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module load r/4.2.1.2 |
To make R 4.2.1 .2 autoload on login
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module initadd r/34.12.1 |
Interactive R use with slurm
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module purge module load r/4.2.1.2 R ... # here will be the interactive commands with R exit |
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When the job completes output will be written to helloworld.Rout
MPI
*If anybody has been using R 3.1.1 with Rmpi and knows what version works with it please let us know.
If you prefer to use one of the other MPI implementations compatible with Rmpi, such as MPICH, feel free to install your local package. This was how OpenMPI was installed in a session of R started with fisbatch (change the values in blue to whatever you want):
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fisbatch
module load r/3.1.1 mpi/openmpi/1.10.1-gcc
R
install.packages('Rmpi', configure.args='--with-Rmpi-include=/apps2/openmpi/1.10.1-gcc/include --with-Rmpi-libpath=/apps2/openmpi/1.10.1-gcc/lib --with-Rmpi-type=OPENMPI')
# When prompted for the mirror, try TX (i.e. 121 at the time of writing) since some mirrors are prob |
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This part is to be updated. |
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#!/bin/bash #SBATCH -p general #SBATCH -n 30 source /etc/profile.d/modules.sh module purge module load r/34.2.31 mpi/openmpi/gcc/64/1.10.1-gcc7 # If MPI tells you that forking is bad uncomment the line below # export OMPI_MCA_mpi_warn_on_fork=0 Rscript mpi.R |
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Each version of R may depend on a different version of MPI, what follows is the known dependencies as of Thu Jun 22 13:30:50 EDT 2017:
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R Version
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MPI Version
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r/3.4.2-gcc540
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mpi/openmpi/1.10.1-gcc
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r/3.3.3
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mpi/openmpi/1.10.1-gcc
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r/3.2.3
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mpi/openmpi/1.10.1-gcc
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r/3.1.1
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Unknown*
*If anybody has been using R 3.1.1 with Rmpi and knows what version works with it please let us know.
If you prefer to use one of the other MPI implementations compatible with Rmpi, such as MPICH, feel free to install your local package. This was how OpenMPI was installed in a session of R started with fisbatch (change the values in blue to whatever you want):
...