In Bisaloo/fundiversity: Easy Computation of Functional Diversity Indices

Note: This vignette presents some performance tests ran between non-parallel and parallel versions of fundiversity functions. Note that to avoid the dependency on other packages, this vignette is pre-computed.

Within fundiversity the computation of most indices can be parallelized using the future package. The goal of this vignette is to explain how to toggle and use parallelization in fundiversity. The functions that currently support parallelization are summarized in the table below:

| Function Name | Index Name | Parallelizable[^1] | Memoizable[^2] | |:----------------------|:---------------|:------------------:|:--------------:| | fd_fric() | FRic | ✅ | ✅ | | fd_fric_intersect() | FRic_intersect | ✅ | ✅ | | fd_fdiv() | FDiv | ✅ | ✅ | | fd_feve() | FEve | ✅ | ❌ | | fd_fdis() | FDis | ✅ | ❌ | | fd_raoq() | Rao's Q | ❌ | ❌ |

[^1]: parallelization through the future backend please refer to the parallelization vignette for details. [^2]: memoization means that the results of the functions calls are cached and not recomputed when recalled, to toggle it off see the fundiversity::fd_fric() Details section.

Note that memoization and parallelization cannot be used at the same time. If the option fundiversity.memoise has been set to TRUE but the computations are parallelized, fundiversity will use unmemoised versions of functions.

The future package provides a simple and general framework to allow asynchronous computation depending on the resources available for the user. The first vignette of future gives a general overview of all its features. The main idea being that the user should write the code once and that it would run seamlessly sequentially, or in parallel on a single computer, or on a cluster, or distributed over several computers. fundiversity can thus run on all these different backends following the user's choice.

library("fundiversity")

data("traits_birds", package = "fundiversity")
data("site_sp_birds", package = "fundiversity")

Running code in parallel

By default the fundiversity code will run sequentially on a single core. To trigger parallelization the user needs to define a future::plan() object with a parallel backend such as future::multisession to split the execution across multiple R sessions.

# Sequential execution
fric1 <- fd_fric(traits_birds)

# Parallel execution
future::plan(future::multisession)  # Plan definition
fric2 <- fd_fric(traits_birds)  # The code resolve in similar fashion

identical(fric1, fric2)
#> [1] TRUE

Within the future::multisession backend you can specify the number of cores on which the function should be parallelized over through the argument workers, you can change it in the future::plan() call:

future::plan(future::multisession, workers = 2)  # Only 2 cores are used
fric3 <- fd_fric(traits_birds)

identical(fric3, fric2)
#> [1] TRUE

To learn more about the different backends available and the related arguments needed, please refer to the documentation of future::plan() and the overview vignette of future.

Performance comparison

We can now compare the difference in performance to see the performance gain thanks to parallelization:

future::plan(future::sequential)
non_parallel_bench <- microbenchmark::microbenchmark(
  non_parallel = {
    fd_fric(traits_birds)
  },
  times = 20
)

future::plan(future::multisession)
parallel_bench <- microbenchmark::microbenchmark(
  parallel = {
    fd_fric(traits_birds)
  },
  times = 20
)

rbind(non_parallel_bench, parallel_bench)
#> Unit: milliseconds
#>          expr      min       lq      mean    median       uq      max neval cld
#>  non_parallel   8.9509   9.2691  14.93812  13.32405  18.4841   33.153    20  a 
#>      parallel 224.7037 248.9997 345.59427 274.59615 304.6889 1660.164    20   b

The non parallelized code runs faster than the parallelized one! Indeed, the parallelization in fundiversity parallelize the computation across different sites. So parallelization should be used when you have many sites on which you want to compute similar indices.

# Function to make a bigger site-sp dataset
make_more_sites <- function(n) {
  site_sp <- do.call(rbind, replicate(n, site_sp_birds, simplify = FALSE))
  rownames(site_sp) <- paste0("s", seq_len(nrow(site_sp)))

  site_sp
}

For example with a dataset 5000 times bigger:

bigger_site <- make_more_sites(5000)

microbenchmark::microbenchmark(
  seq = { 
    future::plan(future::sequential) 
    fd_fric(traits_birds, bigger_site) 
  },
  multisession = { 
    future::plan(future::multisession, workers = 4)
    fd_fric(traits_birds, bigger_site) 
  },
  multicore = { 
    future::plan(future::multicore, workers = 4) 
    fd_fric(traits_birds, bigger_site) 
  }, times = 20
)
#> Unit: seconds
#>          expr      min        lq      mean    median        uq       max neval cld
#>           seq 78.13766 195.17853 184.92560 196.89360 197.90500 200.56116    20  a 
#>  multisession 34.23402  54.44036  53.39172  54.88206  55.19359  61.83829    20   b
#>     multicore 75.43857 192.45136 183.07222 196.48277 201.16889 209.39847    20  a

Session info of the machine on which the benchmark was ran and time it took to run

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Bisaloo/fundiversity documentation built on April 4, 2024, 12:24 a.m.