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doku:rstat [2015/04/28 09:21] – irdoku:rstat [2021/09/29 12:25] (current) – [Example] goldenberg
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 [[http://www.r-project.org/]] [[http://www.r-project.org/]]
  
-We installed the libraries Rmpi, doMPI and foreach and their dependencies on VSC2 and VSC3. +We installed the libraries Rmpi, doMPI and foreach and their dependencies on VSC2 and VSC4. 
-This libraries give you the possibilty to parallelize loops over more nodes with MPI using the foreach function which is very similar to a for loop.+These libraries give you the possibility to parallelize loops over more nodes with MPI using the foreach function which is very similar to a for loop.
  
-Example given a simple for loop:+==== Example ==== 
 + 
 +Given a simple for loop:
 <code> <code>
 for (i in 1:50) {mean(rnorm(1e+07))} for (i in 1:50) {mean(rnorm(1e+07))}
 </code> </code>
  
-sequentially it takes on VSC3:+=== Sequential execution === 
 + 
 +Sequential execution on VSC3 leads to an execution time [s] of:
 <code> <code>
 /opt/sw/R/current/bin/R /opt/sw/R/current/bin/R
Line 19: Line 23:
 </code> </code>
  
-using this script on VSC2:+=== Parallel execution === 
 + 
 +In R, the code **berk-rmpi.R** may be parallelized in the following form:
 <code> <code>
-#$ -N rstat +# basic example with foreach 
-#$ -V +# start R as usual:'R'or via a batch job 
-#$ -pe mpich 16 +library (Rmpi)              
-#$ -l h_rt=01:00:00 +library (doMPI) 
-echo $NSLOTS +cl <- startMPIcluster () 
-mpirun -machinefile $TMPDIR/machines -np 16 ~/sw/rstat/bin/R CMD BATCH berk-rmpi.R+registerDoMPI (cl) 
 + 
 +result <- foreach (i = 1:50) %dopar% { 
 +mean(rnorm(1e+07)) 
 +} 
 + 
 +closeCluster(cl) 
 +mpi.finalize()
 </code> </code>
  
-using this script on VSC3:+On VSC3 the script reads:
 <code> <code>
 #!/bin/sh #!/bin/sh
Line 44: Line 57:
 mpirun R CMD BATCH berk-rmpi.R mpirun R CMD BATCH berk-rmpi.R
 </code> </code>
- +yielding to an execution time [s] of 
-berk-rmpi.R: +
-<code> +
-# basic example with foreach +
-# start R as usual:'R'or via a batch job +
-library (Rmpi) +
-library (doMPI) +
-cl <- startMPIcluster () +
-registerDoMPI (cl) +
- +
-result <- foreach (i = 1:50) %dopar% { +
-mean(rnorm(1e+07)) +
-} +
- +
-closeCluster(cl) +
-mpi.finalize() +
-</code> +
- +
-takes on VSC2:+
 <code> <code>
 > proc.time() > proc.time()
    user  system elapsed     user  system elapsed 
-  8.495   0.264   9.616 +  4.566   0.156   5.750 
 </code> </code>
  • doku/rstat.1430212868.txt.gz
  • Last modified: 2015/04/28 09:21
  • by ir