OpenBLAS routine used from R/Rcpp runs only on a single core in linux

Question

I am trying to run a QR decomposition (LAPACKE_dgeqrf) in R on a linux machine (CentOS) using a C++ program that is interfaced with Rcpp. Unfortunately, I see only 100% using top. This also happens on a Red Hat Enterprise Linux Server. However, the C++ program (with LAPACKE_dgeqrf) runs at nthreads * 100% when started from the terminal (independently outside of R). I compiled OpenBLAS with

NO_AFFINITY=1 

and tried

export OPENBLAS_NUM_THREADS=4
export GOTO_NUM_THREADS=4
export OMP_NUM_THREADS=4
export OPENBLAS_MAIN_FREE=1

Nothing works. Everything works fine on a Mac though. 'mcaffinity()' from the parallel R package returns NULL. I configured R using

configure  'CFLAGS=-g -O3 -Wall -pedantic' 'CXXFLAGS=-g -O3 -Wall -pedantic' 'FCFLAGS=-g -O3' 'F77FLAGS=-g -O3' '--with-system-zlib' '--enable-memory-profiling'

My C++ code:

#include <Rcpp.h>
#include <lapacke.h>
#include <cblas.h>

//[[Rcpp::export]]
Rcpp::NumericMatrix QRopenblas(Rcpp::NumericMatrix X)
{
    // Declare variables 
    int n_rows = X.nrow(), n_cols = X.ncol(), min_mn = std::min(n_rows, n_cols);
    Rcpp::NumericVector tau(min_mn);

    // Perform QR decomposition
    LAPACKE_dgeqrf(CblasColMajor, n_rows, n_cols, X.begin(), n_rows, tau.begin());

    return X;
}

My R code:

PKG_LIBS <- '/pathto/openblas/lib/libopenblas.a' 
PKG_CPPFLAGS <- '-I/pathto/openblas/include'
Sys.setenv(PKG_LIBS = PKG_LIBS , PKG_CPPFLAGS = PKG_CPPFLAGS) 
Rcpp::sourceCpp('/pathto/QRopenblas.cpp', rebuild = TRUE)

n_row <- 4000
n_col <- 4000
A <- matrix(rnorm(n_row * n_col), n_row, n_col)
res <- QRopenblas(A)

Answer 1

I found a solution by rebuilding R and configuring it using

../configure --enable-BLAS-shlib --enable-R-shlib --enable-memory-profiling --with-tcltk=no

Afterwards, I had to replace libRblas.so with the corresponding OpenBLAS file libopenblas.so. Btw, I build OpenBLAS with standard settings (i.e. with affinity). The R function qr() now uses all cores and the C++ programs as well. The reason why this works is that upon startup R is now launched with multiple threads (as verified with cat /proc/pid/status). Without replacing libRblas.so, R is launched with one thread and then upon calling OpenBLAS multiple threads are launched, which are properly pinned to the first core.