Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Multiple calls of future_map() within a single plan() or script result in massive slowdown. #268

Open
padpadpadpad opened this issue Jun 18, 2024 · 0 comments

Comments

@padpadpadpad
Copy link

padpadpadpad commented Jun 18, 2024

I have multiple datasets in a nested tibble, and I am using multiple future_map() calls to fit different non-linear model formulations to each dataset.

For a couple of models it is quicker to use future_map() than map(), but I have found that it becomes very slow (and essentially hangs) when I get to about 7 models.

I have attached a reproducible furrr vs. purrr comparison where furrr outperforms purrr, but when I add more calls furrr basically hangs by the 6 or 7th call or model.

I think it is a memory issue, but I was wondering if there are any recommendations to improving memory usage for multiple future_map() calls.

I tried to look at whether individual models were causing a bottleneck by doing each future_map() call individually within a plan() and using plan(sequential) to close it afterwards, but I still got a huge slowdown in future_map() performance after 6 or 7 calls.

Also I have checked the nested dataframe is not grouped as I know that is a known issue.

Many thanks
Dan


# ---------------------------
# Purpose of script: Compare future_map() and map()
#
# What this script does:
# 1. Compare furrr and purrr for a small dataset
#
# Author: Dr. Daniel Padfield
#
# Date Created: 2024-05-29
#
# Copyright (c) Daniel Padfield, 2024
#
# ---------------------------
#
# Notes:
#
# ---------------------------

# if librarian is not installed, install it
if (!requireNamespace("librarian", quietly = TRUE)){
  install.packages("librarian")
}
# load packages
librarian::shelf(tidyverse, rTPC, nls.multstart, furrr, progressr, microbenchmark)

## ---------------------------

# read in Chlorella TPC data
data("chlorella_tpc")

# fit a few models to the data

# load in data
data("chlorella_tpc")

d <- chlorella_tpc

# compare future_map with map ####

# compare using nls.multstart with 2 models and 10 curves
check_purrr <- microbenchmark(
  purrr = filter(d, curve_id <= 10) %>%
    nest(., data = c(temp, rate)) %>%
    mutate(beta = map(data, possibly(~nls_multstart(rate~beta_2012(temp = temp, a, b, c, d, e),
                                                    data = .x,
                                                    iter = c(6,6,6,6,6),
                                                    start_lower = get_start_vals(.x$temp, .x$rate, model_name = 'beta_2012') * 0.5,
                                                    start_upper = get_start_vals(.x$temp, .x$rate, model_name = 'beta_2012') * 1.5,
                                                    lower = get_lower_lims(.x$temp, .x$rate, model_name = 'beta_2012'),
                                                    upper = get_upper_lims(.x$temp, .x$rate, model_name = 'beta_2012'),
                                                    supp_errors = 'Y',
                                                    convergence_count = FALSE)), NA),
           boatman = map(data, possibly(~nls_multstart(rate~boatman_2017(temp = temp, rmax, tmin, tmax, a,b),
                                                       data = .x,
                                                       iter = c(5,5,5,5,5),
                                                       start_lower = get_start_vals(.x$temp, .x$rate, model_name = 'boatman_2017') * 0.5,
                                                       start_upper = get_start_vals(.x$temp, .x$rate, model_name = 'boatman_2017') * 1.5,
                                                       lower = get_lower_lims(.x$temp, .x$rate, model_name = 'boatman_2017'),
                                                       upper = get_upper_lims(.x$temp, .x$rate, model_name = 'boatman_2017'),
                                                       supp_errors = 'Y',
                                                       convergence_count = FALSE)), NA)),
  times = 1
)

check_purrr

check_furrr <- microbenchmark(
  furrr = {
  plan(multisession, workers = 3)
  
  filter(d, curve_id <= 10) %>%
    nest(., data = c(temp, rate)) %>%
    mutate(beta = future_map(data, possibly(~nls_multstart(rate~beta_2012(temp = temp, a, b, c, d, e),
                                                                     data = .x,
                                                                     iter = c(6,6,6,6,6),
                                                                     start_lower = get_start_vals(.x$temp, .x$rate, model_name = 'beta_2012') * 0.5,
                                                                     start_upper = get_start_vals(.x$temp, .x$rate, model_name = 'beta_2012') * 1.5,
                                                                     lower = get_lower_lims(.x$temp, .x$rate, model_name = 'beta_2012'),
                                                                     upper = get_upper_lims(.x$temp, .x$rate, model_name = 'beta_2012'),
                                                                     supp_errors = 'Y',
                                                                     convergence_count = FALSE, p = p)), NA),
           boatman = future_map(data, possibly(~nls_multstart(rate~boatman_2017(temp = temp, rmax, tmin, tmax, a,b),
                                                                        data = .x,
                                                                        iter = c(5,5,5,5,5),
                                                                        start_lower = get_start_vals(.x$temp, .x$rate, model_name = 'boatman_2017') * 0.5,
                                                                        start_upper = get_start_vals(.x$temp, .x$rate, model_name = 'boatman_2017') * 1.5,
                                                                        lower = get_lower_lims(.x$temp, .x$rate, model_name = 'boatman_2017'),
                                                                        upper = get_upper_lims(.x$temp, .x$rate, model_name = 'boatman_2017'),
                                                                        supp_errors = 'Y',
                                                                        convergence_count = FALSE, p = p)), NA))},
  times = 1
)

check_furrr
check_purrr

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant