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doku:rstat [2015/04/28 12:12] – [Example] irdoku:rstat [2021/09/29 12:24] – [Using R on VSC2 and VSC3 with MPI libraries] 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.
 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. 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.
  
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 === Parallel execution === === Parallel execution ===
  
-The R-code may be parallelized in the following form: +In R, the code **berk-rmpi.R** may be parallelized in the following form:
-   * berk-rmpi.R+
 <code> <code>
 # basic example with foreach # basic example with foreach
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 </code> </code>
  
-On VSC2, a batch job  is submitted by the using the following script:+On VSC2, a batch job  is submitted by using the following script:
 <code> <code>
 #$ -N rstat #$ -N rstat
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 #$ -pe mpich 16 #$ -pe mpich 16
 #$ -l h_rt=01:00:00 #$ -l h_rt=01:00:00
-echo $NSLOTS + 
-mpirun -machinefile $TMPDIR/machines -np 16 ~/sw/rstat/bin/R CMD BATCH berk-rmpi.R+mpirun -machinefile $TMPDIR/machines -np $NSLOTS /opt/sw/R/current/bin/R CMD BATCH berk-rmpi.R
 </code> </code>
 yielding to an execution time [s] of  yielding to an execution time [s] of 
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   4.566   0.156   5.750    4.566   0.156   5.750 
 </code> </code>
- 
  • doku/rstat.txt
  • Last modified: 2021/09/29 12:25
  • by goldenberg