Java cannot load netcdf library

[alaniwi]

I am getting the following error in /esg/content/thredds/logs/serverStartup.log

2017-08-05T10:20:41.961+0100 [     47909][        ] WARN  serverStartup: Nc4Iosp: NetCDF-4 C library not present (jna_path='null', libname='netcdf').
java.lang.UnsatisfiedLinkError: Unable to load library 'netcdf': Native library (linux-x86-64/libnetcdf.so) not found in resource path ([file:/usr/local/apache-tomcat-8.5.9/webapps/thredds/WEB-INF/classes/, file:/usr/local/apache-tomcat-8.5.9/webapps/thredds/WEB-INF/lib/xml-apis-1.4.01.jar, ...

followed by a long list of jar files (snipped).

and the traceback

        at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:277) ~[jna-4.2.2.jar:4.2.2 (b0)]
        at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:403) ~[jna-4.2.2.jar:4.2.2 (b0)]
        at com.sun.jna.Library$Handler.<init>(Library.java:147) ~[jna-4.2.2.jar:4.2.2 (b0)]
        at com.sun.jna.Native.loadLibrary(Native.java:502) ~[jna-4.2.2.jar:4.2.2 (b0)]
        at com.sun.jna.Native.loadLibrary(Native.java:481) ~[jna-4.2.2.jar:4.2.2 (b0)]
        at ucar.nc2.jni.netcdf.Nc4Iosp.load(Nc4Iosp.java:148) [netcdf4-5.0.0-SNAPSHOT.jar:5.0.0-SNAPSHOT]
        at ucar.nc2.jni.netcdf.Nc4Iosp.isClibraryPresent(Nc4Iosp.java:174) [netcdf4-5.0.0-SNAPSHOT.jar:5.0.0-SNAPSHOT]
        at thredds.server.config.TdsInit.readThreddsConfig(TdsInit.java:297) [classes/:5.0.0-SNAPSHOT]
        at thredds.server.config.TdsInit.onApplicationEvent(TdsInit.java:149) [classes/:5.0.0-SNAPSHOT]
        at thredds.server.config.TdsInit.onApplicationEvent(TdsInit.java:89) [classes/:5.0.0-SNAPSHOT]
        at org.springframework.context.event.SimpleApplicationEventMulticaster.invokeListener(SimpleApplicationEventMulticaster.java:167) [spring-context-4.3.9.RELEASE.jar:4.3.9.RELEASE]
        at org.springframework.context.event.SimpleApplicationEventMulticaster.multicastEvent(SimpleApplicationEventMulticaster.java:139) [spring-context-4.3.9.RELEASE.jar:4.3.9.RELEASE]
        at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:393) [spring-context-4.3.9.RELEASE.jar:4.3.9.RELEASE]
        at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:347) [spring-context-4.3.9.RELEASE.jar:4.3.9.RELEASE]
        at org.springframework.context.support.AbstractApplicationContext.finishRefresh(AbstractApplicationContext.java:883) [spring-context-4.3.9.RELEASE.jar:4.3.9.RELEASE]
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:546) [spring-context-4.3.9.RELEASE.jar:4.3.9.RELEASE]
        at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443) [spring-web-4.3.9.RELEASE.jar:4.3.9.RELEASE]
        at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325) [spring-web-4.3.9.RELEASE.jar:4.3.9.RELEASE]
        at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107) [spring-web-4.3.9.RELEASE.jar:4.3.9.RELEASE]
        at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4727) [catalina.jar:8.5.9]
        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5189) [catalina.jar:8.5.9]
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150) [catalina.jar:8.5.9]
        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752) [catalina.jar:8.5.9]
        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728) [catalina.jar:8.5.9]
        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734) [catalina.jar:8.5.9]
        at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1107) [catalina.jar:8.5.9]
        at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig.java:1841) [catalina.jar:8.5.9]
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [?:1.8.0_131]
        at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_131]
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_131]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_131]
        at java.lang.Thread.run(Thread.java:748) [?:1.8.0_131]

[alaniwi]

This is on a recently installed v2.5.12-devel-release

[alaniwi]

If I install netcdf from an RPM, which provides /usr/lib64/libnetcdf.so, this error goes away. (Due to the yum setup on our machines, this finds an RPM that I built for netcdf 4.4.0, but presumably it would be the same if the RPM for 4.1.1 from EPEL was used.)

So it seems that netcdf needs to be included in the RPM dependencies.

[William-Hill]

@alaniwi, What install type did you use? Going to try to reproduce the problem.

[William-Hill]

cc @alaniwi Update on issue from Sean Arms:

"That is just a warning that the TDS could not find the netCDF-C library and should not prevent the TDS from starting up or running properly. If one wishes to have the netCDFSubsetService return netCDF-4 files, you need to link against the netCDF-C library (currently the only way to write netCDF-4 files). If you would like to specify where the C library lives, you can do so in threddsConfig.xml:

http://www.unidata.ucar.edu/software/thredds/current/tds/reference/ThreddsConfigXMLFile.html#netcdfCLibrary

If you do not want netCDF-4 files returned from the NetcdfSubsetService, then it is safe to ignore the message.

That said, I'm not sure why the stack trace is dumping to the log file. Is the TDS failing to start all together?

Cheers,

Sean"

[pchengi]

@William-Hill , how was this resolved? Was something changed in the xml config file?

[William-Hill]

@pchengi I didn't make any changes. The issue is still marked as open. Has the problem been reproduced in test installs?

[pchengi]

@alaniwi , can you please let me know what I need to do to reproduce this issue? If this is not an issue now, I'd like to close this issue.