snap_source/compiled/modules/lib/amd64/libjhdf.so -Dncsa.hdf.hdf5lib.H5.hdflib=/snap_source/compiled/modules/lib/amd64/libjhdf5.so "$@"
Error:
INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters
INFO: org.esa.snap.core.util.EngineVersionCheckActivator: Please check regularly for new updates for the best SNAP experience.
java.lang.UnsatisfiedLinkError: no jhdf5 in java.library.path
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1867)
at java.lang.Runtime.loadLibrary0(Runtime.java:870)
at java.lang.System.loadLibrary(System.java:1122)
at ncsa.hdf.hdf5lib.H5.loadH5Lib(H5.java:339)
at ncsa.hdf.hdf5lib.H5.<clinit>(H5.java:266)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at org.esa.snap.dataio.hdf5.Hdf5ProductWriterPlugIn.loadHdf5Lib(Hdf5ProductWriterPlugIn.java:148)
at org.esa.snap.dataio.hdf5.Hdf5ProductWriterPlugIn.<clinit>(Hdf5ProductWriterPlugIn.java:45)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at java.lang.Class.newInstance(Class.java:442)
at java.util.ServiceLoader$LazyIterator.nextService(ServiceLoader.java:380)
at java.util.ServiceLoader$LazyIterator.next(ServiceLoader.java:404)
at java.util.ServiceLoader$1.next(ServiceLoader.java:480)
at org.esa.snap.core.util.ServiceLoader.loadServices(ServiceLoader.java:40)
at org.esa.snap.core.dataio.ProductIOPlugInManager.<init>(ProductIOPlugInManager.java:209)
at org.esa.snap.core.dataio.ProductIOPlugInManager$Holder.<clinit>(ProductIOPlugInManager.java:214)
at org.esa.snap.core.dataio.ProductIOPlugInManager.getInstance(ProductIOPlugInManager.java:45)
at org.esa.snap.core.gpf.main.CommandLineArgs.detectWriterFormat(CommandLineArgs.java:326)
at org.esa.snap.core.gpf.main.CommandLineArgs.parseArgs(CommandLineArgs.java:191)
at org.esa.snap.core.gpf.main.CommandLineArgs.parseArgs(CommandLineArgs.java:79)
at org.esa.snap.core.gpf.main.CommandLineTool.run(CommandLineTool.java:112)
at org.esa.snap.core.gpf.main.GPT.run(GPT.java:59)
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)
WARNING: org.esa.snap.dataio.hdf5.Hdf5ProductWriterPlugIn: class org.esa.snap.dataio.hdf5.Hdf5ProductWriterPlugIn: HDF-5 library not available: class java.lang.UnsatisfiedLinkError: ncsa.hdf.hdf5lib.H5.H5dont_atexit()I
Executing processing graph
done.
java.lang.NoClassDefFoundError: org/jblas/ComplexDouble
at java.lang.Class.getDeclaredMethods0(Native Method)
at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
at java.lang.Class.getDeclaredMethod(Class.java:2128)
at org.esa.snap.core.gpf.internal.OperatorContext.implementsMethod(OperatorContext.java:509)
at org.esa.snap.core.gpf.internal.OperatorContext.isComputeTileMethodImplemented(OperatorContext.java:481)
at org.esa.snap.core.gpf.internal.OperatorContext.<init>(OperatorContext.java:145)
at org.esa.snap.core.gpf.Operator.<init>(Operator.java:96)
at org.esa.s1tbx.insar.gpf.InterferogramOp.<init>(InterferogramOp.java:65)
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 org.esa.snap.core.gpf.OperatorSpi.createOperator(OperatorSpi.java:134)
at org.esa.snap.core.gpf.graph.NodeContext.initOperator(NodeContext.java:132)
at org.esa.snap.core.gpf.graph.NodeContext.<init>(NodeContext.java:51)
at org.esa.snap.core.gpf.graph.GraphContext.<init>(GraphContext.java:80)
at org.esa.snap.core.gpf.graph.GraphContext.<init>(GraphContext.java:58)
at org.esa.snap.core.gpf.graph.GraphProcessor.executeGraph(GraphProcessor.java:127)
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:59)
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$0(Launcher.java:55)
at org.esa.snap.runtime.Engine.runClientCode(Engine.java:189)
at org.esa.snap.runtime.Launcher.run(Launcher.java:51)
at org.esa.snap.runtime.Launcher.main(Launcher.java:31)
Caused by: java.lang.ClassNotFoundException: org.jblas.ComplexDouble
at java.net.URLClassLoader.findClass(URLClassLoader.java:382)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 35 more
Error: org/jblas/ComplexDouble