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update instructions to use openmpi/1.10.7
(Marked this version for translation) |
(update instructions to use openmpi/1.10.7) |
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module spider r | module spider r | ||
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In this case we choose the latest (as of November, 2017): | In this case we choose the latest (as of November, 2017), and also load the required OpenMPI module: | ||
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module load r/3.4.0 | module load r/3.4.0 | ||
module load openmpi/1.10.7 | |||
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mkdir -p ~/local/R_libs/ | mkdir -p ~/local/R_libs/ | ||
export R_LIBS=~/local/R_libs/ | export R_LIBS=~/local/R_libs/ | ||
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This | This uses OpenMPI version 1.10.7 which is needed to spawn processes correctly (the default MPI module 2.1.1 has a problem with that at present. | ||
====Running==== <!--T:30--> | ====Running==== <!--T:30--> | ||
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#Tell all slaves to return a message identifying themselves. | #Tell all slaves to return a message identifying themselves. | ||
library("Rmpi") | library("Rmpi") | ||
sprintf("TEST mpi.universe.size() = %i", mpi.universe.size()) | sprintf("TEST mpi.universe.size() = %i", mpi.universe.size()) | ||
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#!/bin/bash | #!/bin/bash | ||
#SBATCH --account=def-ppomorsk # replace this with your own account | #SBATCH --account=def-ppomorsk # replace this with your own account | ||
#SBATCH --ntasks=5 # number of MPI processes | #SBATCH --ntasks=5 # number of MPI processes | ||
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#SBATCH --time=0-00:15 # time (DD-HH:MM) | #SBATCH --time=0-00:15 # time (DD-HH:MM) | ||
module load r/3.4.0 | module load r/3.4.0 | ||
module load openmpi/1.10.7 | |||
export R_LIBS=~/local/R_libs/ | export R_LIBS=~/local/R_libs/ | ||
mpirun -np 1 R CMD BATCH test.R test.txt | mpirun -np 1 R CMD BATCH test.R test.txt | ||
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sbatch job.sh | sbatch job.sh | ||
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