From tom@@@k@liber@ @ending from gm@il@com  Tue Jul 17 13:11:23 2018
From: tom@@@k@liber@ @ending from gm@il@com (Tomas Kalibera)
Date: Tue, 17 Jul 2018 13:11:23 +0200
Subject: [Rd] Memory leakage from large lists
In-Reply-To: <CAPPM_gQqPM7eeiaNqpV4fzxk9htZvfBynNx+SXF4DUOmm2ELLA@mail.gmail.com>
References: <CAAuWi_Yz3ssujY_hyEB9jzGjjqe3rmFA=2uJE9PUtqeiphQKeg@mail.gmail.com>
 <CAPPM_gQqPM7eeiaNqpV4fzxk9htZvfBynNx+SXF4DUOmm2ELLA@mail.gmail.com>
Message-ID: <90d95a4d-1ab9-1849-e826-92a53e7765b5@gmail.com>

On 07/17/2018 12:56 PM, Joshua Ulrich wrote:
> 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
Yes. A true memory leak in R would mean that repeated execution of the 
same code (e.g. creation and deletion of the list) would start failing 
due to running out of memory at some (high) iteration number.

Also, gc(verbose=TRUE, full=TRUE) run before and after the code snippet 
suggests there is no leak. Well, a little bit of memory could be added 
initially (e.g. byte-compilation, some internal caching at different 
levels) - and this is why "high iteration number" above - but eventually 
the memory use in cons cells and vectors should become constant and it 
does on my system.

Tomas
> 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
>
>



[Rd] Memory leakage from large lists
Tomas Kalibera