Controller process aborts with "The underlying connection was closed ... An unexpected error occurred on a receive" caused by IIS application pool not responding to ping

Symptom

The following example is from when the user was trying to import structures:

Application Log

Log Name: Application
Source: Cognos Controller
Date: 18/04/2018 14:22:20
Event ID: 0
Task Category: None
Level: Warning
Keywords: Classic
User: N/A
Computer: VBRACONT8AP7
Description:
Error occured at 18/04/2018 14:22:20 in IBM Cognos Controller, Error No=5, Source=FrangoDirect.ImportStructuresD.UpdateImpServer#System.Web.Services, Description=The underlying connection was closed: An unexpected error occurred on a receive.

Log Name: Application
Source: Cognos Controller
Date: 18/04/2018 14:22:21
Event ID: 0
Task Category: None
Level: Warning
Keywords: Classic
User: N/A
Computer: VBRACONT8AP7
Description:
Standard Error
Number: 5
Source: FrangoDirect.ImportStructuresD.UpdateImpServer#System.Web.Services
Description: The underlying connection was closed: An unexpected error occurred on a receive.
at Microsoft.VisualBasic.ErrObject.Raise(Int32 Number, Object Source, Object Description, Object HelpFile, Object HelpContext)
at Cognos.Controller.Common.RaiseErrCli.RaiseError(Int32 lErrNo, String sErrSource, String sErrDesc, String sErrHelpFile, Int32 lErrHelpContext)
at Cognos.Controller.Common.RaiseErrCli.RaiseError(Int32 lErrNo, String sErrSource, String sErrDesc)
at Cognos.Controller.Direct.ImportStructuresD.UpdateImpServer(String sXmlDoc)
at Cognos.Controller.Forms.Form.frmImportStruc.DoImportServer()

Log Name: Application
Source: Cognos Controller
Date: 18/04/2018 14:22:57
Event ID: 0
Task Category: None
Level: Warning
Keywords: Classic
User: N/A
Computer: VBRACONT8AP7
Description:
Standard Error
Source: System.Web.Services
Description: System.Web.Services.Protocols.SoapException: Server was unable to process request. ---> System.Exception: Security Error 1
at Cognos.Controller.Proxy.SoapExtension.ServerExtension.ValidateNativeUser(SoapMessage& message)
at Cognos.Controller.Proxy.SoapExtension.ServerExtension.ValidateUser(SoapMessage& message)
at Cognos.Controller.Proxy.SoapExtension.ServerExtension.ProcessMessage(SoapMessage message)
at System.Web.Services.Protocols.SoapMessage.RunExtensions(SoapExtension[] extensions, Boolean throwOnException)
at System.Web.Services.Protocols.SoapServerProtocol.CreateServerInstance()
at System.Web.Services.Protocols.WebServiceHandler.Invoke()
at System.Web.Services.Protocols.WebServiceHandler.CoreProcessRequest()
--- End of inner exception stack trace ---
at System.Web.Services.Protocols.SoapHttpClientProtocol.ReadResponse(SoapClientMessage message, WebResponse response, Stream responseStream, Boolean asyncCall)
at System.Web.Services.Protocols.SoapHttpClientProtocol.Invoke(String methodName, Object[] parameters)
at Cognos.Controller.ControllerSoapHttpClientProtocol.Invoke(String methodname, Object[] parameters)
at Cognos.Controller.Proxy.FrMiscBT.WSFrMiscBT.SoxT_EndSox(String sGuid, String sUser, String sSourceName, String sTriggerID, String sPerakt, String sBol)
at Cognos.Controller.Direct.SoxD.SoxEnd(String sSourceName, SoxFunctionID iTriggerID, String sPerAkt, String sBol)
at Cognos.Controller.Forms.Form.frmImportStruc.DoSOXEnd()
at Cognos.Controller.Forms.Form.frmImportStruc.IForm_DoClick(Int32 lCmd, String& sTag)

System Log:

Log Name: System
Source: Microsoft-Windows-WAS
Date: 18/04/2018 14:22:18
Event ID: 5010
Task Category: None
Level: Warning
Keywords: Classic
User: N/A
Computer: VBRACONT8AP7
Description:
A process serving application pool '.NET v2.0' failed to respond to a ping. The process id was '9172'.