Unable to stop/start SIA Agent - BOBJ XI 3.1 on RedHat Linux

We have the BOBJXI 3.1 installed on the Red Hat Linux Machines(Custom Installation across Two Red Hat Linux Servers).
Node 1 - Linux BOX 1 - Tomcat and all the BOBJ Services except CMS
Node 2 - Linux BOX 2 - MySql and CMS
Problem Description :
We have two instances of the CMS running on the Linux BOX2.
I have assigned the port 6401 to the CMS2 through CMC,The CMS1 is running with deafult port 6400.
CMS is stopped thorugh the CMC.
Through the command line ccm.sh tool on the Linux BOX2,We tried to stop the CMS.
        ./ccm.sh -stop all or sia agent .The Script is not doing anything .
Unable at start/enable the servers on Node2-Linux BOX 2
        ./ccm.sh - start all
        Message on the Command Prompt:
        Starting all the servers...
        Failed to Register Name Server:Reason:A Server of this name already exists( STU00188)
        ./ccm.sh - enable all
        Creating Session Manager
        Logging into CMS
        err: ERROR could not logon to CMS ( STU00152).
        err: ERROR Description:The System ..can be contacted but their is no CMS running at port 6401.

This looks like an issue with your pid file which is created whent he server starts and should be deleted but may not have been.
Look in <bobj home>/serverpids directory for the pid file that relates to the server process.  If you find that file, delete it.
What I think is happening is the system is checking to see if the pid file exists which should tell it if the server is there.  The pid is there so it says it can't start.  But the actual program isn't there so when you try to use it, it says it's not up.
Hope this helps.

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