multiple definition of `THREAD_NUM' during compilation

[maxdudek]

Hi,

After running make I got the following output and error:

gcc -fopenmp -DNDEBUG -D_FORTIFY_SOURCE=2 -O2  -c -o src/esthmm.o src/esthmm.c
gcc -fopenmp -DNDEBUG -D_FORTIFY_SOURCE=2 -O2  -c -o src/BaumWelch.o src/BaumWelch.c
gcc -fopenmp -DNDEBUG -D_FORTIFY_SOURCE=2 -O2  -c -o src/nrutil.o src/nrutil.c
gcc -fopenmp -DNDEBUG -D_FORTIFY_SOURCE=2 -O2  -c -o src/hmmutils.o src/hmmutils.c
gcc -fopenmp -DNDEBUG -D_FORTIFY_SOURCE=2 -O2  -c -o src/emutils.o src/emutils.c
gcc -fopenmp -DNDEBUG -D_FORTIFY_SOURCE=2 -O2  -c -o src/logmath.o src/logmath.c
gcc -fopenmp -DNDEBUG -D_FORTIFY_SOURCE=2 -O2  -c -o src/fwd_bwd.o src/fwd_bwd.c
gcc -fopenmp -DNDEBUG -D_FORTIFY_SOURCE=2 -O2  -c -o src/viterbi.o src/viterbi.c
gcc -fopenmp -DNDEBUG -D_FORTIFY_SOURCE=2 -O2  -c -o src/fileutils.o src/fileutils.c
gcc -fopenmp -fcommon -lgsl -lgslcblas -o TRACE src/esthmm.o src/nrutil.o \
    src/emutils.o src/hmmutils.o src/logmath.o src/fwd_bwd.o \
    src/BaumWelch.o src/viterbi.o src/fileutils.o -lm
/cm/shared/easybuild/software/binutils/2.38-GCCcore-11.3.0/bin/ld: src/nrutil.o:(.bss+0x0): multiple definition of `THREAD_NUM'; src/esthmm.o:(.bss+0x0): first defined here
/cm/shared/easybuild/software/binutils/2.38-GCCcore-11.3.0/bin/ld: src/nrutil.o:(.bss+0x4): multiple definition of `MAXITERATION'; src/esthmm.o:(.bss+0x4): first defined here
/cm/shared/easybuild/software/binutils/2.38-GCCcore-11.3.0/bin/ld: src/emutils.o:(.bss+0x0): multiple definition of `THREAD_NUM'; src/esthmm.o:(.bss+0x0): first defined here
/cm/shared/easybuild/software/binutils/2.38-GCCcore-11.3.0/bin/ld: src/emutils.o:(.bss+0x4): multiple definition of `MAXITERATION'; src/esthmm.o:(.bss+0x4): first defined here
/cm/shared/easybuild/software/binutils/2.38-GCCcore-11.3.0/bin/ld: src/hmmutils.o:(.bss+0x0): multiple definition of `THREAD_NUM'; src/esthmm.o:(.bss+0x0): first defined here
/cm/shared/easybuild/software/binutils/2.38-GCCcore-11.3.0/bin/ld: src/hmmutils.o:(.bss+0x4): multiple definition of `MAXITERATION'; src/esthmm.o:(.bss+0x4): first defined here
/cm/shared/easybuild/software/binutils/2.38-GCCcore-11.3.0/bin/ld: src/logmath.o:(.bss+0x0): multiple definition of `THREAD_NUM'; src/esthmm.o:(.bss+0x0): first defined here
/cm/shared/easybuild/software/binutils/2.38-GCCcore-11.3.0/bin/ld: src/logmath.o:(.bss+0x4): multiple definition of `MAXITERATION'; src/esthmm.o:(.bss+0x4): first defined here
/cm/shared/easybuild/software/binutils/2.38-GCCcore-11.3.0/bin/ld: src/fwd_bwd.o:(.bss+0x0): multiple definition of `THREAD_NUM'; src/esthmm.o:(.bss+0x0): first defined here
/cm/shared/easybuild/software/binutils/2.38-GCCcore-11.3.0/bin/ld: src/fwd_bwd.o:(.bss+0x4): multiple definition of `MAXITERATION'; src/esthmm.o:(.bss+0x4): first defined here
/cm/shared/easybuild/software/binutils/2.38-GCCcore-11.3.0/bin/ld: src/BaumWelch.o:(.bss+0x0): multiple definition of `THREAD_NUM'; src/esthmm.o:(.bss+0x0): first defined here
/cm/shared/easybuild/software/binutils/2.38-GCCcore-11.3.0/bin/ld: src/BaumWelch.o:(.bss+0x4): multiple definition of `MAXITERATION'; src/esthmm.o:(.bss+0x4): first defined here
/cm/shared/easybuild/software/binutils/2.38-GCCcore-11.3.0/bin/ld: src/viterbi.o:(.bss+0x0): multiple definition of `THREAD_NUM'; src/esthmm.o:(.bss+0x0): first defined here
/cm/shared/easybuild/software/binutils/2.38-GCCcore-11.3.0/bin/ld: src/viterbi.o:(.bss+0x4): multiple definition of `MAXITERATION'; src/esthmm.o:(.bss+0x4): first defined here
/cm/shared/easybuild/software/binutils/2.38-GCCcore-11.3.0/bin/ld: src/fileutils.o:(.bss+0x0): multiple definition of `THREAD_NUM'; src/esthmm.o:(.bss+0x0): first defined here
/cm/shared/easybuild/software/binutils/2.38-GCCcore-11.3.0/bin/ld: src/fileutils.o:(.bss+0x4): multiple definition of `MAXITERATION'; src/esthmm.o:(.bss+0x4): first defined here
collect2: error: ld returned 1 exit status
make: *** [Makefile:14: TRACE] Error 1

After troubleshooting and following this advice I added -fcommon to CFLAGS in the Makefile and that fixed it. Not sure if that will cause other problems down the road but I thought I'd post here in case anyone else has the same problem.

[marinafloresp]

I followed this advice and it didn't work at first, but after I ran make clean and then make again it worked. In case someone else faces this issue.