[R] R crashing after successfully running compiled code
William Dunlap
wdunlap at tibco.com
Wed Oct 31 17:04:04 CET 2012
As long as you use C (or C++ or Fortran ...), using memory that
you don't own is possible. This is one reason people use languages
like R.
(If you program microprocessors or write operating system code
then C's willingness to let you read or write any at address is essential.)
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf
> Of Adam Clark
> Sent: Wednesday, October 31, 2012 8:47 AM
> To: Adam Clark
> Cc: r-help at r-project.org; Prof Brian Ripley
> Subject: Re: [R] R crashing after successfully running compiled code
>
> Aha - got it.
>
> My problem was that I had a pointer (*Aest) that had less memory allocated
> to it than I ended up storing in it (e.g. I had *Aest = 1:100, but stored
> into it values at positions 5:105). With that fixed, all works flawlessly.
>
> Thanks a lot for the help. What I hadn't realized was that .C allowed you
> to exceed memory allocations - I'd have assumed that it would just crash
> while I was running the function as soon as it ran out of space. Instead, I
> guess it must have been writing beyond the space allocated for *Aest, and
> not running into any trouble until R tried to store something else in the
> same spot later (e.g. while plotting a figure).
>
> It was immensely helpful to hear from you all that the function could still
> have a bug, even if it ran successfully. As I understand it, the way
> ".Call" passes variables, this sort of a mistake would not be possible. Is
> this true? I'm tempted to learn the new syntax, but I also like how ".C"
> allows me to keep things looking more or less like normal C code.
>
> Adam
>
> PS - As you mention, Prof. Ripley, I am insane for trying to do this
> without a good debugger. Also, as you point out, valgrind doesn't run on
> Cygwin. If you know of any useful PC debuggers, I'd be most grateful - but
> if all else fails for debugging, I can just run Ubuntu in an Oracle
> VirtualBox.
>
> On Wed, Oct 31, 2012 at 9:38 AM, Adam Clark <atclark at umn.edu> wrote:
>
> > Thanks for the advice.
> >
> > I'll go ahead and dig through my C code. It's helpful to know that my C
> > code can cause R to crash AFTER successfully implementing the code.
> >
> > I have made sure to account for C's vector indexing, and I think I'm
> > allocating my C memory, and passing information back and forth between C
> > and R, as I should. I'm including my input/output stuff below.
> >
> > I tried including options(CBoundsCheck=TRUE) in the script both before
> > and after loading the C function, which doesn't seem to do much. To get it
> > to work, do I actually need to go into the R configuration file and edit
> > the default?
> >
> > It would be exceedingly helpful if anybody could give me tips on where I'm
> > misusing pointers in the example below. That said, I certainly don't expect
> > the R community to debug my C code for me. If I come up with a solution,
> > I'll email it out over the list.
> >
> > In R, I run the script:
> > dyn.load("mycfun.dll")
> > set.seed(1031)
> > A<-1:100
> > B<-runif(100)
> > myfunC<-function(A, B, M, N) {
> > result<-as.double(rep(0, (length(A)- N -(M+1))))
> > plengtht<-as.integer(length(A))
> > Aest<-as.numeric(rep(0, (length(A)- N -(M+1))))
> > distances<-as.numeric(rep(0, length(A)))
> > neighbors<-as.integer(rep(0, (M+1)))
> > u<-as.numeric(rep(0, (M+1)))
> > w<-as.numeric(rep(0, (M+1)))
> > return(.C("mycfun", as.double(A), as.double(B), as.integer(M),
> > as.integer(N),
> > result=as.double(result), as.integer(plengtht), as.double(Aest),
> > as.double(distances),
> > as.integer(neighbors), as.double(u), as.double(w))$result)
> > }
> >
> > fun_result<-myfunC(A,B,3,1)
> >
> >
> > This corresponds to the C code (input output only):
> > #include <R.h>
> > #include <Rmath.h>
> > void mycfun(double *A, double *B, int *pM, int *pN, double *result, int
> > *plengtht,
> > double *Aest, double *distances, int *neighbors, double *u, double *w) {
> > int t, i, j, n, from, to, nneigh;
> > double distsv, sumu, sumaest, corout;
> > int M = *pM;
> > int N = *pN;
> > int lengtht= *plengtht;
> > n=0;
> >
> > ##### running various loops over variables #####
> >
> > result[n]=corout;
> > n=n+1;
> > }
> >
> >
> > ##### END #####
> >
> > I also have two sub-functions that manipulate "neighbors" and "distances"
> > - I can send the i/o for those as well, but they seem much more
> > straightforward, since I don't need to pass all my arguments as pointers. I
> > pass the pointers to internal variables at the beginning because I couldn't
> > index any C arrays using *pM or *pN.
> >
> >
> > Many thanks,
> > Adam
> >
> >
> >
> > On Wed, Oct 31, 2012 at 7:12 AM, Prof Brian Ripley <ripley at stats.ox.ac.uk>wrote:
> >
> >> On Wed, 31 Oct 2012, Duncan Murdoch wrote:
> >>
> >> On 12-10-30 11:13 PM, Adam Clark wrote:
> >>>
> >>>> I'm running R 2.15.1x64, though the same problem persists for 2.13.0x32
> >>>> and
> >>>> 2.13.0x64.
> >>>>
> >>>> I am trying to run compiled C code using the .C convention. The
> >>>> code compiles without problems, dynamically loads within the R
> >>>> workspace with no problems, and even runs and gives correct results with
> >>>> no problems.
> >>>>
> >>>> However, R will randomly crash within a few minutes of successfully
> >>>> using
> >>>> the compiled function.
> >>>>
> >>>> For example, if I run my compiled function using:
> >>>> dyn.load("mycfun.dll")
> >>>> answer<-.C("mycfun", parameters...), I get a completely sensible
> >>>> result that gets stored to "answer".
> >>>> However, if I try to do too many things to "answer", the R exits
> >>>> without warning.
> >>>> I've tried dyn.unload in hopes that R would become stable afterwards,
> >>>> but
> >>>> in this case using the function crashes R without fail.
> >>>>
> >>>> Usually, I can either plot, or view, or save "answer" to a file - but
> >>>> never
> >>>> take more than a single action before R exits. This does not appear to
> >>>> depend on how long R has been open. Initially, I thought it was a bug in
> >>>> the "inline" function, but I'm finding the same problem now that I'm
> >>>> using
> >>>> the dynamically loaded file directly. I'm used to R being insanely
> >>>> stable,
> >>>> and am somewhat mystified by this whole problem.
> >>>>
> >>>> My next move is to learn the ".Call" convention, as I suspect that
> >>>> my problem is related to my "C" function using memory that R doesn't
> >>>> know is used. But - before I invest a while lot more time on this, I'd
> >>>> like to know whether anybody things this is likely to solve the problem.
> >>>> If not, I may just want to run my code entirely in C, and forget the
> >>>> R problem.
> >>>>
> >>>
> >>> I think your C code has a bug in it. The bug might go away when you
> >>> rewrite the function to work within the .Call convention, but it is
> >>> probably easier to find the bug and fix it with the current code.
> >>>
> >>> Things to look for:
> >>>
> >>> Are you fully allocating all arrays in R before passing them to C? The
> >>> C code receives a pointer and will happily write to it, whether that makes
> >>> sense or not.
> >>>
> >>> Are you careful with your limits on vectors? In R, a vector is indexed
> >>> from 1 to n, but the same vector in C is indexed from 0 to n-1. If the C
> >>> code writes to entry n, that will eventually cause problems.
> >>>
> >>
> >> Using R-devel and the following new feature
> >>
> >> * There is a new option, options(CBoundsCheck=), which controls how
> >> .C() and .Fortran() pass arguments to compiled code. If true
> >> (which can be enabled by setting the environment variable
> >> R_C_BOUNDS_CHECK to yes), raw, integer, double and complex
> >> arguments are always copied, and checked for writing off either
> >> end of the array on return from the compiled code (when a second
> >> copy is made). This also checks individual elements of character
> >> vectors passed to .C().
> >>
> >> This is not intended for routine use, but can be very helpful in
> >> finding segfaults in package code.
> >>
> >> makes checking these two points a lot easier.
> >>
> >>
> >> Are you allocating memory in your C code? There are several ways to do
> >>> that, depending on how you want it managed. If you do it one way and
> >>> expect it to be managed in a different way, you'll get problems.
> >>>
> >>
> >> If you can run your code under valgrind (see 'Writing R Extensions') you
> >> will usually get pointed to the exact cause. But that's for Linux, and
> >> with some care MacOS X.
> >>
> >> --
> >> Brian D. Ripley, ripley at stats.ox.ac.uk
> >> Professor of Applied Statistics,
> http://www.stats.ox.ac.uk/~**ripley/<http://www.stats.ox.ac.uk/~ripley/>
> >> University of Oxford, Tel: +44 1865 272861 (self)
> >> 1 South Parks Road, +44 1865 272866 (PA)
> >> Oxford OX1 3TG, UK Fax: +44 1865 272595
> >
> >
> >
> >
> > --
> > Adam Clark
> > University of Minnesota, EEB
> > 100 Ecology Building
> > 1987 Upper Buford Circle
> > St. Paul, MN 55108
> > (857)-544-6782
> >
>
>
>
> --
> Adam Clark
> University of Minnesota, EEB
> 100 Ecology Building
> 1987 Upper Buford Circle
> St. Paul, MN 55108
> (857)-544-6782
>
> [[alternative HTML version deleted]]
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