[R] how to pass matrices from C to R effectively

[Hao Cen]

Hi Duncan,

Thanks for your reply. I am not sure what you meant by "tell your C
function to use the memory that R sent to it". What R can pass to C is a
pointer to an array and the array size, assuming we are taking about the
.C mechanism. Did you mean my C function takes that array pointer and
generate the required matrix along the length of the array? If this is not
what you meant, would you please give me a small example?



Jeff



On Thu, November 12, 2009 6:53 pm, Duncan Murdoch wrote:
> On 12/11/2009 6:45 PM, Hao Cen wrote:
>
>> Hi,
>>
>>
>> I have C code to produce a lot of matrices to be analyzed. As these
>> matrices are large (> 1000*10000) and are a lot (> 1000), I am thinking
>> about how to pass them from C to R effectively.
>>
>> Would you think about the following solution? In R, I create a wrapper
>> function
>>
>> passDataFromCToR = function(row, col) { mat = matrix(0, row, col)
>> .C("passDataFromCToR",mat)[[1]]
>>
>
> That .C call doesn't match the header of the function below:  you didn't
> pass row and col.
>
>> }
>>
>>
>> It wraps the following C function
>> void passDataFromCToR (double *m, int *row, int* col){ mymat = f() // my
>> c function to produce a matrix // then I copy mymat to m element by
>> element via a loop
>>
>> }
>>
>>
>> Then to use these functions, I would write in R
>> mat = passDataFromCToR(1000, 10000)
>>
>> Two issues with this approach are that 1) I have to copy the data once
>> and 2)to the worse, in R I have to know the dimension of the matrices to
>> be passed from C. This information is not always available.
>
> Why would you have to copy the data?  Just tell your C function to use
> the memory that R sent to it, instead of copying entries into it.  (R may
> be doing a copy when you extract the results, though.)
>
> If your C code can't use memory provided to it, then there are no simple
> ways to avoid copying.  The complicated way is to use the .Call interface
> instead of .C.  There are examples in Writing R Extensions. They *will*
> require modifications to your code if it can't take a pointer to the
> memory to use.
>
> For the question of the dimensions being unknown in advance:  Just write
> two functions.  The first does the calculations up to the point where it
> needs the memory, the second works on an appropriately sized array, that
> your R code allocated based on the first result.  Or use the .Call()
> interface.
>
> Duncan Murdoch
>
>
>>
>> I would appreciate if you share with me your thoughts on how to solve
>> this problem better.
>>
>> thanks
>>
>> Jeff
>>
>>
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>
>
>