[Rd] Child thread libR.so

Simon Urbanek
Tue, 25 Aug 2015 02:16:05 -0000

Ryan,

if you read the piece you quoted from more carefully, you'll notice it says
"Rf_initialize_R" - which is quite critical in this matter.

Cheers,
Simon


On Aug 24, 2015, at 9:18 AM, Ryan C Metzger <metzger.rc at gmail.com>
wrote:

> I did some poking around with GDB and confirmed that the advice of
> setting R_CStackLimit after init, which is echoed in the "threading
> issues" section of the R-exts help document, isn't entirely useful
> because init apparently loads the main package which trips over the
> broken stack checking.
>
> Stack trace:
>
> #0  R_SignalCStackOverflow (usage=140732197147604) at errors.c:81
> #1  0x00002aaaab0625b7 in Rf_eval (e=0x1b7592a8, rho=0x1b753960) at
eval.c:545
> #2  0x00002aaaab0871ca in R_ReplFile (fp=0x1b69a830, rho=0x1b753960)
> at main.c:98
> #3  0x00002aaaab087a27 in setup_Rmainloop () at main.c:861
> #4  0x00002aaaab14a98b in Rf_initEmbeddedR (argc=<value optimized
> out>, argv=<value optimized out>) at Rembedded.c:63
>
> On Thu, Aug 20, 2015 at 1:21 PM, Ryan C Metzger <metzger.rc at
gmail.com> wrote:
>> So I'm working on a custom front end to R, in one mode of the front
>> end I dynamically load libR.so into a child worker thread. I'm very
>> careful to make sure it is loaded by a single thread and loaded only
>> once, but since it is a child thread it violates assumptions made by
>> the stack size checking inside of R and I get innumerable errors along
>> the lines of
>>
>> Error: C stack usage  140732526462740 is too close to the limit
>>
>> Digging through this email list (and I also found similar things out
>> on google) I found the following advice from 2009
>>
>> ---------------------------------------- SNIP
>>
------------------------------------------------------------------------------
>>> Hi everyone!
>>>  I meet one problem when embedding R in C code, when I run the the
>>> R code in one child thread ,
>>>  it always print error info:
>>>   Error: C stack usage is too close to the limit
>>>
>>>  I also try to set R_CStackLimit = (uintptr_t)-1 to disable the C
>>> stack check as the R-exts doc say,
>>>  but it still does not work, the error info still exist.
>>>
>>
>> That is the way to do it (and other project use it successfully) - the
>> fact that it doesn't work means that you probably do it at the
wrong
>> place (you must set it *after* Rf_initialize_R).
>>
>> Cheers,
>> Simon
>> ---------------------------------------- SNIP
>>
------------------------------------------------------------------------------
>>
>> my code is as follows
>>
>> ---------------------------------------- SNIP
>>
------------------------------------------------------------------------------
>> void init_r() {
>>    SEXP aperm_function;
>>
>>    const char *init_argv[] = {"MyFront",
"--vanilla", "--slave"};
>>    Rf_initEmbeddedR(sizeof (init_argv) / sizeof (init_argv[0]),
>> (char**) init_argv);
>>
>>    R_CStackLimit = (uintptr_t)-1;
>>
>>    /*
>>     * transposeVector above uses the R builtin function aperm instead
of
>>     * looking it up every time we need deal with transposing a
multidimensional
>>     * intput/output look it up once here and save it off
>>     */
>>    aperm_function = findFun(install("aperm"), R_GlobalEnv);
>>    if (aperm_function == NULL || aperm_function == R_NilValue ||
>> aperm_function == R_UnboundValue) {
>>        aperm_function = NULL;
>>    } else {
>>        aperm_expression = PROTECT(allocVector(LANGSXP, 2));
>>
>>        SETCAR(aperm_expression, aperm_function);
>>    }
>> }
>> ---------------------------------------- SNIP
>>
------------------------------------------------------------------------------
>>
>> but as I say I still get the error and it seems like the call to
>> Rf_initEmbeddedR just never returns. As an experiment I edited
>> config.h.in and removed the define for HAVE_GETRLIMIT and recompiled,
>> thus compiling out the stack checking mechanism entirely. Then
>> everything worked great!, so I know it's the stack checking
mechanism
>> from a child thread that is falling to pieces. So what I have in mind
>> is looking to fix this mechanism so that it works from a child thread
>> if the pthread library is available and submitting a patch. My
>> question is two fold, 1. Is there a way to get this to work without a
>> code change ( I'd like to be able to offer my front end stand alone
>> and not have to bundle R with it ) 2. If I do come up with a diff, how
>> do I go about submitting it back to the r foundation?
>>
>>
>> for completeness the version of R I am using
>>
>>> version
>>               _
>> platform       x86_64-unknown-linux-gnu
>> arch           x86_64
>> os             linux-gnu
>> system         x86_64, linux-gnu
>> status
>> major          3
>> minor          2.1
>> year           2015
>> month          06
>> day            18
>> svn rev        68531
>> language       R
>> version.string R version 3.2.1 (2015-06-18)
>> nickname       World-Famous Astronaut
>>
>> compiled from source with configure options
>> head R-3.2.1/config.log
>> This file contains any messages produced by compilers while
>> running configure, to aid debugging if configure makes a mistake.
>>
>> It was created by R configure 3.2.1, which was
>> generated by GNU Autoconf 2.69.  Invocation command line was
>>
>>  $ ./configure --prefix /u/rmetzger/linux_R_vanilla --enable-R-shlib
>>
>> ## --------- ##
>> ## Platform. ##
>>
>> thank you!
>> Ryan
>
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