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METIS - Serial Graph Partitioning and Fill-reducing Matrix Ordering

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OSError: libmetis.so: undefined symbol: gk_jbufs

gui-salome opened this issue · comments

commented

When attempting to use METIS I am facing this error:
Screenshot 2024-02-02 at 1 00 21 PM

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!

commented

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?

commented

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 #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