Installing Cardinal

[amerallaf]

Hello,

I have been trying to install ardinal with MOOSE's conda Environment, I am folllowing the instructions in the below link:
https://cardinal.cels.anl.gov/with_conda.html

However, I am ending up having the following outcome:

ardinal is using HDF5 from /home/amer/miniforge
Cardinal is using MOOSE from /home/amer/cardinal/contrib/moose
Cardinal is using OpenMC from /home/amer/cardinal/contrib/openmc
Cardinal is using DAGMC from /home/amer/cardinal/contrib/DAGMC
Cardinal is using Moab from /home/amer/cardinal/contrib/moab

Cardinal is compiled with the following MOOSE modules
FLUID_PROPERTIES
HEAT_TRANSFER
NAVIER_STOKES
REACTOR
SOLID_PROPERTIES
STOCHASTIC_TOOLS
THERMAL_HYDRAULICS

Linking libpng: -L/home/amer/miniforge/envs/moose/lib -lpng16
Rebuilding symlinks in /home/amer/cardinal/contrib/moose/framework/build/header_symlinks
Creating Unity Directory /home/amer/cardinal/contrib/moose/framework/build/unity_src
Copying default MOOSE configuration to: /home/amer/cardinal/contrib/moose/framework/include/base/MooseConfig.h...
cp: relocation error: /lib/x86_64-linux-gnu/libacl.so.1: symbol getxattr version ATTR_1.0 not defined in file libattr.so.1 with link time reference
Compiling C++ (in opt mode) /home/amer/cardinal/contrib/moose/framework/contrib/pcre/src/pcrecpp.cc...
make: *** [/home/amer/cardinal/contrib/moose/framework/moose.mk:158: /home/amer/cardinal/contrib/moose/framework/include/base/MooseConfig.h] Error 127
make: *** Waiting for unfinished jobs....
mv: relocation error: /lib/x86_64-linux-gnu/libacl.so.1: symbol getxattr version ATTR_1.0 not defined in file libattr.so.1 with link time reference

What should I do to make it work?

[milljm]

The error does seem to be related to altering LD_LIBRARY_PATH. It may be that the system you are on contains a wildly different libattr.so version.

Can you try the following, see if setting LD_LIBRARY_PATH is not necessary?

Exit your terminal (to remove what we asked you to do with the exporting of this variable), and then do:

cd cardinal
export ENABLE_NEK=false
export HDF5_ROOT=$CONDA_PREFIX
make -j8

basically everything except exporting LD_LIBRARY_PATH...

[amerallaf]

Thank you again, the attched text file shows the outcome of what you asked me to try.

output4.txt

[milljm]

Thats one of the more clean outputs of diagnotics I've seen. I am not detecting anything out of the ordinary.

I suspect you have third party tools installed in /usr/local that are getting in the way however. I am not sure why there would be an issue with fmt. From what I am finding on the internet, its a pretty simple library. We can try to install it, then attempt to build Cardinal again. But I suspect we will run into another error of the same nature (some other binary in /usr/local next getting in our way). We will deal with what ever next comes up, in the same manner!

Regardless, doesn't hurt to try. Please perform the following:

conda activate moose  # if not already
conda install fmt
cd ~/cardinal
git submodule foreach --recursive git clean -xfd
git clean -xfd
export ENABLE_NEK=false
export HDF5_ROOT=$CONDA_PREFIX
make -j 4            # looks like you have 4 available cores according to diagnostic output

It is necessary to run the clean commands (and thus start over), because I suspect OpenMC is using pkg-config to locate the necessary paths to link fmt properly. Consider the following as an example I ran into on my machine:

$ pkg-config --libs --cflags fmt
Package fmt was not found in the pkg-config search path.
Perhaps you should add the directory containing `fmt.pc'
to the PKG_CONFIG_PATH environment variable
No package 'fmt' found

$ conda install fmt
$ pkg-config --libs --cflags fmt
-L/data/milljm/host_conda/envs/moose/lib -lfmt

[aprilnovak]

It was a while ago that we needed to add that LD_LIBRARY_PATH aspect for the OpenMC builds with conda. I think it was related to OpenMC's submodules for fmt, etc. conflicting with system versions (for instance, see this issue: openmc-dev/openmc#2536). Perhaps @pshriwise has a better memory than me?

[amerallaf]

Hello @milljm and @aprilnovak, now I have Cardinal working well.

So what I did in the end is uninstalling and reinstalling my Ubuntu (WSL), and start from zero.

I installed MOOSE with Conda environment, based on the following link:
https://mooseframework.inl.gov/getting_started/installation/conda.html

Then I did follow what @milljm instructed me previously:
export ENABLE_NEK=false
export HDF5_ROOT=$CONDA_PREFIX
make -j 8

So no "export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH"

And now I have a working Cardinal.

Thank you so much @milljm for your time and help.

[milljm]

I was going to suggest that moving away from Ubuntu 18 might help, and that WSL makes that an easy process... What Ubuntu version did you end up going with? I am curious so that we may use this information in future discussions.

[amerallaf]

The current version is Ubuntu 22.04.3 LTS, previously it was 18.04.6 LTS.