building SMuFin problems

[corleo]

Dear all,

I am encountering problems during the make.

mpic++ -o SMuFin main.cpp alphabet.o amino.o array8.o array.o direct.o genarray.o genhash.o gmem.o gs2k.o hash.o mathutil.o mystring.o parse.o seqgen.o stack.o stree.o trace.o util.o blind2.o deep2.o ds.o globals.o helped.o shallow.o getway_s asm bwa.a samtools.a -lz -lmpi -lgomp

/tmp/cctH5QXT.o: In function `process_det_mut_block(void*)':

main.cpp:(.text+0xe27): undefined reference to `gsuffixfilteraux(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, int> > >&, char*, unsigned long, char*, unsigned long, char*, unsigned long, std::vector<_SNV, std::allocator<_SNV> >*)'

blind2.o: In function `insert_suffix':

blind2.c:(.text+0x4f9): undefined reference to `new_node__blind_ssort'

blind2.c:(.text+0x5bd): undefined reference to `new_node__blind_ssort'

deep2.o: In function `qs_unrolled_lcp':

deep2.c:(.text+0x315): undefined reference to `cmp_unrolled_lcp'

deep2.c:(.text+0x3b9): undefined reference to `cmp_unrolled_lcp'

helped.o: In function `split_group':

helped.c:(.text+0x14c3): undefined reference to `vecswap2'

helped.c:(.text+0x1524): undefined reference to `vecswap2'

shallow.o: In function `shallow_mkq':

shallow.c:(.text+0x19c): undefined reference to `med3func'

shallow.c:(.text+0x1e2): undefined reference to `med3func'

shallow.c:(.text+0x227): undefined reference to `med3func'

shallow.c:(.text+0x243): undefined reference to `med3func'

shallow.c:(.text+0x46a): undefined reference to `vecswap2'

shallow.c:(.text+0x4c8): undefined reference to `vecswap2'

shallow.o: In function `shallow_mkq16':

shallow.c:(.text+0x6c6): undefined reference to `med3func'

shallow.c:(.text+0x70c): undefined reference to `med3func'

shallow.c:(.text+0x751): undefined reference to `med3func'

shallow.c:(.text+0x76d): undefined reference to `med3func'

shallow.c:(.text+0xa00): undefined reference to `vecswap2'

shallow.c:(.text+0xa5e): undefined reference to `vecswap2'

shallow.o: In function `shallow_mkq32':

shallow.c:(.text+0xc5c): undefined reference to `med3func'

shallow.c:(.text+0xca2): undefined reference to `med3func'

shallow.c:(.text+0xce7): undefined reference to `med3func'

shallow.c:(.text+0xd03): undefined reference to `med3func'

shallow.c:(.text+0x1050): undefined reference to `vecswap2'

shallow.c:(.text+0x10ae): undefined reference to `vecswap2'

shallow.o: In function `shallow_inssort_lcp':

shallow.c:(.text+0x12d0): undefined reference to `cmp_unrolled_shallow_lcp'

collect2: error: ld returned 1 exit status

Makefile:3: recipe for target 'SMuFin' failed

make: *** [SMuFin] Error 1

I don t understand why there are problems with these 5 functions linking.

ubuntu version 15.10

gcc 5.2

open MPI works perfectly.

Could please help me to solve this annoying issue?

Kind regards

[SMuFin]

Dear corleo,

Can you tell me what OpenMPI version are you using, please?

Thank you,

[corleo]

Thank you for the reply,

the version is openmpi-1.5.5