Github user serranom commented on the issue:

    https://github.com/apache/twill/pull/23
  
    I have discovered the cause of the intermittent failure.
    
    This code (starting on line 703 of ApplicationMasterService, comments added 
by me):
    
          /*
           * The provisionRequest will either contain a single container 
(ALLOCATE_ONE_INSTANCE_AT_A_TIME), or all the
           * containers to satisfy the expectedContainers count. In the later 
case, the provision request is complete once
           * all the containers have run at which point we poll() to remove the 
provisioning request.
           */
          if (expectedContainers.getExpected(runnableName) == 
runningContainers.count(runnableName) ||
            
provisioning.peek().getType().equals(AllocationSpecification.Type.ALLOCATE_ONE_INSTANCE_AT_A_TIME))
 {
            provisioning.poll();
          }
    
    There is a case when instances are failing (but not simultaneously) where 
the retries for the instances will be spread over two invocations of 
`ApplicationMasterService.handleCompleted`.  This means they will be part of 
separate `RunnableContainerRequests` and thus will be provisioned separately.  
But because the code above does not anticipate this case, the first 
provisionRequest will never appear to be satisfied, never be polled and the 
total can never be met.  This is an existing bug, since I think it could happen 
before my new code -- its just that my test tickles it.  If there is agreement, 
I can file a new JIRA and PR request or just fix it with this PR.   Let me know.


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