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doku:rstat [2015/04/28 12:07] – [Example] ir | doku:rstat [2021/09/29 12:25] (current) – [Example] 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. | ||
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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** |
- | * berk-rmpi.R | + | |
< | < | ||
# basic example with foreach | # basic example with foreach | ||
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</ | </ | ||
- | + | On VSC3 the script | |
- | using this script | + | |
- | < | + | |
- | #$ -N rstat | + | |
- | #$ -V | + | |
- | #$ -pe mpich 16 | + | |
- | #$ -l h_rt=01: | + | |
- | echo $NSLOTS | + | |
- | mpirun -machinefile $TMPDIR/ | + | |
- | </ | + | |
- | + | ||
- | using this script on VSC3: | + | |
< | < | ||
#!/bin/sh | #!/bin/sh | ||
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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() | ||
| | ||
- | | + | |
</ | </ |