Heads up: I posted this question on Stackoverflow yesterday (http://stackoverflow.com/questions/26484103/using-a-custom-memory-allocation-function-in-r). So far I haven’t gotten a response and I thought this could be an even better place to ask such a question.
I would like to be able to use my own memory allocation function for certain data structures (real valued vectors and arrays) in R. The reason for this is that I need my data to be 64bit aligned and I would like to use the numa library for having control over which memory node is used (I'm working on compute nodes with four 12-core AMD Opteron 6174 CPUs). Now I have two functions for allocating and freeing memory: numa_alloc_onnode and numa_free(courtesy of http://stackoverflow.com/questions/8154162/numa-aware-cache-aligned-memory-allocation). I'm using R version 3.1.1, so I have access to the function allocVector3(src/main/memory.c), which seems to me as the intended way of adding a custom memory allocator. I also found the struct R_allocator in src/include/R_ext However it is not clear to me how to put these pieces together. Let's say, in R, I want the result res of an evaluation such as res <- Y - mean(Y) to be saved in a memory area allocated with my own function, how would I do this? Can I integrate allocVector3 directly at the R level? I assume I have to go through the R-C interface. As far as I know, I cannot just return a pointer to the allocated area, but have to pass the result as an argument. So in R I call something like n <- length(Y) res <- numeric(length=1) .Call("R_allocate_using_myalloc", n, res) res <- Y - mean(Y) and in C #include <R.h> #include <Rinternals.h> #include <numa.h> SEXP R_allocate_using_myalloc(SEXP R_n, SEXP R_res){ PROTECT(R_n = coerceVector(R_n, INTSXP)); PROTECT(R_res = coerceVector(R_res, REALSXP)); int *restrict n = INTEGER(R_n); R_allocator_t myAllocator; myAllocator.mem_alloc = numa_alloc_onnode; myAllocator.mem_free = numa_free; myAllocator.res = NULL; myAllocator.data = ???; R_res = allocVector3(REALSXP, n, myAllocator); UNPROTECT(2); return R_res; } Unfortunately I cannot get beyond a variable has incomplete type 'R_allocator_t' compilation error (I had to remove the .data line since I have no clue as to what I should put there). Also the function signature for numa_alloc_onnode is (size_t size, int node). How do I pass the number of the memory node to the numa_alloc_onnode? Is that somehow done through the .data field? Does any of the above code make sense? Is there an easier way of achieving what I want to? It seems a bit odd to have to allocate a small vector in R and the change its location in memory in C just to be able to both control the memory allocation and have the vector available in R... I'm trying to avoid using Rcpp, as I'm modifying a fairly large package and do not want to convert all C calls and thought that mixing different C interfaces could perform sub-optimally. Any help is greatly appreciated. ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
