IfcOpenShell BIMserver plugin
If you see org.bimserver.plugins.renderengine.RenderEngineException: java.io.EOFException in the geometry generation report, have a look at BIMserver issue #633 for a possible reason and solution. Updating gcc and libstdc++ may solve the issue.
If you see java.lang.Exception: Missing objects in model in the geometry generation report, IfcOpenShell was not able to generate geometry for these products. This may happen when you use an older version of IfcOpenShell. In that case it may help to update IfcOpenShell to a newer version through the "build version" (previously "commit sha") plugin setting as described in BIMserver issue #1207.