Build RStan
From HPC
Build RStan as a qsub job
Notes
- RStan requires a newer version of GCC so that must be loaded as a module.
- You can change the module load line for R to which ever version you prefer.
- Once job finishes you can look a build.out to check for completion.
- The build.R will modify the R Makevars file to add CXX14FLAGS and CXX14
QSUB script
#!/bin/bash #$ -N R_BUILD_JOB #$ -M email@lshtm.ac.uk -m be #$ -q short.q #$ -l mem_free=4G,h_vmem=4.2G #$ -V -cwd module load gcc/6.5.0 module load R/3.5.3 which R which gcc R CMD BATCH build.R build.out
build.R
dotR <- file.path(Sys.getenv("HOME"), ".R") if (!file.exists(dotR)) dir.create(dotR) M <- file.path(dotR, "Makevars") if (!file.exists(M)) file.create(M) cat("\nCXX14FLAGS=-O2 -march=native -mtune=native -fPIC", "CXX14=g++", # or clang++ but you may need a version postfix file = M, sep = "\n", append = TRUE) install.packages("rstan", type = "source", repos = "https://cloud.r-project.org/", dependencies = TRUE)