From hp@ge@ @end|ng |rom |redhutch@org  Tue Apr  7 18:51:36 2020
From: hp@ge@ @end|ng |rom |redhutch@org (=?UTF-8?B?SGVydsOpIFBhZ8Oocw==?=)
Date: Tue, 7 Apr 2020 09:51:36 -0700
Subject: [Rd] Hard memory limit of 16GB under Windows?
In-Reply-To: <CAJuCY5x-sC94EofCqSKNbTGANHyY6p=f8YAbLVLAOvOcnEsY3g@mail.gmail.com>
References: <emfb436b8b-b4cb-41bc-a183-5c31984721ee@bioinfo5>
 <1e00202b-4529-3488-800b-cdf3a81bfc58@gmail.com>
 <em4318d77f-0ea6-4099-892f-73c3c5302375@bioinfo5>
 <CAJuCY5x-sC94EofCqSKNbTGANHyY6p=f8YAbLVLAOvOcnEsY3g@mail.gmail.com>
Message-ID: <6c1125d0-c59b-744a-84ed-81a723020341@fredhutch.org>

Agreed. I don't see any evidence of a "hard limit" here. It just looks 
like the code you're running has exhausted the memory of your machine. 
It doesn't require creating a lot of 12.6 Gb vectors to do that, even on 
a machine with a lot of memory ;-)

H.

On 4/7/20 08:05, Thierry Onkelinx via R-devel wrote:
> Dear Samuel,
> 
> The most important information from your mail was the actual error message:
> "cannot allocate vector of size 12.6 Gb".
> 
> You'll need to know what code generated this error message. And then figure
> out if the code does something sensible. Often that is not the case when
> you get a similar error message.
> 
> Best regards,
> 
> ir. Thierry Onkelinx
> Statisticus / Statistician
> 
> Vlaamse Overheid / Government of Flanders
> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
> FOREST
> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> thierry.onkelinx at inbo.be
> Havenlaan 88 bus 73, 1000 Brussel
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> 
> ///////////////////////////////////////////////////////////////////////////////////////////
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> than asking him to perform a post-mortem examination: he may be able to say
> what the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
> ///////////////////////////////////////////////////////////////////////////////////////////
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> 
> 
> Op di 7 apr. 2020 om 16:16 schreef Samuel Granjeaud IR/Inserm <
> samuel.granjeaud at inserm.fr>:
> 
>> Hi Tomas,
>>
>> Many thanks for your answer.
>>
>> Here is a copy of a fresh session under RStudio, and after a copy under
>> Rgui.
>> Strangely enough the result of memory.limit() is not the same. Without
>> your question I would not have looked to RGui, being used to work with
>> RStudio.
>>
>> The value under RGui sounds to correspond to the total RAM of the
>> computer. It makes me noticing that the value is in MB.
>>
>> The value under Rstudio was so huge (1.759219e+13) that I just
>> interpreted it as GB. But I was totally wrong. So in fact I don't know
>> what it refers to. The documentation says "For a 64-bit versions of R
>> under 64-bit Windows the limit is currently 8Tb.", but it looks like
>> being 16TB, which my computer don't have of course.
>>
>> I still have to understand why my colleague has a problem of memory
>> allocation (cannot allocate vector of size 12.6 Gb).
>>
>> Sorry for the wrong interpretation, but thanks for the help,
>> Samuel
>>
>> --- RStudio
>>
>> R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
>> Copyright (C) 2020 The R Foundation for Statistical Computing
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>>   > memory.limit()
>> [1] 1.759219e+13
>>   > sessionInfo()
>> R version 3.6.3 (2020-02-29)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> Running under: Windows 10 x64 (build 18363)
>>
>> Matrix products: default
>>
>> locale:
>> [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
>> LC_MONETARY=French_France.1252 LC_NUMERIC=C
>> [5] LC_TIME=French_France.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_3.6.3 tools_3.6.3
>>   >
>>
>> --- RGui
>>
>> R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
>> Copyright (C) 2020 The R Foundation for Statistical Computing
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>>   > ls()
>> character(0)
>>   > memory.limit()
>> [1] 32627
>>   > sessionInfo()
>> R version 3.6.3 (2020-02-29)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> Running under: Windows 10 x64 (build 18363)
>>
>> Matrix products: default
>>
>> locale:
>> [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
>> LC_MONETARY=French_France.1252
>> [4] LC_NUMERIC=C                   LC_TIME=French_France.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_3.6.3
>>   >
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=r6WLJ5dXWo2qb7mQwONaCxYeeWgKwycd3y89JoqY-oY&s=ABvG3sGKR5ln27FVCM8dlmZ82X93ZCTigbMxHeBEb6E&e=
>>
> 
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-- 
Herv? Pag?s

Program in Computational Biology
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[Rd] Hard memory limit of 16GB under Windows?
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