From henrik.bengtsson at gmail.com  Sat Jun  4 21:40:41 2016
From: henrik.bengtsson at gmail.com (Henrik Bengtsson)
Date: Sat, 4 Jun 2016 12:40:41 -0700
Subject: [Rd] RProfmem output format
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I'm picking up this 5-year old thread.

1. About the four memory allocations without a stacktrace

I think the four memory allocations without a stacktrace reported by Rprofmem():

> Rprofmem(); x <- raw(2000); Rprofmem("")
> cat(readLines("Rprofmem.out", n=5, warn=FALSE), sep="\n")
192 :360 :360 :1064 :2040 :"raw"

are due to some initialization of R that is independent of Rprofmem(),
because they can be avoided if one allocates some memory before (in a
fresh R session):

> z <- raw(1000); dummy <- gc()
> Rprofmem(); x <- raw(2000); Rprofmem("")
> cat(readLines("Rprofmem.out", n=5, warn=FALSE), sep="\n")
2040 :"raw"


2. About missing newlines when stacktrace is empty

As a refresher, the problem is that memory allocations an empty
stracktrace are reported without newlines, i.e.

192 :360 :360 :1064 :2040 :"raw"

The question is why this is not reported as:

192 :
360 :
360 :
1064 :
2040 :"raw"

This was/is because C function R_OutputStackTrace() - part of
src/main/memory.c  - looks like:

static void R_OutputStackTrace(FILE *file)
{
    int newline = 0;
    RCNTXT *cptr;

    for (cptr = R_GlobalContext; cptr; cptr = cptr->nextcontext) {
        if ((cptr->callflag & (CTXT_FUNCTION | CTXT_BUILTIN))
           && TYPEOF(cptr->call) == LANGSXP) {
           SEXP fun = CAR(cptr->call);
           if (!newline) newline = 1;
           fprintf(file, "\"%s\" ",
               TYPEOF(fun) == SYMSXP ? CHAR(PRINTNAME(fun)) :
               "<Anonymous>");
        }
    }
    if (newline) fprintf(file, "\n");
}


Thomas, your last comment was:

> Yes. It's obviously better to always print a newline, and so clearly
> deliberate not to, that I suspect there may have been a good reason.
> If I can't work it out (after my grant deadline this week) I will just
> assume it's wrong.

When I search the code and the commit history
(https://github.com/wch/r-source/commit/3d5eb2a09f2d75893efdc8bbf1c72d17603886a0),
it appears that this was there from the very first commit.  Also,
searching the code for usages of R_OutputStackTrace(), I only find
R_ReportAllocation() and R_ReportNewPage(), both part of of
src/main/memory.c (see below).

static void R_ReportAllocation(R_size_t size)
{
    if (R_IsMemReporting) {
if(size > R_MemReportingThreshold) {
   fprintf(R_MemReportingOutfile, "%lu :", (unsigned long) size);
   R_OutputStackTrace(R_MemReportingOutfile);
}
    }
    return;
}

static void R_ReportNewPage(void)
{
    if (R_IsMemReporting) {
fprintf(R_MemReportingOutfile, "new page:");
R_OutputStackTrace(R_MemReportingOutfile);
    }
    return;
}


Could it be that when you wrote it you had another usage for
R_OutputStackTrace() in mind as well?  If so, it makes sense that
R_OutputStackTrace() shouldn't output a newline if the stack trace was
empty.  But if the above is the only usage, to me it looks pretty safe
to always add a newline.

> sessionInfo()
R version 3.3.0 Patched (2016-05-26 r70682)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

/Henrik


On Sun, May 15, 2011 at 1:16 PM, Thomas Lumley <tlumley at uw.edu> wrote:
> On Mon, May 16, 2011 at 1:02 AM, Hadley Wickham <hadley at rice.edu> wrote:
>> So what causes allocations when the call stack is empty?  Something
>> internal?  Does the garbage collector trigger allocations (i.e. could
>> it be caused by moving data to contiguous memory)?
>
> The garbage collector doesn't move anything, it just swaps pointers in
> a linked list.
>
> The lexer, parser, and evaluator all have  to do some work before a
> function context is set up for the top-level function, so I assume
> that's where it is happening.
>
>> Any ideas what the correct thing to do with these memory allocations?
>> Ignore them because they're not really related to the function they're
>> attributed to?  Sum them up?
>>
>>> I don't see why this is done, and I may well be the person who did it
>>> (I don't have svn on this computer to check), but it is clearly
>>> deliberate.
>>
>> It seems like it would be more consistent to always print a newline,
>> and then it would obvious those allocations occurred when the call
>> stack was empty.  This would make parsing the file a little bit
>> easier.
>
> Yes. It's obviously better to always print a newline, and so clearly
> deliberate not to, that I suspect there may have been a good reason.
> If I can't work it out (after my grant deadline this week) I will just
> assume it's wrong.
>
>
>    -thomas
>
> --
> Thomas Lumley
> Professor of Biostatistics
> University of Auckland
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] RProfmem output format
Henrik Bengtsson