[Rcpp-devel] Conversion of Rcpp::Vector Rcpp::List and Rcpp::Matrix to std objects - OpenMP

[Asis Hallab]

Dear Dirk, Simon and Rcpp Experts.

This is a message following up the thread about using OpenMP
directives with Rcpp to construct probability matrices in parallel.

I followed Dirk's hint and implemented the parallel matrix generation
using just C++'s STL and the "#pragma omp parallel for" for the loop
of the heaviest work load in each iteration, that is the generation of
a matrix.

Good news: The code compiles and runs without errors.

Bad news: Even though the conversion of a large RcppList and its
contained NumericMatrix objects does only take less then half a
second, the parallel code with 10 cores runs approximately 10 times
slower than the serial pure Rcpp implementation.

Serial implementation
 user  system elapsed
  9.657   0.100   9.785

Parallel implementation on 10 cores
   user  system elapsed
443.095  26.437 100.132

Parallel implementation on 20 cores
   user  system elapsed
719.173  35.418  85.663

Again: I measured the time required to convert the Rcpp objects and
this is only half a second.
Back conversion I did not even implement yet, I just wrap the
resulting std::map< std string, std::vector< std::vector<double> >.

Does anyone have an idea what is going on?

The code can be reviewed on github:
https://github.com/asishallab/PhyloFun_Rccp/blob/OpenMP

You'll find very short installation and test run instructions in the
README.textile.

Kind regards and all the best!