I am struggling to use OpenMP with R and data.table on an M2 Mac Running macOS Ventura 13.3.1. I am following the instructions at https://mac.r-project.org/openmp/. Any help would be greatly appreciated.
In summary:
~.R/Makevars in line with the instructions~.R/Makevars is loading in RI believe that I have successfully installed OpenMP in line with the instructions as suggested by the following output:
file.exists(
"/usr/local/lib/libomp.dylib",
"/usr/local/include/ompt.h",
"/usr/local/include/omp.h",
"/usr/local/include/omp-tools.h"
)
# TRUE TRUE TRUE TRUE
When I try to compile the following openmp_test.c
#include <stdio.h>
#include <omp.h>
int main() {
#pragma omp parallel
{
int thread_id = omp_get_thread_num();
printf("Hello from thread %d\n", thread_id);
}
return 0;
}
with clang -Xclang -fopenmp -lomp openmp_test.c -o openmp_test
I can run the program with ./openmp_test and get the output
Hello from thread 2
Hello from thread 0
Hello from thread 3
Hello from thread 8
Hello from thread 1
Hello from thread 4
Hello from thread 11
Hello from thread 7
Hello from thread 10
Hello from thread 6
Hello from thread 9
Hello from thread 5
readLines("~/.R/Makevars")
# [1] "CPPFLAGS += -Xclang -fopenmp"
# [2] "LDFLAGS += -lomp"
# [3] "TEST = test1234"
~.R/Makevars is loading in RI'm not sure exactly how ~.R/Makevars works, but it doesn't seem that these environment variables are loading in R:
Sys.getenv("CPPFLAGS")
# [1] ""
Sys.getenv("LDFLAGS")
# [1] ""
Sys.getenv("TEST")
# [1] ""
In shell,
ls -al ~/.R/Makevars
# -rw------- 1 chandler 62 May 31 07:08 /Users/chandler/.R/Makevars
I have also, tried to change the permissions of the file
chmod 600 ~/.R/Makevars
And I've tried to update my .Renviron to
R_MAKEVARS_USER=~/.R/Makevars
Now
Sys.getenv("R_MAKEVARS_USER")
# [1] "~/.R/Makevars"
I am not sure of the expected output, but none of these approaches seem to be solving the issue.
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Denver
tzcode source: internal
attached base packages:
[1] stats graphics grDevices
[4] utils datasets methods
[7] base
loaded via a namespace (and not attached):
[1] compiler_4.3.0
I ended up following the instructions here and was able to get data.table working with OpenMP:
https://github.com/Rdatatable/data.table/issues/5419#issuecomment-1465023581
For the data.table installation, my ~/.R/Makevars file looked liked this:
LDFLAGS += -L/opt/homebrew/opt/libomp/lib -lomp
CPPFLAGS += -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp
To get other packages working with OpenMP, I installed the GNU Fortran compiler as suggested here: https://mac.r-project.org/tools/
To install the fst package, I first had to uncomment out the CPPFLAGS line in ~/.R/Makevars and add the lines for fst here.
So, my ~/.R/Makevars looked like this:
LDFLAGS += -L/opt/homebrew/opt/libomp/lib -lomp
## CPPFLAGS += -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp
CXX1X=/opt/homebrew/Cellar/gcc/13.1.0/bin/g++-13 -fopenmp
CXX98=/opt/homebrew/Cellar/gcc/13.1.0/bin/g++-13 -fopenmp
CXX11=/opt/homebrew/Cellar/gcc/13.1.0/bin/g++-13 -fopenmp
CXX14=/opt/homebrew/Cellar/gcc/13.1.0/bin/g++-13 -fopenmp
CXX17=/opt/homebrew/Cellar/gcc/13.1.0/bin/g++-13 -fopenmp
I then installed the fst package by invoking R in the terminal and using install.packages("fstcore", type="source") and `install.packages("fst", type="source").
I similarly installed the fixest package: install.packages("fixest", type="source")
I removed the comment in front CPPFLAGS, so my final ~/.R/Makevars looks like this:
LDFLAGS += -L/opt/homebrew/opt/libomp/lib -lomp
CPPFLAGS += -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp
CXX1X=/opt/homebrew/Cellar/gcc/13.1.0/bin/g++-13 -fopenmp
CXX98=/opt/homebrew/Cellar/gcc/13.1.0/bin/g++-13 -fopenmp
CXX11=/opt/homebrew/Cellar/gcc/13.1.0/bin/g++-13 -fopenmp
CXX14=/opt/homebrew/Cellar/gcc/13.1.0/bin/g++-13 -fopenmp
CXX17=/opt/homebrew/Cellar/gcc/13.1.0/bin/g++-13 -fopenmp
In the end, everything seems to work:
library(data.table); library(fst); library(fixest);
data.table::getDTthreads()
# [1] 6
fst::threads_fst()
# [1] 12
fixest::getFixest_nthreads()
# [1] 6
So, for me, in ~/.R/Makevars, the line
CPPFLAGS += -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp
is necessary to install data.table but needs to commented out to install other packages that also rely on OpenMP
I re-installed these packages. I first installed data.table using install.packages("data.table", type=source) with the following ~.R/Makevars:
LDFLAGS += -L/opt/homebrew/opt/libomp/lib -lomp
CPPFLAGS += -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp
I then updated my ~./Makevars to the following:
LDFLAGS += -L/opt/homebrew/opt/libomp/lib -lomp
CPPFLAGS += -I/opt/homebrew/opt/libomp/include -Xclang -fopenmp
CXX1X=/opt/homebrew/Cellar/gcc/14.2.0/bin/g++-14 -fopenmp
CXX98=/opt/homebrew/Cellar/gcc/14.2.0/bin/g++-14 -fopenmp
CXX11=/opt/homebrew/Cellar/gcc/14.2.0/bin/g++-14 -fopenmp
CXX14=/opt/homebrew/Cellar/gcc/14.2.0/bin/g++-14 -fopenmp
CXX17=/opt/homebrew/Cellar/gcc/14.2.0/bin/g++-14 -fopenmp
I then installed install.packages("fstcore", type="source"), install.packages("fst", type="source"), and install.packages("fixest", type="source").