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NetCDF library is missing in thredds image #206

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thorseye opened this issue Jun 14, 2023 · 0 comments · Fixed by #207
Open

NetCDF library is missing in thredds image #206

thorseye opened this issue Jun 14, 2023 · 0 comments · Fixed by #207

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@thorseye
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After deployment (Kubernetes), the log output for the thredds container shows that we are missing libnetcdf.so:

2023-06-14T09:29:20.338661Z thredds INFO 2023-06-14T09:29:20.338+0000 [    115590][        ] INFO  serverStartup: TdsInit: catalogWriting.useBytesForDataSize= false
2023-06-14T09:29:20.751712Z thredds INFO 2023-06-14T09:29:20.744+0000 [    115996][        ] WARN  serverStartup: Nc4Iosp: NetCDF-4 C library not present (jna_path='null', libname='netcdf').
2023-06-14T09:29:20.751745Z thredds INFO java.lang.UnsatisfiedLinkError: Unable to load library 'netcdf':
2023-06-14T09:29:20.751761Z thredds INFO libnetcdf.so: cannot open shared object file: No such file or directory
2023-06-14T09:29:20.751764Z thredds INFO libnetcdf.so: cannot open shared object file: No such file or directory
2023-06-14T09:29:20.837744Z thredds INFO Native library (linux-x86-64/libnetcdf.so) not found in resource path ([file:/opt/tomcat/webapps/thredds/WEB-INF/classes/, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/asm-analysis-9.2.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/velocity-1.7.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/aws-query-protocol-2.17.290.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/xmlbeans-3.1.0.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/jfreechart-1.0.19.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/spring-security-config-5.7.8.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/chronicle-values-2.23.3.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/sis-metadata-1.0.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/spring-security-core-5.7.8.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/httpmime-4.5.13.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/jcl-over-slf4j-1.7.28.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/re2j-1.3.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/cdm-mcidas-5.5.4-SNAPSHOT.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/spring-aop-5.3.27.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/jakarta.activation-api-1.2.1.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/cdm-image-5.5.4-SNAPSHOT.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/jakarta.xml.bind-api-2.3.2.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/edal-cdm-1.5.0.6-SNAPSHOT.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/failureaccess-1.0.1.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/log4j-core-2.17.1.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/opendap-5.5.4-SNAPSHOT.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/log4j-web-2.17.1.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/bufr-5.5.4-SNAPSHOT.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/jffi-1.3.9-native.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/jackson-core-2.14.0-rc1.jar, file:/opt/tomcat/webapps/t
2023-06-14T09:29:20.837790Z thredds INFO   at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:307) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.837794Z thredds INFO   at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:467) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.837796Z thredds INFO   at com.sun.jna.Library$Handler.<init>(Library.java:192) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.837803Z thredds INFO   at com.sun.jna.Native.load(Native.java:622) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.837805Z thredds INFO   at com.sun.jna.Native.load(Native.java:596) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.837808Z thredds INFO   at ucar.nc2.ffi.netcdf.NetcdfClibrary.load(NetcdfClibrary.java:126) [netcdf4-5.5.4-SNAPSHOT.jar:5.5.4-SNAPSHOT]
2023-06-14T09:29:20.837810Z thredds INFO   at ucar.nc2.ffi.netcdf.NetcdfClibrary.isLibraryPresent(NetcdfClibrary.java:74) [netcdf4-5.5.4-SNAPSHOT.jar:5.5.4-SNAPSHOT]
2023-06-14T09:29:20.837813Z thredds INFO   at ucar.nc2.ffi.netcdf.NetcdfClibrary.getForeignFunctionInterface(NetcdfClibrary.java:81) [netcdf4-5.5.4-SNAPSHOT.jar:5.5.4-SNAPSHOT]
2023-06-14T09:29:20.837817Z thredds INFO   at ucar.nc2.jni.netcdf.Nc4Iosp.<clinit>(Nc4Iosp.java:62) [netcdf4-5.5.4-SNAPSHOT.jar:5.5.4-SNAPSHOT]
2023-06-14T09:29:20.837819Z thredds INFO   at thredds.server.config.TdsInit.readThreddsConfig(TdsInit.java:300) [classes/:5.5-SNAPSHOT]
2023-06-14T09:29:20.837822Z thredds INFO   at thredds.server.config.TdsInit.onApplicationEvent(TdsInit.java:138) [classes/:5.5-SNAPSHOT]
2023-06-14T09:29:20.837825Z thredds INFO   at thredds.server.config.TdsInit.onApplicationEvent(TdsInit.java:67) [classes/:5.5-SNAPSHOT]
2023-06-14T09:29:20.837828Z thredds INFO   at org.springframework.context.event.SimpleApplicationEventMulticaster.doInvokeListener(SimpleApplicationEventMulticaster.java:176) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837830Z thredds INFO   at org.springframework.context.event.SimpleApplicationEventMulticaster.invokeListener(SimpleApplicationEventMulticaster.java:169) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837833Z thredds INFO   at org.springframework.context.event.SimpleApplicationEventMulticaster.multicastEvent(SimpleApplicationEventMulticaster.java:143) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837836Z thredds INFO   at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:421) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837838Z thredds INFO   at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:378) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837840Z thredds INFO   at org.springframework.context.support.AbstractApplicationContext.finishRefresh(AbstractApplicationContext.java:940) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837843Z thredds INFO   at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:586) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837845Z thredds INFO   at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:399) [spring-web-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837847Z thredds INFO   at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:278) [spring-web-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837850Z thredds INFO   at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:103) [spring-web-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837852Z thredds INFO   at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4763) [catalina.jar:8.5.81]
2023-06-14T09:29:20.837855Z thredds INFO   at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5232) [catalina.jar:8.5.81]
2023-06-14T09:29:20.837857Z thredds INFO   at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183) [catalina.jar:8.5.81]
2023-06-14T09:29:20.837859Z thredds INFO   at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:753) [catalina.jar:8.5.81]
2023-06-14T09:29:20.837862Z thredds INFO   at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:727) [catalina.jar:8.5.81]
2023-06-14T09:29:20.837864Z thredds INFO   at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:695) [catalina.jar:8.5.81]
2023-06-14T09:29:20.837869Z thredds INFO   at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1177) [catalina.jar:8.5.81]
2023-06-14T09:29:20.837871Z thredds INFO   at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig.java:1925) [catalina.jar:8.5.81]
2023-06-14T09:29:20.837874Z thredds INFO   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) [?:?]
2023-06-14T09:29:20.837876Z thredds INFO   at java.util.concurrent.FutureTask.run(FutureTask.java:264) [?:?]
2023-06-14T09:29:20.837878Z thredds INFO   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) [?:?]
2023-06-14T09:29:20.837880Z thredds INFO   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) [?:?]
2023-06-14T09:29:20.837883Z thredds INFO   at java.lang.Thread.run(Thread.java:829) [?:?]
2023-06-14T09:29:20.837885Z thredds INFO   Suppressed: java.lang.UnsatisfiedLinkError: libnetcdf.so: cannot open shared object file: No such file or directory
2023-06-14T09:29:20.837888Z thredds INFO           at com.sun.jna.Native.open(Native Method) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.837890Z thredds INFO           at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:197) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.837892Z thredds INFO           at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:467) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.837895Z thredds INFO           at com.sun.jna.Library$Handler.<init>(Library.java:192) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.837897Z thredds INFO           at com.sun.jna.Native.load(Native.java:622) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.837899Z thredds INFO           at com.sun.jna.Native.load(Native.java:596) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.837910Z thredds INFO           at ucar.nc2.ffi.netcdf.NetcdfClibrary.load(NetcdfClibrary.java:126) [netcdf4-5.5.4-SNAPSHOT.jar:5.5.4-SNAPSHOT]
2023-06-14T09:29:20.837913Z thredds INFO           at ucar.nc2.ffi.netcdf.NetcdfClibrary.isLibraryPresent(NetcdfClibrary.java:74) [netcdf4-5.5.4-SNAPSHOT.jar:5.5.4-SNAPSHOT]
2023-06-14T09:29:20.837915Z thredds INFO           at ucar.nc2.ffi.netcdf.NetcdfClibrary.getForeignFunctionInterface(NetcdfClibrary.java:81) [netcdf4-5.5.4-SNAPSHOT.jar:5.5.4-SNAPSHOT]
2023-06-14T09:29:20.837917Z thredds INFO           at ucar.nc2.jni.netcdf.Nc4Iosp.<clinit>(Nc4Iosp.java:62) [netcdf4-5.5.4-SNAPSHOT.jar:5.5.4-SNAPSHOT]
2023-06-14T09:29:20.837920Z thredds INFO           at thredds.server.config.TdsInit.readThreddsConfig(TdsInit.java:300) [classes/:5.5-SNAPSHOT]
2023-06-14T09:29:20.837922Z thredds INFO           at thredds.server.config.TdsInit.onApplicationEvent(TdsInit.java:138) [classes/:5.5-SNAPSHOT]
2023-06-14T09:29:20.837924Z thredds INFO           at thredds.server.config.TdsInit.onApplicationEvent(TdsInit.java:67) [classes/:5.5-SNAPSHOT]
2023-06-14T09:29:20.837927Z thredds INFO           at org.springframework.context.event.SimpleApplicationEventMulticaster.doInvokeListener(SimpleApplicationEventMulticaster.java:176) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837929Z thredds INFO           at org.springframework.context.event.SimpleApplicationEventMulticaster.invokeListener(SimpleApplicationEventMulticaster.java:169) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837931Z thredds INFO           at org.springframework.context.event.SimpleApplicationEventMulticaster.multicastEvent(SimpleApplicationEventMulticaster.java:143) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837934Z thredds INFO           at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:421) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837936Z thredds INFO           at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:378) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837938Z thredds INFO           at org.springframework.context.support.AbstractApplicationContext.finishRefresh(AbstractApplicationContext.java:940) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837940Z thredds INFO           at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:586) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837945Z thredds INFO           at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:399) [spring-web-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837948Z thredds INFO           at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:278) [spring-web-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837950Z thredds INFO           at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:103) [spring-web-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.837953Z thredds INFO           at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4763) [catalina.jar:8.5.81]
2023-06-14T09:29:20.837955Z thredds INFO           at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5232) [catalina.jar:8.5.81]
2023-06-14T09:29:20.837957Z thredds INFO           at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183) [catalina.jar:8.5.81]
2023-06-14T09:29:20.837960Z thredds INFO           at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:753) [catalina.jar:8.5.81]
2023-06-14T09:29:20.837964Z thredds INFO           at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:727) [catalina.jar:8.5.81]
2023-06-14T09:29:20.837966Z thredds INFO           at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:695) [catalina.jar:8.5.81]
2023-06-14T09:29:20.837969Z thredds INFO           at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1177) [catalina.jar:8.5.81]
2023-06-14T09:29:20.837971Z thredds INFO           at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig.java:1925) [catalina.jar:8.5.81]
2023-06-14T09:29:20.837973Z thredds INFO           at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) [?:?]
2023-06-14T09:29:20.837975Z thredds INFO           at java.util.concurrent.FutureTask.run(FutureTask.java:264) [?:?]
2023-06-14T09:29:20.837978Z thredds INFO           at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) [?:?]
2023-06-14T09:29:20.837980Z thredds INFO           at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) [?:?]
2023-06-14T09:29:20.837982Z thredds INFO           at java.lang.Thread.run(Thread.java:829) [?:?]
2023-06-14T09:29:20.837985Z thredds INFO   Suppressed: java.lang.UnsatisfiedLinkError: libnetcdf.so: cannot open shared object file: No such file or directory
2023-06-14T09:29:20.837987Z thredds INFO           at com.sun.jna.Native.open(Native Method) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.837989Z thredds INFO           at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:210) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.837992Z thredds INFO           at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:467) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.837994Z thredds INFO           at com.sun.jna.Library$Handler.<init>(Library.java:192) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.837997Z thredds INFO           at com.sun.jna.Native.load(Native.java:622) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.838000Z thredds INFO           at com.sun.jna.Native.load(Native.java:596) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.838003Z thredds INFO           at ucar.nc2.ffi.netcdf.NetcdfClibrary.load(NetcdfClibrary.java:126) [netcdf4-5.5.4-SNAPSHOT.jar:5.5.4-SNAPSHOT]
2023-06-14T09:29:20.838005Z thredds INFO           at ucar.nc2.ffi.netcdf.NetcdfClibrary.isLibraryPresent(NetcdfClibrary.java:74) [netcdf4-5.5.4-SNAPSHOT.jar:5.5.4-SNAPSHOT]
2023-06-14T09:29:20.838008Z thredds INFO           at ucar.nc2.ffi.netcdf.NetcdfClibrary.getForeignFunctionInterface(NetcdfClibrary.java:81) [netcdf4-5.5.4-SNAPSHOT.jar:5.5.4-SNAPSHOT]
2023-06-14T09:29:20.838010Z thredds INFO           at ucar.nc2.jni.netcdf.Nc4Iosp.<clinit>(Nc4Iosp.java:62) [netcdf4-5.5.4-SNAPSHOT.jar:5.5.4-SNAPSHOT]
2023-06-14T09:29:20.838012Z thredds INFO           at thredds.server.config.TdsInit.readThreddsConfig(TdsInit.java:300) [classes/:5.5-SNAPSHOT]
2023-06-14T09:29:20.838015Z thredds INFO           at thredds.server.config.TdsInit.onApplicationEvent(TdsInit.java:138) [classes/:5.5-SNAPSHOT]
2023-06-14T09:29:20.838020Z thredds INFO           at thredds.server.config.TdsInit.onApplicationEvent(TdsInit.java:67) [classes/:5.5-SNAPSHOT]
2023-06-14T09:29:20.838022Z thredds INFO           at org.springframework.context.event.SimpleApplicationEventMulticaster.doInvokeListener(SimpleApplicationEventMulticaster.java:176) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838025Z thredds INFO           at org.springframework.context.event.SimpleApplicationEventMulticaster.invokeListener(SimpleApplicationEventMulticaster.java:169) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838027Z thredds INFO           at org.springframework.context.event.SimpleApplicationEventMulticaster.multicastEvent(SimpleApplicationEventMulticaster.java:143) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838030Z thredds INFO           at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:421) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838032Z thredds INFO           at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:378) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838036Z thredds INFO           at org.springframework.context.support.AbstractApplicationContext.finishRefresh(AbstractApplicationContext.java:940) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838038Z thredds INFO           at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:586) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838041Z thredds INFO           at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:399) [spring-web-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838043Z thredds INFO           at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:278) [spring-web-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838045Z thredds INFO           at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:103) [spring-web-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838047Z thredds INFO           at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4763) [catalina.jar:8.5.81]
2023-06-14T09:29:20.838050Z thredds INFO           at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5232) [catalina.jar:8.5.81]
2023-06-14T09:29:20.838052Z thredds INFO           at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183) [catalina.jar:8.5.81]
2023-06-14T09:29:20.838055Z thredds INFO           at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:753) [catalina.jar:8.5.81]
2023-06-14T09:29:20.838057Z thredds INFO           at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:727) [catalina.jar:8.5.81]
2023-06-14T09:29:20.838059Z thredds INFO           at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:695) [catalina.jar:8.5.81]
2023-06-14T09:29:20.838061Z thredds INFO           at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1177) [catalina.jar:8.5.81]
2023-06-14T09:29:20.838064Z thredds INFO           at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig.java:1925) [catalina.jar:8.5.81]
2023-06-14T09:29:20.838066Z thredds INFO           at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) [?:?]
2023-06-14T09:29:20.838068Z thredds INFO           at java.util.concurrent.FutureTask.run(FutureTask.java:264) [?:?]
2023-06-14T09:29:20.838071Z thredds INFO           at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) [?:?]
2023-06-14T09:29:20.838073Z thredds INFO           at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) [?:?]
2023-06-14T09:29:20.838075Z thredds INFO           at java.lang.Thread.run(Thread.java:829) [?:?]
2023-06-14T09:29:20.838187Z thredds INFO   Suppressed: java.io.IOException: Native library (linux-x86-64/libnetcdf.so) not found in resource path ([file:/opt/tomcat/webapps/thredds/WEB-INF/classes/, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/asm-analysis-9.2.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/velocity-1.7.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/aws-query-protocol-2.17.290.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/xmlbeans-3.1.0.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/jfreechart-1.0.19.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/spring-security-config-5.7.8.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/chronicle-values-2.23.3.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/sis-metadata-1.0.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/spring-security-core-5.7.8.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/httpmime-4.5.13.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/jcl-over-slf4j-1.7.28.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/re2j-1.3.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/cdm-mcidas-5.5.4-SNAPSHOT.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/spring-aop-5.3.27.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/jakarta.activation-api-1.2.1.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/cdm-image-5.5.4-SNAPSHOT.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/jakarta.xml.bind-api-2.3.2.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/edal-cdm-1.5.0.6-SNAPSHOT.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/failureaccess-1.0.1.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/log4j-core-2.17.1.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/opendap-5.5.4-SNAPSHOT.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/log4j-web-2.17.1.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/bufr-5.5.4-SNAPSHOT.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/jffi-1.3.9-native.jar, file:/opt/tomcat/webapps/thredds/WEB-INF/lib/jackson-core-2.14.0-r
2023-06-14T09:29:20.838202Z thredds INFO           at com.sun.jna.Native.extractFromResourcePath(Native.java:1145) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.838205Z thredds INFO           at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:281) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.838207Z thredds INFO           at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:467) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.838209Z thredds INFO           at com.sun.jna.Library$Handler.<init>(Library.java:192) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.838212Z thredds INFO           at com.sun.jna.Native.load(Native.java:622) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.838214Z thredds INFO           at com.sun.jna.Native.load(Native.java:596) ~[jna-5.12.1.jar:5.12.1 (b0)]
2023-06-14T09:29:20.838217Z thredds INFO           at ucar.nc2.ffi.netcdf.NetcdfClibrary.load(NetcdfClibrary.java:126) [netcdf4-5.5.4-SNAPSHOT.jar:5.5.4-SNAPSHOT]
2023-06-14T09:29:20.838219Z thredds INFO           at ucar.nc2.ffi.netcdf.NetcdfClibrary.isLibraryPresent(NetcdfClibrary.java:74) [netcdf4-5.5.4-SNAPSHOT.jar:5.5.4-SNAPSHOT]
2023-06-14T09:29:20.838226Z thredds INFO           at ucar.nc2.ffi.netcdf.NetcdfClibrary.getForeignFunctionInterface(NetcdfClibrary.java:81) [netcdf4-5.5.4-SNAPSHOT.jar:5.5.4-SNAPSHOT]
2023-06-14T09:29:20.838229Z thredds INFO           at ucar.nc2.jni.netcdf.Nc4Iosp.<clinit>(Nc4Iosp.java:62) [netcdf4-5.5.4-SNAPSHOT.jar:5.5.4-SNAPSHOT]
2023-06-14T09:29:20.838231Z thredds INFO           at thredds.server.config.TdsInit.readThreddsConfig(TdsInit.java:300) [classes/:5.5-SNAPSHOT]
2023-06-14T09:29:20.838234Z thredds INFO           at thredds.server.config.TdsInit.onApplicationEvent(TdsInit.java:138) [classes/:5.5-SNAPSHOT]
2023-06-14T09:29:20.838236Z thredds INFO           at thredds.server.config.TdsInit.onApplicationEvent(TdsInit.java:67) [classes/:5.5-SNAPSHOT]
2023-06-14T09:29:20.838240Z thredds INFO           at org.springframework.context.event.SimpleApplicationEventMulticaster.doInvokeListener(SimpleApplicationEventMulticaster.java:176) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838242Z thredds INFO           at org.springframework.context.event.SimpleApplicationEventMulticaster.invokeListener(SimpleApplicationEventMulticaster.java:169) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838244Z thredds INFO           at org.springframework.context.event.SimpleApplicationEventMulticaster.multicastEvent(SimpleApplicationEventMulticaster.java:143) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838247Z thredds INFO           at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:421) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838250Z thredds INFO           at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:378) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838252Z thredds INFO           at org.springframework.context.support.AbstractApplicationContext.finishRefresh(AbstractApplicationContext.java:940) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838254Z thredds INFO           at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:586) [spring-context-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838257Z thredds INFO           at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:399) [spring-web-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838259Z thredds INFO           at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:278) [spring-web-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838261Z thredds INFO           at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:103) [spring-web-5.3.27.jar:5.3.27]
2023-06-14T09:29:20.838264Z thredds INFO           at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4763) [catalina.jar:8.5.81]
2023-06-14T09:29:20.838266Z thredds INFO           at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5232) [catalina.jar:8.5.81]
2023-06-14T09:29:20.838268Z thredds INFO           at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183) [catalina.jar:8.5.81]
2023-06-14T09:29:20.838270Z thredds INFO           at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:753) [catalina.jar:8.5.81]
2023-06-14T09:29:20.838273Z thredds INFO           at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:727) [catalina.jar:8.5.81]
2023-06-14T09:29:20.838275Z thredds INFO           at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:695) [catalina.jar:8.5.81]
2023-06-14T09:29:20.838278Z thredds INFO           at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1177) [catalina.jar:8.5.81]
2023-06-14T09:29:20.838280Z thredds INFO           at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig.java:1925) [catalina.jar:8.5.81]
2023-06-14T09:29:20.838282Z thredds INFO           at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) [?:?]
2023-06-14T09:29:20.838284Z thredds INFO           at java.util.concurrent.FutureTask.run(FutureTask.java:264) [?:?]
2023-06-14T09:29:20.838289Z thredds INFO           at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) [?:?]
2023-06-14T09:29:20.838291Z thredds INFO           at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) [?:?]
2023-06-14T09:29:20.838294Z thredds INFO           at java.lang.Thread.run(Thread.java:829) [?:?]
2023-06-14T09:29:20.838675Z thredds INFO 2023-06-14T09:29:20.838+0000 [    116090][        ] INFO  serverStartup: Nc4Iosp: set log level: old=-1 new=0
2023-06-14T09:29:20.843646Z thredds INFO 2023-06-14T09:29:20.843+0000 [    116095][        ] INFO  serverStartup: TdsInit: Aggregation.setTypicalDatasetMode= penultimate
2023-06-14T09:29:20.943117Z thredds INFO 2023-06-14T09:29:20.942+0000 [    116194][        ] INFO  serverStartup: TdsInit: CdmCache= /opt/tomcat/content/thredds/cache/cdm scour = 3600 maxSize = 1000000000
2023-06-14T09:29:21.038084Z thredds INFO [2023-06-14T09:29:21.037+0000] Started a DiskCache2 scour task on /opt/tomcat/content/thredds/cache/agg every 1440 minutes for files older than 129600 minutes
2023-06-14T09:29:21.038636Z thredds INFO [2023-06-14T09:29:21.038+0000] Started a DiskCache2 scour task on /opt/tomcat/content/thredds/cache/aggNew/ every 1440 minutes for files older than 129600 minutes
2023-06-14T09:29:21.237662Z thredds INFO 2023-06-14T09:29:21.139+0000 [    116391][        ] INFO  serverStartup: TdsInit: AggregationCache= /opt/tomcat/content/thredds/cache/agg scour = 86400 maxAgeSecs = 7776000
2023-06-14T09:29:21.239226Z thredds INFO 2023-06-14T09:29:21.238+0000 [    116490][        ] INFO  serverStartup: TdsInit: GribIndex=DiskCache2{cachePathPolicy=NestedDirectory, alwaysUseCache=false, cachePathPolicyParam='null', root='/opt/tomcat/content/thredds/cache/grib/', scourEveryMinutes=0, persistMinutes=129600, fail=false}
2023-06-14T09:29:21.940733Z thredds INFO [2023-06-14T09:29:21.940+0000] Started a DiskCache2 scour task on /opt/tomcat/content/thredds/cache/ncSubsetCache/ every 10 minutes for files older than 5 minutes
2023-06-14T09:29:22.140501Z thredds INFO 2023-06-14T09:29:22.140+0000 [    117392][        ] INFO  serverStartup: thredds.server.ncss.controller.NcssDiskCacheNcss.Cache= /opt/tomcat/content/thredds/cache/ncSubsetCache/ scour = 600 maxAgeSecs = 300
2023-06-14T09:29:22.143180Z thredds INFO 2023-06-14T09:29:22.142 +0000 [    117394][        ] INFO  - thredds.featurecollection.cache.GridInventoryCacheChronicle - Creating cache directory at /opt/tomcat/content/thredds/cache/collection
2023-06-14T09:29:22.143607Z thredds INFO 2023-06-14T09:29:22.143 +0000 [    117395][        ] INFO  - thredds.featurecollection.cache.GridInventoryCacheChronicle - Creating new grid inventory cache file at /opt/tomcat/content/thredds/cache/collection/GridDatasetInv.dat
2023-06-14T09:29:22.143774Z thredds INFO 2023-06-14T09:29:22.143 +0000 [    117395][        ] INFO  - thredds.featurecollection.cache.GridInventoryCacheChronicle - Grid inventory cache built with: maxEntries=1000, maxBloatFactor=1, averageValueSize=4096
2023-06-14T09:29:22.548868Z thredds INFO WARNING: An illegal reflective access operation has occurred
2023-06-14T09:29:22.548898Z thredds INFO WARNING: Illegal reflective access using Lookup on net.openhft.chronicle.core.Jvm (file:/opt/tomcat/webapps/thredds/WEB-INF/lib/chronicle-core-2.23.36.jar) to class java.lang.reflect.AccessibleObject
2023-06-14T09:29:22.548903Z thredds INFO WARNING: Please consider reporting this to the maintainers of net.openhft.chronicle.core.Jvm
2023-06-14T09:29:22.548906Z thredds INFO WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
2023-06-14T09:29:22.548909Z thredds INFO WARNING: All illegal access operations will be denied in a future release
2023-06-14T09:29:22.644987Z thredds INFO 2023-06-14T09:29:22.644 +0000 [    117896][        ] DEBUG - net.openhft.chronicle.core.Jvm - No system.properties file found
2023-06-14T09:29:22.645252Z thredds INFO 2023-06-14T09:29:22.645 +0000 [    117897][        ] INFO  - net.openhft.chronicle.core.Jvm - Chronicle core loaded from file:/opt/tomcat/webapps/thredds/WEB-INF/lib/chronicle-core-2.23.36.jar
2023-06-14T09:29:23.243318Z thredds INFO 2023-06-14T09:29:23.243 +0000 [    118495][        ] DEBUG - net.openhft.chronicle.bytes.internal.BytesInternal - java.lang.reflect.InaccessibleObjectException: Unable to make public static int jdk.internal.util.ArraysSupport.vectorizedMismatch(java.lang.Object,long,java.lang.Object,long,int,int) accessible: module java.base does not "exports jdk.internal.util" to unnamed module @702f38b2
2023-06-14T09:29:23.764474Z thredds INFO 172.29.97.1 - - [14/Jun/2023:09:29:17 +0000] "GET /thredds/catalog/catalog.html HTTP/1.1" 200 3574 "-" "kube-probe/1.22" "-" [0.004]

The simple solution to this should be to install netcdf in the thredds Dockerfile.
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Install netcdf thorseye/esgf-docker
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@thorseye