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Hi,
There is one more configuration you need to make to resolve this issue.
Right Click on Process in workbench->Configure->Advanced(tab)->Timeout, there are two options:
1:Default: Specifies to use the application server's transaction time-out setting.
2:Number Of Seconds: Specifies to wait the number of seconds specified before rolling back a transaction.
Either increase the server transaction time out(varies according to server) in server configuration file or select second option.
Note:Selecting second option is advisable because it will have impact on single process
Thanks
Abhishek