WebSphere Application Server & Liberty

We upgraded our WAS ND servers to v9.0.5.17. During the upgrade we had issues with Installation Manager. We tried replacing the contents for ./eclipse with the files from another server that was working and we were able to upgrade the servers but when we try to start the nodeagent, it fails with java.lang.ClassNotFoundException. 

We see the following errors in the SystemOut.log:

WSVR0661W: Some bundles failed to resolve during the nodeagent server startup. The server logged OSGi bundle diagnostics to the
WAS_PROFILE_ROOT//servers/nodeagent/configuration/diag-xxx.log file.

WSVR0009E: Error occurred during startup
com.ibm.ws.exception.RuntimeError: Unable to start the CoordinatorComponentImpl
at com.ibm.ws.hamanager.runtime.CoordinatorComponentImpl.start(CoordinatorComponentImpl.java:320)
at com.ibm.ws.runtime.component.ContainerHelper.startComponents(ContainerHelper.java:540)
at com.ibm.ws.runtime.component.ContainerImpl.startComponents(ContainerImpl.java:627)
at com.ibm.ws.runtime.component.ContainerImpl.start(ContainerImpl.java:618)
at com.ibm.ws.runtime.component.ServerImpl.start(ServerImpl.java:555)
at com.ibm.ws.runtime.WsServerImpl.bootServerContainer(WsServerImpl.java:325)
at com.ibm.ws.runtime.WsServerImpl.start(WsServerImpl.java:238)
at com.ibm.ws.runtime.WsServerImpl.main(WsServerImpl.java:711)
at com.ibm.ws.runtime.WsServer.main(WsServer.java:59)
...
Caused by: java.lang.NoClassDefFoundError: javax.portlet.PortletRequest
Caused by: java.lang.ClassNotFoundException: javax.portlet.PortletRequest cannot be found by com.ibm.ws.runtime_10.0.0
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:501)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:421)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:412)
at org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader.loadClass(DefaultClassLoader.java:107)
at java.lang.ClassLoader.loadClass(ClassLoader.java:876)

Comparing the WAS_INSTALL_ROOT/plugins directrory between the working and the failing environment. All the contents(including the file sizes) were exactly the same except for one jar file:com.ibm.ws.org.jboss.logging.3.3.0_1.0.17.jar.

How can we fix the errors and get the nodeagent started?

Most likely someone deleted that file accidentally or there was a bad install. 
Please try putting a copy from the working server onto the failing server and then run osgiCfgInit.sh -all(from directory path <WAS-HOME>/bin ), and try starting your nodeagent again.