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| doku:rstat [2015/04/28 12:05] – [Example] ir | doku:rstat [2021/09/29 12:24] – [Using R on VSC2 and VSC3 with MPI libraries] goldenberg | ||
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| [[http:// | [[http:// | ||
| - | 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. | ||
| Line 25: | Line 25: | ||
| === Parallel execution === | === Parallel execution === | ||
| - | The R-code may be parallelized in the following form: | + | In R, the code **berk-rmpi.R** |
| - | - berk-rmpi.R | + | |
| < | < | ||
| # basic example with foreach | # basic example with foreach | ||
| # start R as usual:' | # start R as usual:' | ||
| - | library (Rmpi) | + | library (Rmpi) |
| library (doMPI) | library (doMPI) | ||
| cl <- startMPIcluster () | cl <- startMPIcluster () | ||
| Line 43: | Line 42: | ||
| </ | </ | ||
| - | + | On VSC2, a batch job is submitted by using the following | |
| - | using this script | + | |
| < | < | ||
| #$ -N rstat | #$ -N rstat | ||
| Line 50: | Line 48: | ||
| #$ -pe mpich 16 | #$ -pe mpich 16 | ||
| #$ -l h_rt=01: | #$ -l h_rt=01: | ||
| - | echo $NSLOTS | ||
| - | mpirun -machinefile $TMPDIR/ | ||
| - | </ | ||
| - | using this script on VSC3: | + | mpirun -machinefile $TMPDIR/ |
| + | </ | ||
| + | yielding to an execution time [s] of | ||
| + | < | ||
| + | > proc.time() | ||
| + | | ||
| + | 8.495 | ||
| + | </ | ||
| + | On VSC3 the script reads: | ||
| < | < | ||
| #!/bin/sh | #!/bin/sh | ||
| Line 69: | Line 72: | ||
| mpirun R CMD BATCH berk-rmpi.R | mpirun R CMD BATCH berk-rmpi.R | ||
| </ | </ | ||
| - | + | yielding to an execution time [s] of | |
| - | + | ||
| - | takes on VSC2: | + | |
| < | < | ||
| > proc.time() | > proc.time() | ||
| | | ||
| - | | + | |
| </ | </ | ||