[Rcpp-devel] Pointer troubles
Sebastian Weber
sebastian.weber at frias.uni-freiburg.de
Wed Aug 3 17:13:19 CEST 2011
Hi!
Reading this thread, I hit on some questions which would help me understand Rcpp a lot better.
> We have the Rcpp::XPtr template class that is parameterized by the class of the pointer, the XPtr object acts as a smart pointer, so can be passed down to whatever C++ function that needs a pointer. It also adds the necessary wrapping so that you can pass the object back to R as an external pointer.
Hmm, I understand that XPtr is always a "strong" pointer in the sense that XPtr will delete the object once it gets out of scope. Is that right? If so, how can I get a weak pointer? I.e. tell XPtr to never call a finalizer at all since the ownership is handled at a different spot in my code.
Moreover, I saw that basically the whole class_-declaration mechanism boils down to stuff things into XPtr, right? So on the C++ side one has actually pointers to wrapped classes which are held by XPtr. How can I now obtain these pointers and what is the type of the wrapped classes? The problem is that I have to deal with a wrapped class A, but might also fool around with A* in my code...
Cheers,
Sebastian
>
> With the XPtr class, you would write your code something like this:
>
> SEXP getIntPointer(){
> int *test = new int; *test = 6;
>
> XPtr<int> retVal(test) ;
> return retVal ;
> }
>
> SEXP doubleIntPointer(SEXP test){
> XPtr<int> test2(test) ;
> return wrap( *test2 * 2 ) ;
> }
>
> You don't need intObjFinalizer because this is the same as the default finalizer that is shipped for free with XPtr:
>
> template <typename T>
> void standard_delete_finalizer(T* obj){
> delete obj ;
> }
>
> template <typename T, void Finalizer(T*) >
> void finalizer_wrapper(SEXP p){
> if( TYPEOF(p) == EXTPTRSXP ){
> T* ptr = (T*) R_ExternalPtrAddr(p) ;
> Finalizer(ptr) ;
> }
> }
>
>
> You don't need int2SEXP because the XPtr constructor deals with it.
>
> You don't need the SEXP2int because the XPtr dereferences itself to the actual underlying pointer class.
>
> HTH,
>
> Romain
>
> Le 03/08/11 12:13, Willem Ligtenberg a écrit :
>> Hi Dirk and list,
>>
>> Indeed it might have been a bit too complicated.
>> I think I have another example, which explains my troubles without
>> requiring OpenCL.
>> In this case, I want to return a pointer to an integer value to R and
>> the double the integer value in another function.
>> (I know this is stupid to do, but it is a toy example)
>>
>> // Stuff to expose the int to R
>> static void intObjFinalizer(SEXP ref){
>> if(TYPEOF(ref) == EXTPTRSXP){
>> int *o = static_cast<int*> (R_ExternalPtrAddr(ref));
>> if (o) delete o;
>> }
>> }
>>
>> SEXP int2EXP(int *o){
>> SEXP xp = R_MakeExternalPtr(o, R_NilValue, R_NilValue);
>> R_RegisterCFinalizerEx(xp, intObjFinalizer, TRUE);
>> return xp;
>> }
>>
>> int *SEXP2int(SEXP o){
>> if(TYPEOF(o) != EXTPTRSXP)
>> Rf_error("invalid object");
>> return (int*) R_ExternalPtrAddr(o);
>> }
>>
>> SEXP getIntPointer(){
>> int test = 6;
>> SEXP retVal = int2EXP(&test);
>> std::cout<< test<< "\n";
>> int test2 = *SEXP2int(retVal);
>> std::cout<< test2<< "\n";
>> return retVal;
>> }
>>
>> SEXP doubleIntPointer(SEXP test){
>> int test2 = *SEXP2int(test);
>> std::cout<< test2;
>> return Rcpp::wrap(test2*2);
>> }
>>
>> By the way, I use a module to expose these functions:
>>
>> RCPP_MODULE(ropencl){
>> using namespace Rcpp ;
>> function( "getIntPointer" ,&getIntPointer , "getIntPointer" ) ;
>> function( "doubleIntPointer" ,&doubleIntPointer , "doubleIntPointer" ) ;
>> }
>>
>> When I now execute getIntPointer() from R, it seems to work fine, both
>> the initial integer and the value that I get back from
>> *SEXP2int(retVal); are 6. (Although when I exit R after only this call
>> I get the following: *** glibc detected *** /usr/lib64/R/bin/exec/R:
>> free(): invalid pointer: 0x00007fffd1a587cc ***)
>>
>> However, when I now use doubleIntPointer(getIntPointer()) in R, I get
>> some wrong result (a different value each time I restart R).
>>
>> Does this make it a bit more clear what I want to do, or the problems
>> that I am facing?
>>
>> Kind regards,
>>
>> Willem
>>
>> On Tue, Aug 2, 2011 at 15:24, Dirk Eddelbuettel<edd at debian.org> wrote:
>>>
>>> Hi Willem,
>>>
>>> Thanks a pretty long and complicated post. Could we possibly break it down
>>> into smaller pieces?
>>>
>>> On 2 August 2011 at 11:45, Willem Ligtenberg wrote:
>>> | Hi,
>>> |
>>> | I am trying to wrap around OpenCL.
>>> | But I am running into some problems when I try to return pointers to
>>> | R. Later I want to be able to use these pointers in other c functions.
>>> | As an example I have the following code:
>>> |
>>> | #include "createContext.h"
>>> | #include<CL/opencl.h>
>>> | #include<Rcpp.h>
>>> |
>>> | // Stuff to expose the cl_platform_id to R
>>> | static void cl_platform_idObjFinalizer(SEXP ref){
>>> | if(TYPEOF(ref) == EXTPTRSXP){
>>> | cl_platform_id *o = static_cast<cl_platform_id*> (R_ExternalPtrAddr(ref));
>>> | if (o) delete o;
>>> | }
>>> | }
>>> |
>>> | SEXP cl_platform_id2EXP(cl_platform_id *o){
>>> | SEXP xp = R_MakeExternalPtr(o, R_NilValue, R_NilValue);
>>> | R_RegisterCFinalizerEx(xp, cl_platform_idObjFinalizer, TRUE);
>>> | return xp;
>>> | }
>>> |
>>> | cl_platform_id *SEXP2cl_platform_id(SEXP o){
>>> | if(TYPEOF(o) != EXTPTRSXP)
>>> | Rf_error("invalid object");
>>> | return (cl_platform_id*) R_ExternalPtrAddr(o);
>>> | }
>>> |
>>> | This bit I have found posted on this mailing list earlier.
>>> | This is to expose a pointer to a cl_platform_id object in memory (and
>>> | this should also take care of the clean up).
>>> |
>>> | Now I have the following method to get a list of platform_ids:
>>> |
>>> | SEXP getPlatformIDs(){
>>> | //returns a list of platform ids
>>> | cl_uint num_platforms = 0;
>>> | clGetPlatformIDs(0, 0,&num_platforms);
>>> | std::vector<cl_platform_id> platforms(num_platforms);
>>> | clGetPlatformIDs(num_platforms, platforms.empty() ? NULL :
>>> |&platforms.front(),&num_platforms);
>>> | //for each platform in platforms add its pointer to the return list
>>> | Rcpp::List result(platforms.size());
>>> | for (int i=0; i<platforms.size(); i++){
>>> | cl_platform_id tempPlatformID = platforms[i];
>>> | result[i] = cl_platform_id2EXP(&tempPlatformID);
>>> | }
>>> | return result;
>>> | }
>>> |
>>> | And I want to get the name of the platform as follows:
>>> |
>>> | SEXP getPlatformName(SEXP sPlatformID){
>>> | char cBuffer[1024];
>>> | cl_platform_id platformID = *SEXP2cl_platform_id(sPlatformID);
>>> | clGetPlatformInfo (platformID, CL_PLATFORM_NAME, sizeof(cBuffer),
>>> | cBuffer, NULL);
>>> | Rcpp::CharacterVector ab(1);
>>> | ab[0] = cBuffer;
>>> | return ab;
>>>
>>> You could use wrap() on std::string or char* if you just want to return a
>>> single string. No need for a CharacterVector of size 1.
>>>
>>> | }
>>> |
>>> | The whole lot compiles, but gives a runtime error. When I try the
>>> | following in R:
>>> | library(ROpenCL)
>>> | platformIDs<- getPlatformIDs()
>>> | print(getPlatformName(platformIDs[[1]]))
>>> |
>>> | *** caught segfault ***
>>> | address 0x51, cause 'memory not mapped'
>>> |
>>> | Now when I put all this together in one method which just returns the
>>> | platform name, it works:
>>> |
>>> | SEXP getPlatformIDs2(){
>>> | //returns a list of platform ids
>>> | cl_uint num_platforms = 0;
>>> | clGetPlatformIDs(0, 0,&num_platforms);
>>> | std::vector<cl_platform_id> platforms(num_platforms);
>>> | clGetPlatformIDs(num_platforms, platforms.empty() ? NULL :
>>> |&platforms.front(),&num_platforms);
>>> | char cBuffer[1024];
>>> | clGetPlatformInfo (platforms[0], CL_PLATFORM_NAME,
>>> | sizeof(cBuffer), cBuffer, NULL);
>>> | Rcpp::CharacterVector ab(1);
>>> | ab[0] = cBuffer;
>>> | return ab;
>>> | }
>>> |
>>> | This results in:
>>> | getPlatformIDs2()
>>> | [1] "NVIDIA CUDA"
>>> |
>>> | Could someone check if I am taking the pointer to and from R in the correct way?
>>>
>>> I can't as I do not know the OpenCL API.
>>>
>>> One thought is that maybe you do not you really need external pointers as you
>>> are just copying IDs around. Can you simplify what you are trying to do?
>>>
>>> Cheers, Dirk
>>>
>>> --
>>> Gauss once played himself in a zero-sum game and won $50.
>>> -- #11 at http://www.gaussfacts.com
>>>
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>
>
> --
> Romain Francois
> Professional R Enthusiast
> +33(0) 6 28 91 30 30
> http://romainfrancois.blog.free.fr
> http://romain-francois.com
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>
>
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--
Sebastian Weber
Group of Cell Communication and Control
Freiburg Institute for Advanced Studies - FRIAS
School of Life Sciences - LIFENET
Albert-Ludwigs-Universität Freiburg
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79104 Freiburg
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