[R-sig-hpc] cores vs. slots vs. slaves

[Dirk Eddelbuettel]

On 6 October 2011 at 15:07, Jeff Howbert wrote:
| We are seeing some odd behavior in the allocation of R tasks to MPI slots
| under OpenMPI.  All of the following takes place on a parallel compute
| system we built and run on Amazon Web Services.  Hardware is two AWS cluster
| compute nodes (cc1.4xlarge), each with 8 cores.  We designate one node as
| the "head" node, and the other as the "client" node.
| 
|  
| 
| Scenario A: We request, via the hostfile, 8 slots on the head node and 8
| slots on the client node.  We then spawn an R cluster using RMPI, with 1
| master and 15 slaves.  The master (rank 0) and 8 slaves (rank 1-8), i.e. a
| total of 9 R tasks, appear on the head node, and only 7 slaves (rank 9-15)
| appear on the client node.
| 
|  
| 
| Scenario B: We request, via the hostfile, 7 slots on the head node and 8
| slots on the client node.  We then spawn an R cluster using RMPI, with 1
| master and 15 slaves (same as Scenario A).  The master (rank 0) and 7 slaves
| (rank 1-7), i.e. a total of 8 R tasks, appear on the head node, and 8 slaves
| (rank 8-15) appear on the client node.
| 
|  
| 
| We have run several parallel jobs under both scenarios, and Scenario A is
| always considerably slower (c. 40%) than Scenario B, suggesting that in
| Scenario A there really are more slots (9?) than available cores (8) on the
| head node.
| 
|  
| 
| Does anyone have insight into the source of this behavior?  Is it OpenMPI,
| RMPI, or some interaction between the two?  Thanks.

I'd bet it is the Open MPI layer.  Rmpi, after all, just requests into MPI
via the MPI.  Can you cook up a simple C client program which you can test
the same way?

Dirk
  
 
| Jeff Howbert
| 
| Brian Pratt
| 
| Insilicos LLC
| 
|  
| 
| 
| 	[[alternative HTML version deleted]]
| 
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