[Jellyfish] successfully compiled on Mac, but linking error on Ubuntu

Question

[CodeRush]

Hi all,

I tried to use Jellyfish. Everything went well in [make] and [make install]. The executable bin file also works. What I want is to compile my own code against the Jellyfish include files and the shared libraries.

I tried to compile the following simple code, which is very simple, with only one declaration of hash_counter.

#include <iostream>    
#include <jellyfish/mer_dna.hpp>
#include <jellyfish/thread_exec.hpp>
#include <jellyfish/hash_counter.hpp>
#include <jellyfish/stream_manager.hpp>
#include <jellyfish/mer_overlap_sequence_parser.hpp>
#include <jellyfish/mer_iterator.hpp>

typedef jellyfish::cooperative::hash_counter<jellyfish::mer_dna>  mer_hash_type;

int main(int argc, char *argv[]) {
  jellyfish::mer_dna::k(25); // Set length of mers (k=25)
  const uint64_t hash_size    = 10000000; // Initial size of hash.
  const uint32_t num_reprobes = 126;
  const uint32_t num_threads  = 16; // Number of concurrent threads
  const uint32_t counter_len  = 7;  // Minimum length of counting field
  const bool     canonical    = true; // Use canonical representation

  // create the hash
  mer_hash_type mer_hash(hash_size, jellyfish::mer_dna::k()*2, counter_len, num_threads, num_reprobes);

  return 0;
}

This code can be successfully compiled on Mac with the command below,

$g++ -std=c++11 -I/home/jellyfish_lib/include/jellyfish-2.2.5  -L/home/jellyfish_lib/lib -lpthread -ljellyfish-2.0 test.c -o test

but failed when compiled on Ubuntu (with g++ 4.9), with the following errors:

/tmp/ccKzjmVq.o: In function `main':
test.c:(.text+0x56): undefined reference to `jellyfish::quadratic_reprobes'
/tmp/ccKzjmVq.o: In function `jellyfish::random_bits()':
test.c:(.text._ZN9jellyfish11random_bitsEv[_ZN9jellyfish11random_bitsEv]+0xa): undefined reference to `jellyfish::random_bits(int)'
/tmp/ccKzjmVq.o: In function `allocators::mmap::~mmap()':
test.c:(.text._ZN10allocators4mmapD2Ev[_ZN10allocators4mmapD5Ev]+0x14): undefined reference to `allocators::mmap::free()'
/tmp/ccKzjmVq.o: In function `jellyfish::RectangularBinaryMatrix::RectangularBinaryMatrix(unsigned int, unsigned int)':
test.c:(.text._ZN9jellyfish23RectangularBinaryMatrixC2Ejj[_ZN9jellyfish23RectangularBinaryMatrixC5Ejj]+0x1d): undefined reference to `jellyfish::RectangularBinaryMatrix::alloc(unsigned int, unsigned int)'
/tmp/ccKzjmVq.o: In function `jellyfish::RectangularBinaryMatrix::RectangularBinaryMatrix(jellyfish::RectangularBinaryMatrix const&)':
test.c:(.text._ZN9jellyfish23RectangularBinaryMatrixC2ERKS0_[_ZN9jellyfish23RectangularBinaryMatrixC5ERKS0_]+0x23): undefined reference to `jellyfish::RectangularBinaryMatrix::alloc(unsigned int, unsigned int)'
/tmp/ccKzjmVq.o: In function `jellyfish::RectangularBinaryMatrix::randomize_pseudo_inverse()':
test.c:(.text._ZN9jellyfish23RectangularBinaryMatrix24randomize_pseudo_inverseEv[_ZN9jellyfish23RectangularBinaryMatrix24randomize_pseudo_inverseEv]+0x24): undefined reference to `jellyfish::RectangularBinaryMatrix::randomize_pseudo_inverse(unsigned long (*)())'
/tmp/ccKzjmVq.o: In function `jellyfish::locks::pthread::barrier::barrier(unsigned int)':
test.c:(.text._ZN9jellyfish5locks7pthread7barrierC2Ej[_ZN9jellyfish5locks7pthread7barrierC5Ej]+0x1f): undefined reference to `pthread_barrier_init'
/tmp/ccKzjmVq.o: In function `jellyfish::locks::pthread::barrier::~barrier()':
test.c:(.text._ZN9jellyfish5locks7pthread7barrierD2Ev[_ZN9jellyfish5locks7pthread7barrierD5Ev]+0x14): undefined reference to `pthread_barrier_destroy'
/tmp/ccKzjmVq.o: In function `jellyfish::large_hash::array_base<jellyfish::mer_dna_ns::mer_base_static<unsigned long, 0>, unsigned long, atomic::gcc, jellyfish::large_hash::array<jellyfish::mer_dna_ns::mer_base_static<unsigned long, 0>, unsigned long, atomic::gcc, allocators::mmap> >::array_base(unsigned long, unsigned short, unsigned short, unsigned short, jellyfish::RectangularBinaryMatrix, unsigned long const*)':
test.c:(.text._ZN9jellyfish10large_hash10array_baseINS_10mer_dna_ns15mer_base_staticImLi0EEEmN6atomic3gccENS0_5arrayIS4_mS6_N10allocators4mmapEEEEC2EmtttNS_23RectangularBinaryMatrixEPKm[_ZN9jellyfish10large_hash10array_baseINS_10mer_dna_ns15mer_base_staticImLi0EEEmN6atomic3gccENS0_5arrayIS4_mS6_N10allocators4mmapEEEEC5EmtttNS_23RectangularBinaryMatrixEPKm]+0x269): undefined reference to `jellyfish::RectangularBinaryMatrix::pseudo_inverse() const'
/tmp/ccKzjmVq.o: In function `jellyfish::large_hash::array<jellyfish::mer_dna_ns::mer_base_static<unsigned long, 0>, unsigned long, atomic::gcc, allocators::mmap>::alloc_data(unsigned long)':
test.c:(.text._ZN9jellyfish10large_hash5arrayINS_10mer_dna_ns15mer_base_staticImLi0EEEmN6atomic3gccEN10allocators4mmapEE10alloc_dataEm[_ZN9jellyfish10large_hash5arrayINS_10mer_dna_ns15mer_base_staticImLi0EEEmN6atomic3gccEN10allocators4mmapEE10alloc_dataEm]+0x1f): undefined reference to `allocators::mmap::realloc(unsigned long)'
collect2: error: ld returned 1 exit status

It seems something went wrong during linking. Does anyone have experience about this?

Answer 1

[kloetzl]

During linking, the order of your parameters is important. Try this:

g++ -std=c++11 -I/home/jellyfish_lib/include/jellyfish-2.2.5  -L/home/jellyfish_lib/lib test.c -o test -lpthread -ljellyfish-2.0

Hope that's it.

[CodeRush]

Great! It seems work! At least no error appeared and the executable file got generated. Let me check further. I just explictly translated the command into the compile command I posted and didn't noted the order of parameters. Do you know why it works on Mac but not on Ubuntu? Maybe due to the compiler? Thank you so much

[kloetzl]

I am unsure why it works on Mac. Maybe clang does things differently. Also the order in with you define the libraries -lfoo -lbar matters.