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r-administration.md

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R Update.

Updating default R version to newer release, following step need to be done.

  • Notify downtime in MS Team, need to mention about the R update as well.
  • Make a note of all servers default R version --> ll /usr/bin/R
  • Need to restore the default versions after R update.
  1. Check the active sessions.
  2. Notify in MS Team that the downtime has started.
  3. Suspend all the active sessions --> rstudio-server suspend-all
  4. Stop RStudio --> rstudio-server stop
  5. Update R with --> yum install --enablerepo="rhel-7-server-optional-rpms" R
  6. Finally restart RStudio server --> rstudio-server restart
  7. Check the new R version with --> R
  • After update make all server default R versions as previous.
  • Open RStudio server and check new version is there or not.

Compiling Vanilla R with OpenBLAS

For compiling VanillaR with openBLAS, following steps are done.

  1. Go to the following link https://sourceforge.net/projects/openblas/files/v0.3.3/OpenBLAS%200.3.3%20version.tar.gz
  2. Download the file and extract the file in /mnt (For ease of use, we are keeping it on /mnt)
  3. Create a directory in /opt/OpenBLAS
  4. Go to that extracted file and export the following.
  • export OPENBLAS_NUM_THREADS=7
  • export GOTO_NUM_THREADS=7
  • export OMP_NUM_THREADS=7
  1. sudo make
  2. sudo make PREFIX=/opt/OpenBLAS install
  3. Confirm that all files came in /opt/OpenBLAS
  4. Next step is to rename libRblas.so for that,Go to /opt/vanillaR/R-3.4.3/lib64/R/lib and rename libRblas.so to libRblas.so_back
  5. For renaming use mv libRblas.so libRblas.so_back command
  6. Now we need to softlink, for that do, ln -s /opt/OpenBLAS/lib/libopenblas.so /opt/R-3.4.3/lib64/R/lib/libRblas.so
  7. Confirm whether the OpenBLAS is linked by benchmark test.