From jo@h@m@ulrich @ending from gm@il@com  Tue Jul 17 12:56:37 2018
From: jo@h@m@ulrich @ending from gm@il@com (Joshua Ulrich)
Date: Tue, 17 Jul 2018 05:56:37 -0500
Subject: [Rd] Memory leakage from large lists
In-Reply-To: <CAAuWi_Yz3ssujY_hyEB9jzGjjqe3rmFA=2uJE9PUtqeiphQKeg@mail.gmail.com>
References: <CAAuWi_Yz3ssujY_hyEB9jzGjjqe3rmFA=2uJE9PUtqeiphQKeg@mail.gmail.com>
Message-ID: <CAPPM_gQqPM7eeiaNqpV4fzxk9htZvfBynNx+SXF4DUOmm2ELLA@mail.gmail.com>

This looks like a case of FAQ 7.42:
https://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-is-R-apparently-not-releasing-memory_003f

On Mon, Jul 16, 2018 at 2:32 PM, Daniel Raduta <datudar at gmail.com> wrote:
> Hello,
>
> I am experiencing a very noticeable memory leak when using large lists of
> large data. The code below creates a list of matrices, yet the memory does
> not free up after removing that item and performing a garbage collection.
> Is there a something I can do to prevent this memory leak? Any help would
> be greatly appreciated. By the way, if you execute the code, please run it
> in a new R session.
>
> # Start of code
> ================================================================
>
> # Function that returns memory being used
> MemoryUsed <- function(){
>   pid <- Sys.getpid()
>   system(paste0("top -n 1 -p ", pid, " -b"), intern = TRUE)[c(7,8)]
> }
>
> # Initial memory (VIRT memory equals about 400,000 bytes on my machine)
> MemoryUsed()
>
> # Create a large list of large data, remove it, and perform garbarge
> collection
> ncols <- 100
> nrows <- 10000
> mat <- matrix(seq(nrows * ncols), nrow = nrows, ncol = ncols)
> ls <- lapply(1:1000, function(x) as.data.frame(mat))
> rm(list = setdiff(ls(), 'MemoryUsed'))
> invisible(gc())
>
> # Final memory (now, VIRT memory equals about 4,600,000 bytes on my machine)
> MemoryUsed()
>
> # End of code
> ==================================================================
>
> My session info is:
>
> R version 3.4.4 (2018-03-15)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 16.04.3 LTS
>
> Matrix products: default
> BLAS: /usr/lib/libblas/libblas.so.3.6.0
> LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] compiler_3.4.4 tools_3.4.4    yaml_2.1.19
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



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[Rd] Memory leakage from large lists
Joshua Ulrich