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launch cluster interactively?
3 messages · Whit Armstrong, Dirk Eddelbuettel, Huang-Wen Chen
On 16 September 2009 at 12:25, Whit Armstrong wrote:
| Is it no longer possible to start a cluster interactively with MPI? | I just tried to run an old script interactively, but it now fails. | | warmstrong at research:~$ R | > library(Rmpi) | > library(snow) | > cl <- makeCluster(4,"MPI") | [research:08918] [[33202,1],0] routed:binomial: Connection to lifeline | [[33202,0],0] lost | warmstrong at research:~$ | | our MPI setup works with slurm and orterun. I just can't seem to start the | cluster from an existing R session. | | R 2.8.1, openMPI 1.3, ubuntu 9.04. My memory is a little foggy about the issues, but I think that Open MPI 1.3 changed something here. I think you need the 'outer call' setup I use is most (all ?) of my tutorial examples -- and littler is good for that scripting use. That said, there are snow and Rmpi setup functions where you explicitly list hostnames. Those may work too. Posting of working examples is encouraged :) Dirk
Three out of two people have difficulties with fractions.
I solved the same problem by modifying system-wide hostfile. Starting the cluster by orterun is fine but not insides R/Rmpi/snow. This is because local settings, such as ~/.openmpi or environment variables, are ignored in Rmpi. Another way is to add host/hostfile into the 'info' object (via mpi.info.add) while you start the cluster. The latter might require openmpi 1.3 because it didn't work for me.
Whit Armstrong wrote:
Is it no longer possible to start a cluster interactively with MPI? I just tried to run an old script interactively, but it now fails. warmstrong at research:~$ R
library(Rmpi) library(snow) cl <- makeCluster(4,"MPI")
[research:08918] [[33202,1],0] routed:binomial: Connection to lifeline [[33202,0],0] lost warmstrong at research:~$ our MPI setup works with slurm and orterun. I just can't seem to start the cluster from an existing R session. R 2.8.1, openMPI 1.3, ubuntu 9.04. Thanks, Whit [[alternative HTML version deleted]]