inst/extdata/scripts/cluster_setup.R

In kylieainslie/MoreVac: Modelling Repeat Vaccination

### For cluster
# getting started
 # install.packages("drat") # if you don't have it already
 # drat:::add("mrc-ide")
 # install.packages("provisionr")
 # install.packages("didehpc")
 # install.packages("buildr)

# setwd('/Volumes/kainslie/cluster')
setwd('Q:/cluster')
# set up your details and which cluster you want (big or small)
options(didehpc.username = "kainslie",
        didehpc.cluster = "big")

# dont really know what these lines do but you need them
context::context_log_start()
root <- "contexts"

# setting up the context: what files need to be sourced for your function to work, what packages you need
# package sources only required here because the package I am using is not on CRAN
ctx <- context::context_save(path = root,
                             packages = c("morevac","Rcpp","dplyr",
                                          "data.table","rdist", "Matrix"),
                             package_sources =
                               provisionr::package_sources(github = "kylieainslie/morevac@coudeville",
                                                           cran = "https://cran.ma.imperial.ac.uk/")
)

# this line should give you a login prompt
obj <- didehpc::queue_didehpc(ctx)

# run a single job
# 'job' is the thing I am running on the cluster
job <- obj$enqueue(run_sims_all(params_file = "param_values.csv", out_file = "sim"))
job2 <- obj$enqueue(run_sims_all(params_file = "param_values_16.csv", out_file = "sim16_"))

# bulk jobs
library(morevac)
library(lhs)
params <- create_params_file(n_sim = 100, n_indiv = 30000, lhc_size = 1000, out_file = "param_values",
                            vac_cutoff = 10, seed = 1234)

job_bulk2 <- obj$enqueue_bulk(params[40:50,], run_sims_clust, do_call = TRUE)