Undefined references

[Torbjørn Opheim]

I have built GKLib version
make config prefix=/usr/local/
sudo make install

Then I build METIS
make config shared=1 cc=gcc prefix=/usr/local
sudo make install

when I try to build colmap I get:
[97%] Linking CXX executable colmap
/usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_randint32' /usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_mcorePop'
/usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_rmpath' /usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_free'
/usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_mcoreCreate' /usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_CPUSeconds'
/usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_jbufs' /usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_siguntrap'
/usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_idxsmalloc' /usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_cur_jbufs'
/usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_errexit' /usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_malloc_init'
/usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_mcoreDestroy' /usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_randinit'
/usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_realloc' /usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_log2'
/usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_mcorePush' /usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_malloc_cleanup'
/usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_mcoreMalloc' /usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to gk_sigtrap'
/usr/bin/ld: /usr/local/lib/libmetis.so: undefined reference to `gk_malloc'
collect2: error: ld returned 1 exit status
make[2]: *** [src/colmap/exe/CMakeFiles/colmap_main.dir/build.make:278: src/colmap/exe/colmap] Error 1
make[1]: *** [CMakeFiles/Makefile2:668: src/colmap/exe/CMakeFiles/colmap_main.dir/all] Error 2
make: *** [Makefile:136: all] Error 2

nm -D /usr/local/lib/libmetis.so | grep gk_
U gk_CPUSeconds
U gk_cur_jbufs
U gk_errexit
U gk_free
U gk_idxsmalloc
U gk_jbufs
U gk_log2
U gk_malloc
U gk_malloc_cleanup
U gk_malloc_init
U gk_mcoreCreate
U gk_mcoreDestroy
U gk_mcoreMalloc
U gk_mcorePop
U gk_mcorePush
U gk_randinit
U gk_randint32
U gk_realloc
U gk_rmpath
U gk_sigtrap
U gk_siguntrap

[Gavin Rohrer]

it looks like gklib isn't being linked. Make sure there is a gklib shared object in your usr/local/lib after you build it

[Torbjørn Opheim]

I specified /usr/local on both installs, but it didn't work.

I ended up installing using yay instead and it worked.

[David Miguel Susano Pinto]

it looks like gklib isn't being linked. Make sure there is a gklib shared object in your usr/local/lib after you build it

The way to do this when building GKlib is:

make config CONFIG_FLAGS='-D BUILD_SHARED_LIBS=ON'
make
make install

In my specific case I need a bunch more flags. I found other people needing the same, so here they are:

make config CONFIG_FLAGS='-D CMAKE_C_FLAGS="-D_POSIX_C_SOURCE=200809L" -D CMAKE_INSTALL_PREFIX='$HOME'/.local -D CMAKE_BUILD_TYPE=Release -D BUILD_SHARED_LIBS=ON'

Then METIS can be installed with:

LDFLAGS="-Wl,-rpath -Wl,$HOME/.local/lib  -L${HOME}/.local/lib" make config shared=1 prefix=$HOME/.local gklib_path=$HOME/.local
make
make install

[David Miguel Susano Pinto]

The fix in #77 is much nicer (and complete) than some of the dark magic used on those flags.

[Yang-Xijie]

Just some notes:

sudo apt-get update
sudo apt-get install build-essential git cmake vim

git clone https://github.com/KarypisLab/GKlib.git
cd GKlib
make config prefix="~/local" CONFIG_FLAGS='-D CMAKE_INSTALL_PREFIX='$HOME'/local -D BUILD_SHARED_LIBS=ON'
make install

# cd ..
git clone https://github.com/KarypisLab/METIS.git
cd METIS
make config shared=1 prefix=~/local
make install

mkdir demo
cd demo
mkdir src
vim src/main.cpp
# ...
vim Makefile
# ...

A demo cpp main file to test with: https://gist.github.com/erikzenker/c4dc42c8d5a8c1cd3e5a

Makefile:

run: build
    LD_LIBRARY_PATH=~/local/lib ./build/main
build: clean
    mkdir -p build
    g++ src/*.cpp -std=c++11 -I ~/local/include -L ~/local/lib -lmetis -lGKlib -W -Wall -O3 -o ./build/main

clean:
    rm ./build/main || true