scratch/test-open-mp.R

In pbs-assess/sdmTMB: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'

library(sdmTMB)
library(ggplot2)

mesh <- make_mesh(pcod_2011, c("X", "Y"), cutoff = 10)
options(sdmTMB.cores = 4)
tictoc::tic()
fit <- sdmTMB(density ~ 0 + depth_scaled + depth_scaled2 + as.factor(year),
  data = pcod_2011, time = "year", mesh = mesh, family = tweedie(link = "log"))
tictoc::toc()

# ------

tests <- expand.grid(iter = 1, i = 1:6)
df <- purrr::pmap_dfr(tests, function(iter, i) {
  cat(i, "\n")
  options(sdmTMB.cores = i)
  tictoc::tic()
  fit <- sdmTMB(density ~ 0 + depth_scaled + depth_scaled2 + as.factor(year),
    data = pcod_2011, time = "year", mesh = mesh, family = tweedie(link = "log"))
  a <- tictoc::toc()
  data.frame(iter = iter, n_threads = i, time = unname(a$toc - a$tic))
})
ggplot(df, aes(n_threads, time)) + geom_point()

options(sdmTMB.cores = 5)
fit <- sdmTMB(density ~ 0 + depth_scaled + depth_scaled2 + as.factor(year),
  data = pcod_2011, time = "year", mesh = mesh, family = tweedie(link = "log"), silent = FALSE)
fit$control$parallel

nd <- subset(qcs_grid, year %in% unique(pcod_2011$year))

tictoc::tic()
fit$control$parallel <- 4
p <- predict(fit, return_tmb_object = TRUE, newdata = nd)
tictoc::toc()

tictoc::tic()
fit$control$parallel <- 1
p <- predict(fit, return_tmb_object = TRUE, newdata = nd)
tictoc::toc()

tictoc::tic()
p$fit_obj$control$parallel <- 4
ind <- get_index(p, bias_correct = FALSE)
tictoc::toc()

tictoc::tic()
p$fit_obj$control$parallel <- 1
ind <- get_index(p, bias_correct = FALSE)
tictoc::toc()

tictoc::tic()
fit$control$parallel <- 4
p <- predict(fit, return_tmb_object = TRUE, newdata = nd, nsim = 500)
tictoc::toc()

tictoc::tic()
fit$control$parallel <- 1
p <- predict(fit, return_tmb_object = TRUE, newdata = nd, nsim = 500)
tictoc::toc()