[Rcpp-devel] Sparse matrices with RcppArmadillo

[Romain Francois]

Thanks for the valuable information.

I will look into it more seriously at some point when I have some more 
time.

Romain

Le 09/12/12 14:40, c s a écrit :
> Hi Romain & Doug,
>
> Two points to note:
>
> (1)
> When poking around internal Armadillo pointers and arrays for sparse
> matrices, please take into account that the col_ptrs array is slightly
> longer than specified by the Compressed Sparse Column (CSC) format.
>
> However, this should not cause any problems when interfacing with
> external libraries. If you use the set_size() function before writing
> to the values[], row_indices[] and col_ptrs[] arrays, everything
> should be okay.
>
> The col_ptrs array is slightly longer in order to allow robust
> iterators.  Specifically, instead of the col_ptrs array having a size
> of ncols+1 (as specified by CSC), it has a size of ncols+2.  The extra
> element is always set to std::numeric_limits<uword>::max().  As such,
> be careful not to overwrite this magic number.
>
> For more details within the code, see the function
> SpMat<eT>::init(uword in_rows, uword in_cols), on line 3635 in
> "SpMat_meat.hpp".
>
> (2)
> If you need to allocate memory for the values[] and row_indices[]
> arrays, you need to use the memory::acquire_chunked() function.  This
> is an alternative memory allocation mechanism designed to reduce the
> burden of inserting or removing a non-zero element.  The rest of the
> sparse matrix memory management code relies on this.  See the code in
> file "memory.hpp" for more details.
>
>
> On Sun, Dec 9, 2012 at 5:55 AM, Romain Francois
> <romain at r-enthusiasts.com> wrote:
>> Yes. Conrad left a back door open so that we can add things **inside** the
>> SpMat template, similar to what we have done in dense matrix classes.
>>
>> Going from there I was looking at the copy constructor of a SpMat, which
>> eventually is a call to init:
>>
>> /**
>>   * Copy from another matrix.
>>   */
>> template<typename eT>
>> inline
>> void
>> SpMat<eT>::init(const SpMat<eT>& x)
>>    {
>>    arma_extra_debug_sigprint();
>>
>>    // Ensure we are not initializing to ourselves.
>>    if (this != &x)
>>      {
>>      init(x.n_rows, x.n_cols);
>>
>>      // values and row_indices may not be null.
>>      if (values != NULL)
>>        {
>>        memory::release(values);
>>        memory::release(row_indices);
>>        }
>>
>>      access::rw(values)      = memory::acquire_chunked<eT> (x.n_nonzero + 1);
>>      access::rw(row_indices) = memory::acquire_chunked<uword>(x.n_nonzero +
>> 1);
>>
>>      // Now copy over the elements.
>>      arrayops::copy(access::rwp(values),      x.values,      x.n_nonzero +
>> 1);
>>      arrayops::copy(access::rwp(row_indices), x.row_indices, x.n_nonzero +
>> 1);
>>      arrayops::copy(access::rwp(col_ptrs),    x.col_ptrs,    x.n_cols + 1);
>>
>>      access::rw(n_nonzero) = x.n_nonzero;
>>      }
>>    }
>>
>> So it all looks very doable.
>>
>> Romain
>


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