From x|@oy@n@yu @end|ng |rom gm@||@com  Tue Apr  6 00:27:10 2021
From: x|@oy@n@yu @end|ng |rom gm@||@com (xiaoyan yu)
Date: Mon, 5 Apr 2021 18:27:10 -0400
Subject: [Rd] R extension memory leak detection question
In-Reply-To: <CAJf4E3pJiF4U=w89P1UH6jDFbNM6Mwxu=r8EDfGjbtNmeLesuw@mail.gmail.com>
References: <CANjVfJ2xXfinnpYgEoH_0dwvG=29FFMinuV+1cOueSrRMNyq9A@mail.gmail.com>
 <b0b80c39-2931-cd4e-ef6f-5cff9e9678c8@gmail.com>
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Message-ID: <CANjVfJ3gc7+U2-ep4-CeJWDHa7SivkqvBx2sxkD3tA1mdv5DMQ@mail.gmail.com>

Thank you all for your help.
We embedded R in our program and found the memory in the process
accumulated while our expectation is that the memory will go down after
each R evaluation.
I started to write a test program with only a few lines of R embedded codes
and found the memory never went down even after R library is unloaded.
Please find more details in the readme and test program at
https://github.com/xiaoyanyuvt/RMemTest

Thanks,
Xiaoyan


On Fri, Mar 19, 2021 at 2:21 PM Lionel Henry <lionel at rstudio.com> wrote:

> > Still, memory leaks are possible if the program forgets about a
> > pointer to some piece of memory no longer needed, and keeps that
> > pointer in say some global structure. Such memory leaks would not be
> > found using address sanitizer.
>
> We had a few cases of this in the past. Given the difficulty of
> tracing the leaking references, we wrote this package for taking
> snapshots of the R heap and finding dominators and shortest paths
> between nodes:
>
> Repo: https://github.com/r-lib/memtools
> Vignette: https://memtools.r-lib.org/articles/memtools.html
>
> One issue that complicates taking snapshots is that R doesn't expose
> the GC roots. In practice, only the precious list is needed I think.
> Would you consider a patch that allows retrieving the precious list
> for debugging purposes via a `.Internal()` call?
>
> Best,
> Lionel
>
>
> On 3/15/21, Tomas Kalibera <tomas.kalibera at gmail.com> wrote:
> > On 3/12/21 7:43 PM, xiaoyan yu wrote:
> >> I am writing C++ program based on R extensions and also try to test the
> >> program with google address sanitizer.
> >>
> >> I thought if I don't protect the variable from the allocation API such
> as
> >> Rf_allocVector, there will be a memory leak. However, the address
> >> sanitizer
> >> didn't report it. Is my understanding correct? Or I will see the memory
> >> leak only if I compile R source code with the address sanitizer.
> >
> > Yes, you should use special options for compilation and linking to use
> > address sanitizer. See Writing R Extensions, section 4.3.3.
> >
> > If you allocate an R object using Rf_allocVector(), but don't protect
> > it, it means this object is available for the garbage collector to
> > reclaim. So it is not a memory leak.
> >
> > Memory leaks with a garbage collector are much less common than without,
> > because if the program loses a pointer to some piece of memory, that
> > piece will automatically be reclaimed (not leaked). Still, memory leaks
> > are possible if the program forgets about a pointer to some piece of
> > memory no longer needed, and keeps that pointer in say some global
> > structure. Such memory leaks would not be found using address sanitizer.
> >
> > Address sanitizer/Undefined behavior sanitizer can sometimes find errors
> > caused by that the program forgets to protect an R object, but this is
> > relatively rare, as they don't understand R heap specifically, so you
> > cannot assume that if you create such example, the error will always be
> > found.
> >
> > Best
> > Tomas
> >
> >>
> >>   Please help!
> >>
> >> Thanks,
> >> Xiaoyan
> >>
> >>      [[alternative HTML version deleted]]
> >>
> >> ______________________________________________
> >> R-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>

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[Rd] R extension memory leak detection question
xiaoyan yu