Error while building R from source with gcc OpenMP support - r

Question

I am trying to compile R in a Redhat linux environment on a HPC cluster. I have used environment modules to install recent versions of a number of tools including GCC 5.2.0. I cannot get R to build from the source. It fails with undefined reference to `GOMP_parallel'. When I compile with the --disable-openmp option it compiles fine.
array.o: In function `do_colsum':
array.c:(.text+0x5829): undefined reference to `GOMP_parallel'
collect2: error: ld returned 1 exit status
make[3]: *** [R.bin] Error 1
make[3]: Leaving directory `/scratch/kokul/240763.hpc5/R- 3.2.3/src/main'
make[2]: *** [R] Error 2
make[2]: Leaving directory `/scratch/kokul/240763.hpc5/R- 3.2.3/src/main'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/scratch/kokul/240763.hpc5/R-3.2.3/src'
make: *** [R] Error 1
A couple of questions
What are the advantages of having openMP enabled, I am assuming this will enhance the performance?
How do I fix the error I encounter while building? Is this related to linking the correct library? -fopenmp is correctly used while building. libgomp.* files are also in the $LIBRARY_PATH and $LD_LIBRARY_PATH.
It might be a simple thing I am missing, but I have tried to search for a proper answer without success.
Advanced thanks for any help.

Answer 1

I am having the same problem:
gcc -Wl,--export-dynamic -fopenmp -L/usr/local/lib -o R.bin Rmain.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o ls ../unix/*.o ../appl/*.o ../nmath/*.o ../extra/tre/libtre.a -L../../lib -lRblas -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -lgfortran -lm -lquadmath -lreadline -lpcre -llzma -lbz2 -lz -lrt -ldl -lm
array.o: In function do_colsum':
/home/myaccount/Downloads/R-patched/src/main/array.c:1437: undefined reference toGOMP_parallel'
collect2: error: ld returned 1 exit status
Makefile:144: recipe for target 'R.bin' failed
This is a configuration problem from R (autotools problem). My computer has both gcc 4.8 (came with OS) and the latest version gcc 5.2 (I build from source). The gcc 5.2 is located in /usr/local
I saw that R is mixing these two up, and not picking up the 5.2 library locations.
I changed the Makefile (this is only one time fix since the make file is generated by the autotool).
First go to src/main directory. Then edit the Makefile:
143 $(R_binary): $(R_bin_OBJECTS) $(R_bin_DEPENDENCIES)
144 $(MAIN_LINK) -o $# $(R_bin_OBJECTS) $(R_bin_LDADD)
Edite line 144:
144 $(MAIN_LINK) -o $# $(R_bin_OBJECTS) -L/usr/local/lib64 -lgomp $(R_bin_LDADD)
This fixed my problem. I had a hard time filing a bug with the R project. If the R developers saw this, could they fix this at the auto configure level? The auto probing just have to be a little bit smarter.