My question is based on a project I have partially done, but there is still
something I'm not clear.
My goal is to create a R package contains GPU functions (some are from Nividia
cuda library, some are my self-defined CUDA functions)
My design is quite different from current R's GPU package, I want to create a R
object (external pointer) point to GPU address, and run my GPU function direct
on GPU side without transferring forth and back between CPU and GPU.
I used the R external pointer to implement my design. But I found I have memory
leak problems on GPU side, I can still fix it by running gc() function
explicitly in R side, but I'm just wondering if I missed something in my C
code. Would you please indicate my mistake, because this is my first time write
a R package, and I could possibly made some terrible mistakes.
actually, I have wrote bunch of GPU functions which can run on GPU side with
the object created by following create function, but the memory leak kills me
if I need to deal with some huge dataset.
Here is my create function, I create a gpu pointer x, and allocate GPU memory
for x, then make a R external pointer ext based on x, and copy the cpu vector
input to my gpu external pointer ext,
/*
define function to create a vector in GPU
by transferring a R's vector to GPU.
input is R's vector and its length,
output is a R external pointer
pointing to GPU vector(device)
*/
SEXP createGPU(SEXP input, SEXP n)
{
int *lenth = INTEGER(n);
PROTECT (input = AS_NUMERIC (input));
double * temp;
temp = REAL(input);
double *x; ##here is the step which causes the memory leak
cudacall(cudaMalloc((void**)&x, *lenth * sizeof(double)));
//protect the R external pointer from finalizer
SEXP ext = PROTECT(R_MakeExternalPtr(x, R_NilValue, R_NilValue));
R_RegisterCFinalizerEx(ext, _finalizer, TRUE);
//copying CPU to GPU
cublascall(cublasSetVector(*lenth, sizeof(double), temp, 1,
R_ExternalPtrAddr(ext), 1));
UNPROTECT(2);
return ext;
}
here is my finalized for my create function,
/*
define finalizer for R external pointer
input is R external pointer, function will finalize the pointer
when it is not in use.
*/
static void _finalizer(SEXP ext)
{
if (!R_ExternalPtrAddr(ext))
return;
double * ptr= (double *) R_ExternalPtrAddr(ext);
Rprintf("finalizer invoked once \n");
cudacall(cudaFree(ptr));
R_ClearExternalPtr(ext);
}
My create function can run smoothly, but if I run the create function too many
times, it shows out of memory for my GPU device, which clearly implies memory
leak problem. Can anybody help? Help alot in advance!
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