I want to run R in parallel on HPC clusters using MPI. I understand the makeCluster function from package snow can be used to specify the number of nodes. For example: makeCluster(2,type="MPI") means 2 nodes. Without specifying the type to "MPI", makeCluster(2) would mean 2 cores on a single node.
Is there a way to specify both the number of nodes and cores?
How many cores on each node at default would be used if specifying the type to MPI?
The snow and parallel packages do not to the best of my knowledge expose this -- as it gets hardware-dependent very quickly.
No, if your MPI implementation is, say, OpenMPI then you can specify this in your server's MPI configuration. There is a pretty rich grammar for this, and the hwloc library should give you hardware locality.
But R at the very end of this only knows 'number of worker nodes' and passes the how and which down to the particular implementation you pick.
