CODEWITHSUNDEEP
ropenmp
StevenMurray
StevenMurray

Reputation: 752

Using openMP in fortran and R - where do I set -fopenmp?

I've read a bit from the Writing R Extensions manual but I can't quite figure this out - where do I put the -fopenmp flag in makevars? I can set

PKG_FCFLAGS = -fopenmp

which compiles fine. But I'm not sure if I should also be setting it for PKG_LIBS and PKG_CPPFLAGS ?

When I try for PKG_LIBS it gives me an error

i686-apple-darwin8-gfortran-4.2: libgomp.spec: No such file or directory

But if I just use it in PKG_FCFLAGS then even though it compiles fine, when I try to use the routine in R, it says

Error in dyn.load("correlate.so") : 
unable to load shared object '/Users/Steven/Documents/PhD/npsR/correlate.so':
dlopen(/Users/Steven/Documents/PhD/npsR/correlate.so, 6): Symbol not found: _GOMP_parallel_end
Referenced from: /Users/Steven/Documents/PhD/npsR/correlate.so
Expected in: dynamic lookup

So obviously the gomp library has not been linked correctly. Any ideas?

Cheers.

Upvotes: 1

Views: 1203

Answers (2)

StevenMurray
StevenMurray

Reputation: 752

So I have solved this issue (though I have opened up another can of worms now...). I'm not sure exactly what I did which solved the issue but I'll list what I did do here.

After finding that the fortran program itself would not compile and link with openMP (not counting in R at all) I figured it was something to do with the gfortran installation. So what I did was:

  • Uninstalled R
  • Uninstalled gfortran
  • Downloaded gcc and gfortran from http://r.research.att.com/tools/gcc-42-5666.3-darwin11.pkg
  • Installed the updated gcc+gfortran (gfortran v4.2.4)
  • Installed R 2.15.1
  • Set the line PATH = /usr/bin:$PATH in my .bash_profile
  • Set two lines in Makevars: PKG_FCFLAGS = -fopenmp and PKG_LIBS = -fopenmp. It seems both of these are necessary.

Then it worked! By the way, this is on OS X 10.7 (Lion).

Thanks for everyone's help.

Upvotes: 0

Spacedman
Spacedman

Reputation: 94307

Luke Tierney's pnmath package http://homepage.stat.uiowa.edu/~luke/R/experimental/ uses OpenMP and has the following in its Makevars:

PKG_CFLAGS=-fopenmp
PKG_LIBS=-lgomp

and Makevars.win:

PKG_CFLAGS=-fopenmp
PKG_LIBS=-mthreads -lgomp -lpthreadGC2

You seem to be on a Mac so maybe neither work. But setting PKG_LIBS=-lgomp looks critical.

Upvotes: 3

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