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I have been having trouble with the Fast Artificial Neural Network (FANN) library. I can't seem to get it completely working on my system. I think I am missing some dependency, but I can't seem to figure out how to fix it.

I am on Ubuntu, but I decided to clone the repository from GitHub rather than use apt-get. I cloned to the directory /home/lucas/includes/fann and from that directory I performed cmake ., and finally sudo make install like instructed at the GitHub readme.

Some parts of the library work, but some crash. Here is my example file:

#include <iostream>
#include <fann.h>
#include <fann_cpp.h>

using namespace std;
using namespace FANN;

int main(int argc, char** argv) {
    fann_type** input_data;
    //training_data training_data;
    return 0;
}

Here is my CMake file:

cmake_minimum_required(VERSION 2.8.4)
project(FANN_sin)

set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")

include_directories(/usr/local/include/)
include_directories(/usr/local/lib/)

set(SOURCE_FILES main.cpp)
add_executable(FANN_sin ${SOURCE_FILES})

target_link_libraries(FANN_sin /usr/local/lib/libfann.a)

When I run the code with the training_data training_data commented out, it compiles and runs. However, when I try to run with that part uncommented, the project won't make.

Here are the errors:

/usr/local/lib/libfann.a(floatfann.c.o): In function `fann_train_epoch_batch_parallel._omp_fn.1':
floatfann.c:(.text+0x20): undefined reference to `omp_get_num_threads'
floatfann.c:(.text+0x28): undefined reference to `omp_get_thread_num'
/usr/local/lib/libfann.a(floatfann.c.o): In function `fann_train_epoch_irpropm_parallel._omp_fn.3':
floatfann.c:(.text+0x116): undefined reference to `omp_get_num_threads'
floatfann.c:(.text+0x11e): undefined reference to `omp_get_thread_num'
/usr/local/lib/libfann.a(floatfann.c.o): In function `fann_train_epoch_quickprop_parallel._omp_fn.5':
floatfann.c:(.text+0x304): undefined reference to `omp_get_num_threads'
floatfann.c:(.text+0x30c): undefined reference to `omp_get_thread_num'
/usr/local/lib/libfann.a(floatfann.c.o): In function `fann_train_epoch_sarprop_parallel._omp_fn.7':
floatfann.c:(.text+0x592): undefined reference to `omp_get_num_threads'
floatfann.c:(.text+0x59a): undefined reference to `omp_get_thread_num'
/usr/local/lib/libfann.a(floatfann.c.o): In function `fann_train_epoch_batch_parallel._omp_fn.0':
floatfann.c:(.text+0xf375): undefined reference to `omp_get_num_threads'
floatfann.c:(.text+0xf37d): undefined reference to `omp_get_thread_num'
floatfann.c:(.text+0xf3dd): undefined reference to `GOMP_barrier'
/usr/local/lib/libfann.a(floatfann.c.o): In function `fann_train_epoch_irpropm_parallel._omp_fn.2':
floatfann.c:(.text+0xf4c5): undefined reference to `omp_get_num_threads'
floatfann.c:(.text+0xf4cd): undefined reference to `omp_get_thread_num'
floatfann.c:(.text+0xf52d): undefined reference to `GOMP_barrier'
/usr/local/lib/libfann.a(floatfann.c.o): In function `fann_train_epoch_quickprop_parallel._omp_fn.4':
floatfann.c:(.text+0xf615): undefined reference to `omp_get_num_threads'
floatfann.c:(.text+0xf61d): undefined reference to `omp_get_thread_num'
floatfann.c:(.text+0xf67d): undefined reference to `GOMP_barrier'
/usr/local/lib/libfann.a(floatfann.c.o): In function `fann_train_epoch_sarprop_parallel._omp_fn.6':
floatfann.c:(.text+0xf765): undefined reference to `omp_get_num_threads'
floatfann.c:(.text+0xf76d): undefined reference to `omp_get_thread_num'
floatfann.c:(.text+0xf7cd): undefined reference to `GOMP_barrier'
/usr/local/lib/libfann.a(floatfann.c.o): In function `fann_train_epoch_batch_parallel':
floatfann.c:(.text+0x13a9a): undefined reference to `omp_set_dynamic'
floatfann.c:(.text+0x13aa1): undefined reference to `omp_set_num_threads'
floatfann.c:(.text+0x13ac5): undefined reference to `GOMP_parallel_start'
floatfann.c:(.text+0x13ad4): undefined reference to `GOMP_parallel_end'
floatfann.c:(.text+0x13b09): undefined reference to `omp_set_dynamic'
floatfann.c:(.text+0x13b10): undefined reference to `omp_set_num_threads'
floatfann.c:(.text+0x13b48): undefined reference to `GOMP_parallel_start'
floatfann.c:(.text+0x13b57): undefined reference to `GOMP_parallel_end'
/usr/local/lib/libfann.a(floatfann.c.o): In function `fann_train_epoch_irpropm_parallel':
floatfann.c:(.text+0x13e6d): undefined reference to `omp_set_dynamic'
floatfann.c:(.text+0x13e74): undefined reference to `omp_set_num_threads'
floatfann.c:(.text+0x13e98): undefined reference to `GOMP_parallel_start'
floatfann.c:(.text+0x13ea7): undefined reference to `GOMP_parallel_end'
floatfann.c:(.text+0x13f09): undefined reference to `omp_set_dynamic'
floatfann.c:(.text+0x13f10): undefined reference to `omp_set_num_threads'
floatfann.c:(.text+0x13f79): undefined reference to `GOMP_parallel_start'
floatfann.c:(.text+0x13f88): undefined reference to `GOMP_parallel_end'
/usr/local/lib/libfann.a(floatfann.c.o): In function `fann_train_epoch_quickprop_parallel':
floatfann.c:(.text+0x142ad): undefined reference to `omp_set_dynamic'
floatfann.c:(.text+0x142b4): undefined reference to `omp_set_num_threads'
floatfann.c:(.text+0x142d8): undefined reference to `GOMP_parallel_start'
floatfann.c:(.text+0x142e7): undefined reference to `GOMP_parallel_end'
floatfann.c:(.text+0x14355): undefined reference to `omp_set_dynamic'
floatfann.c:(.text+0x1435c): undefined reference to `omp_set_num_threads'
floatfann.c:(.text+0x143dd): undefined reference to `GOMP_parallel_start'
floatfann.c:(.text+0x143ec): undefined reference to `GOMP_parallel_end'
/usr/local/lib/libfann.a(floatfann.c.o): In function `fann_train_epoch_sarprop_parallel':
floatfann.c:(.text+0x1470d): undefined reference to `omp_set_dynamic'
floatfann.c:(.text+0x14714): undefined reference to `omp_set_num_threads'
floatfann.c:(.text+0x14738): undefined reference to `GOMP_parallel_start'
floatfann.c:(.text+0x14747): undefined reference to `GOMP_parallel_end'
floatfann.c:(.text+0x1483d): undefined reference to `omp_set_dynamic'
floatfann.c:(.text+0x14844): undefined reference to `omp_set_num_threads'
floatfann.c:(.text+0x1492a): undefined reference to `GOMP_parallel_start'
floatfann.c:(.text+0x14939): undefined reference to `GOMP_parallel_end'
/usr/local/lib/libfann.a(floatfann.c.o): In function `fann_train_epoch_batch_parallel._omp_fn.0':
floatfann.c:(.text+0xf4a4): undefined reference to `GOMP_barrier'
/usr/local/lib/libfann.a(floatfann.c.o): In function `fann_train_epoch_irpropm_parallel._omp_fn.2':
floatfann.c:(.text+0xf5f4): undefined reference to `GOMP_barrier'
/usr/local/lib/libfann.a(floatfann.c.o): In function `fann_train_epoch_quickprop_parallel._omp_fn.4':
floatfann.c:(.text+0xf744): undefined reference to `GOMP_barrier'
/usr/local/lib/libfann.a(floatfann.c.o): In function `fann_train_epoch_sarprop_parallel._omp_fn.6':
floatfann.c:(.text+0xf894): undefined reference to `GOMP_barrier'
collect2: error: ld returned 1 exit status
make[2]: *** [FANN_sin] Error 1
make[1]: *** [CMakeFiles/FANN_sin.dir/all] Error 2
make: *** [all] Error 2

I researched the errors, and I assume they are referring GOMP, an OpenMP implementation for GCC. I currently have GCC version 4.8.4. I have the support library package libgomp1 from apt-get installed also, so I'm not sure what the problem is.

Did I miss something? Thanks.

sfjac
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Lucas
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  • Where is gomp1 installed? – john elemans Jan 12 '16 at 22:44
  • dpkg -L shows the .so file in /usr/lib/x86_64-linux-gnu – Lucas Jan 12 '16 at 22:49
  • I don't see you linking in the GOMP library when compiling. Can you post the actual call to the compiler(I'm not a hawk at Cmake)? – Banan Jan 13 '16 at 08:44
  • CMake won't link in every library that's installed on your computer, that might be thousands of libraries! If you need to link GOMP, tell CMake so. Also, it's quite common that there are two or more libraries that implement the same symbols, the most common example being static and dynamic versions of the same library. – MSalters Jan 13 '16 at 10:01
  • CMake generates a really long Makefile, and I don't see that actual compiler call while looking through it. I will have to try to figure that one out when I get the chance. – Lucas Jan 13 '16 at 15:37
  • As for CMake not linking every library, the FANN library comes with its own CMake file. When I build and install that library, it should have done all the linking it needed to function I thought. Then I try to include a FANN file in my project using CMAKE and it gives that error. However, if I compile from the command line using g++ and using -lfann it works. So, I'm not sure exactly where the problem is. – Lucas Jan 13 '16 at 15:38
  • I did find a workaround. I put a copy of FANN inside my project and did the make, but I didn't install it. Next, I set the target_link_libraries to point to the .so file instead of the .a inside the projects own FANN folder. It seems to work for now. – Lucas Jan 13 '16 at 15:43
  • Sometimes libraries needs you to link other libraries to function, e.g., liblapack needs you to also link libblas to work. The call to the compiler should be shown somewhere in the terminal when you type 'make'. You can try to specifically add libgomp to your CMake file. – Banan Jan 14 '16 at 09:03

0 Answers0