Hi all, Here is an R script that uses Armadillo to decompose a large matrix and print the first 10 eigenvalues.
library(RcppArmadillo) library(Rcpp) src <- r"(#include <RcppArmadillo.h> // [[Rcpp::depends(RcppArmadillo)]] // [[Rcpp::export]] arma::vec getEigenValues(arma::mat M) { return arma::eig_sym(M); })" size <- 10000 m <- matrix(rnorm(size^2), size, size) m <- m * t(m) # This line compiles the above code with the -fopenmp flag. sourceCpp(code = src, verbose = TRUE, rebuild = TRUE) result <- getEigenValues(m) print(result[1:10]) When I run this code on server A, I see that arma can implicitly leverage all available cores by running top -H. However, on server B it can only use one core despite multiple being available: there is just one process entry in top -H. Both processes successfully exit and return an answer. The process on server B is of course much slower. Here is the compilation on server A: /usr/local/lib/R/bin/R CMD SHLIB --preclean -o 'sourceCpp_2.so' 'file197c21cbec564.cpp' g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I../inst/include -fopenmp -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I"/tmp/RtmpwhGRi3/sourceCpp-x86_64-pc-linux-gnu-1.0.9" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c file197c21cbec564.cpp -o file197c21cbec564.o g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o sourceCpp_2.so file197c21cbec564.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR and here it is for server B: /sw/R/R-4.2.3/lib64/R/bin/R CMD SHLIB --preclean -o 'sourceCpp_2.so' 'file158165b9c4ae1.cpp' g++ -std=gnu++11 -I"/sw/R/R-4.2.3/lib64/R/include" -DNDEBUG -I../inst/include -fopenmp -I"/home/my_username/.R/library/Rcpp/include" -I"/home/ my_username/.R/library/RcppArmadillo/include" -I"/tmp/RtmpvfPt4l/sourceCpp-x86_64-pc-linux-gnu-1.0.10" -I/usr/local/include -fpic -g -O2 -c file158165b9c4ae1.cpp -o file158165b9c4ae1.o g++ -std=gnu++11 -shared -L/sw/R/R-4.2.3/lib64/R/lib -L/usr/local/lib64 -o sourceCpp_2.so file158165b9c4ae1.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/sw/R/R-4.2.3/lib64/R/lib -lR I thought that the -fopenmp flag should let arma implicitly parallelize matrix computations. Any hints as to why this may not work on server B? The actual code I'm running is an R package that includes RcppArmadillo and RcppEnsmallen. Server B is the login node to an hpc cluster, but the code does not use all cores on the compute nodes either. Best, Robin
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