OSError: libmetis.so: undefined symbol: gk_jbufs

When attempting to use METIS I am facing this error:

I installed METIS in Ubuntu 20.04 by:

git clone git@github.com:KarypisLab/GKlib.git
git clone https://github.com/KarypisLab/METIS.git

cd GKlib
make config cc=gcc prefix=~/local
make
make install

cd ../METIS
make config shared=1 cc=gcc prefix=~/local i64=1 r64=1
make
make install

My cmake is version 3.2. The runtime error arises when using the python metis package.

I could not figure out a way to solve this issue, any assistance would be greatly appreciated. Thank you!

[gfaster]

It looks like GKlib isn't being linked properly. I would try running one of the executables that metis provides - if that also has an error then it means there was something wrong during build. I'm not familiar with how the _dlopen prints its error, but it looks like there is only a single symbol missing - are you able to get a verbose output?

[carandraug]

This is caused because of a series of issues:

1. GKLib does not build shared libraries by default, use:

   make config CONFIG_FLAGS='-D BUILD_SHARED_LIBS=ON'
   

   (or add it to ther other flags you probably need) when building GKlib

2. METIS does not link to GKLib even if it exists. You need to apply the fix in link metis to gklib #77, or:

    sed -i '/add_library(metis ${METIS_LIBRARY_TYPE} ${metis_sources})/ s/$/\ntarget_link_libraries(metis GKlib)/' libmetis/CMakeLists.txt
   

   before building

3. depending where you install GKLib you may need to tell the linker where to find GKLib (the gklib_path is not enough). I add to do:

   sed -i '/^CONFIG_FLAGS \?= / s,$, -DCMAKE_BUILD_RPATH=${HOME}/.local/lib -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON,' Makefile
   

[petehogan]

was this ever resolved? same problem on ubuntu 24

[gfaster]

This repository has not received any commits for 2 years, so it has not been fixed.

[petehogan]

This repository has not received any commits for 2 years, so it has not been fixed.

I got it sorted out. Loosely following instructions posted by caradruag.

[karypis]

Fixed in commit d358278. Added target_link_libraries(metis GKlib) to libmetis/CMakeLists.txt so that GKlib symbols are resolved when building libmetis as a shared library.

Note: you must build GKlib and METIS with the same compiler (both gcc or both clang) to avoid TLS symbol mismatch issues.