Running into an "undefined symbol" issue with the installation

[ybadr16]

I tried the installing cardinal without moose's conda environment guide, everything went smoothly with the exception of a few timeouts issues during the cloning phase of the dependencies file (resolved by switching the protocol to ssh in .gitmodules), the installation produced the exe cardinal-opt successfully. However, whenever I run it i get the following:
mpiexec -np 2 ../../../../../cardinal-opt -i openmc_master.i --n-threads=2
../../../../../cardinal-opt: symbol lookup error: /home/youssef/cardinal/lib/libcardinal-opt.so.0: undefined symbol: _ZN6openmc8settings12libmesh_commE
../../../../../cardinal-opt: symbol lookup error: /home/youssef/cardinal/lib/libcardinal-opt.so.0: undefined symbol: _ZN6openmc8settings12libmesh_commE

or for another command
./cardinal-opt --help
./cardinal-opt: symbol lookup error: /home/youssef/cardinal/lib/libcardinal-opt.so.0: undefined symbol: _ZN6openmc8settings12libmesh_commE

I have tried re-installing libmesh, which did not seem to work. I am unsure what to do to solve the problem.

[aprilnovak]

Hi @ybadr16 , sorry for the delayed response - I was traveling internationally last week so am catching up on emails now.

I think I'll need to see a bit more info to help debug this. Can you please do the following (re-build Cardinal, and save the console output to a file) and attach out.txt here:

cd cardinal
rm -rf build/ install/
./scripts/get-dependencies.sh

make -j8 MAKEFLAGS=-j8 >> out.txt 2>&1 

[ybadr16]

This is the script.
One more thing i discovered is that it is running if i run it through python, but if i run it with openmc targeting settings.xml i get the output i provided above.

(I changed the format to .txt because github comments do not support .py).
openmctest (copy).txt

[pshriwise]

I'm late to the party here, but @ybadr16 could you post the output of the following command:

$ ldd /home/youssef/cardinal/lib/libcardinal-opt.so.0

[ybadr16]

Here is the output
libraries.txt

[pshriwise]

This line is jumping out at me:

libopenmc.so => /usr/local/lib/libopenmc.so (0x00007b6cb6c00000)

And doesn't appear to be the OpenMC library that is generated by a Cardinal build. This is most likely why that symbol is declared missing by the libcardinal-opt library at runtime.

Can you provide the output of

$ env

as well?

[ybadr16]

This is possibly because I have another install from source for openmc?

Here is the env output
env.txt

[ybadr16]

Yeah that was it. Unsure how to resolve the conflict, but moving libopenmc.so from /usr/local/lib resolved the issue and now cardinal works fine. Any ideas on how can i keep both without causing any conflict?

[ybadr16]

Okay so, I added
$ export LD_LIBRARY_PATH=/home/youssef/cardinal/install/lib:$LD_LIBRARY_PATH
to my bash_profile. Whenever i want to use cardinal i just source it. This resolves the issue.

[pshriwise]

That would do the trick, yep. I generally recommend trying to avoid setting the LD_LIBRARY_PATH variable at all b/c it can override the paths to other libraries embedded in the .so files, but I know that's not always possible and if this keep you moving, great!