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| doku:rstat [2015/04/14 12:50] – created ssenoner | 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. |
| - | This libraries give you the possibilty | + | These libraries give you the possibility |
| - | Example | + | ==== Example |
| + | |||
| + | Given a simple for loop: | ||
| < | < | ||
| for (i in 1:50) {mean(rnorm(1e+07))} | for (i in 1:50) {mean(rnorm(1e+07))} | ||
| </ | </ | ||
| - | sequentially it takes on VSC3: | + | === Sequential execution === |
| + | |||
| + | Sequential execution | ||
| < | < | ||
| / | / | ||
| Line 19: | Line 23: | ||
| </ | </ | ||
| - | using this script | + | === Parallel execution === |
| + | |||
| + | In R, the code **berk-rmpi.R** may be parallelized in the following form: | ||
| + | < | ||
| + | # basic example with foreach | ||
| + | # start R as usual:' | ||
| + | library (Rmpi) | ||
| + | library (doMPI) | ||
| + | cl <- startMPIcluster () | ||
| + | registerDoMPI (cl) | ||
| + | |||
| + | result <- foreach (i = 1:50) %dopar% { | ||
| + | mean(rnorm(1e+07)) | ||
| + | } | ||
| + | |||
| + | closeCluster(cl) | ||
| + | mpi.finalize() | ||
| + | </ | ||
| + | |||
| + | On VSC2, a batch job is submitted by using the following | ||
| < | < | ||
| #$ -N rstat | #$ -N rstat | ||
| Line 25: | 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 36: | Line 64: | ||
| #SBATCH --tasks-per-node=16 | #SBATCH --tasks-per-node=16 | ||
| - | module unload intel | ||
| module unload intel-mpi/5 | module unload intel-mpi/5 | ||
| - | module load intel/ | ||
| module load intel-mpi/ | module load intel-mpi/ | ||
| + | module load R | ||
| export I_MPI_FABRICS=shm: | export I_MPI_FABRICS=shm: | ||
| - | mpirun | + | mpirun R CMD BATCH berk-rmpi.R |
| </ | </ | ||
| - | + | yielding to an execution time [s] of | |
| - | berk-rmpi.R: | + | |
| - | < | + | |
| - | # basic example with foreach | + | |
| - | # start R as usual:' | + | |
| - | library (Rmpi) | + | |
| - | library (doMPI) | + | |
| - | cl <- startMPIcluster () | + | |
| - | registerDoMPI (cl) | + | |
| - | clusterSize (cl) | + | |
| - | + | ||
| - | result <- foreach (i = 1:50) %dopar% { | + | |
| - | mean(rnorm(1e+07)) | + | |
| - | } | + | |
| - | + | ||
| - | closeCluster(cl) | + | |
| - | mpi.finalize() | + | |
| - | </ | + | |
| - | + | ||
| - | takes on VSC2: | + | |
| < | < | ||
| > proc.time() | > proc.time() | ||
| | | ||
| - | | + | |
| </ | </ | ||