Parallel computing with phangorn
Klaus Schliep
University of Graz, Graz University of Technologyklaus.schliep@gmail.com
2026-01-25
Source:vignettes/Parallel.Rmd
Parallel.RmdChanges in phangorn 3.0
Several function in phangorn make use of parallel computing. With the new version 3 we move to using the future and future.apply package (Bengtsson 2021).
Before we were using the mclapply() function in in
bootstrap.pml(), bootstrap.phyDat(),
modelTest(). The disadvantage of mclapply() is
that it works not for Windows and its usage is not recommended inside a
GUI like RStudio. The future package allows the user to define its
backend and can so be adjusted to the hardware and operating system of
the user. Now also on Windows one can use parallel processing. It is
very likely that several other function will allow the future framework
in future. By default processes are running sequential. To run a
function in parallel we just need to call the function plan specifying
the backend and than the function which allows the parallel
processing.
library(phangorn)
library(future)
data("Laurasiatherian")
plan(multisession, workers = 2)
mt <- modelTest(Laurasiatherian, model = c("JC", "F81", "K80", "HKY", "SYM", "GTR"))
plan(sequential) # run sequential againIt is good practice to clean up and set the backend to sequential after using parallel processing.
A few things to consider. When running processes in parallel the memory footprint might be larger compared to the sequential computation. Furthermore some of the linear algebra routines build in R might implicitly use parallel computing. So check how many cores are in use. If too many cores are used parallel code might even slow down.
For more see the man page for plan help(plan), the
vignettes vignette(package="future") and other
documentation of the future package.
Session info
## R version 4.5.2 (2025-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
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## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
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## [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
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## time zone: UTC
## tzcode source: system (glibc)
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## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
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## loaded via a namespace (and not attached):
## [1] digest_0.6.39 desc_1.4.3 R6_2.6.1 fastmap_1.2.0
## [5] xfun_0.56 cachem_1.1.0 knitr_1.51 htmltools_0.5.9
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## [13] pkgdown_2.2.0 textshaping_1.0.4 jquerylib_0.1.4 systemfonts_1.3.1
## [17] compiler_4.5.2 tools_4.5.2 ragg_1.5.0 bslib_0.9.0
## [21] evaluate_1.0.5 yaml_2.3.12 otel_0.2.0 jsonlite_2.0.0
## [25] rlang_1.1.7 fs_1.6.6 htmlwidgets_1.6.4