Error when installing PETSc and libMesh

[5trayheart]

I'm currently installing cardinal without MOOSE's conda environment to use all the features of cardinal, see the following link.
https://cardinal.cels.anl.gov/without_conda.html

However, I am having trouble installing PETSc and libMesh. I recently found a similar problem with #27115 and tried deinit and rinit of moose, but that didn't solve the problem. It says in cardinal to contact moose's discussion regarding PETSc and libMesh, so I came here.
Please save me.

Here is the output from my terminal.

./contrib/moose/scripts/update_and_rebuild_petsc.sh

/home/linux/cardinal/contrib/moose/scripts
INFO: Checking for HDF5...
INFO: HDF5 installation location was set using HDF5_ROOT=/home/linux/mambaforge3
##========================================================================================
                         Configuring PETSc to compile on your system
##========================================================================================
##========================================================================================
                                     ***** WARNING *****
  Using default C optimization flags "-g -O". You might consider manually setting optimal
  optimization flags for your system with COPTFLAGS="optimization flags" see
  config/examples/arch-*-opt.py for examples
##========================================================================================
##========================================================================================
                                     ***** WARNING *****
  Using default Cxx optimization flags "-g -O". You might consider manually setting optimal
  optimization flags for your system with CXXOPTFLAGS="optimization flags" see
  config/examples/arch-*-opt.py for examples
##========================================================================================
##========================================================================================
                                     ***** WARNING *****
  Using default FC optimization flags "-g -O". You might consider manually setting optimal
  optimization flags for your system with FOPTFLAGS="optimization flags" see
  config/examples/arch-*-opt.py for examples
##========================================================================================
TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:168)
##*********************************************************************************************
           UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
##---------------------------------------------------------------------------------------------
                     --with-hdf5-dir=/home/linux/mambaforge3 did not work
##*********************************************************************************************

There was an error. Exiting...

[GiudGiud]

Hello

How did you get HDF5 installed at this location? Where did you find these instructions pointing to this folder for HDF5?

Guillaume

[milljm]

@5trayheart, enlighten of @oanaoana comment about a blank environment, please disregard my notion of deleting/removing the Conda environment. Lets create a blank one instead.

Still, please follow my other directions however (about installing zlib, libz, etc)

[5trayheart]

@oanaoana Does that mean to build petsc, use git clean -xfd again, and install with sudo apt-get install the packages not found by petsc one by one?

*********************************************************************************************
           UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
---------------------------------------------------------------------------------------------
        CMake not found, needed to build METIS. Rerun configure with --download-cmake.
*********************************************************************************************

[milljm]

With PETSc, one can usually supply what it is asking. But in your case, we're going to need Cmake for more than just PETSc's contribs. So in this case, I would install it via the system;

sudo apt install cmake

(and anything else that comes up). We want to use Conda as little as possible, since you have a system MPI Wrapper installed.

[milljm]

@milljm you labored with me on getting this going so, so I only accept shared glory. It remains to be seen about HDF5 cause I didn't have that issue. Does MOOSE tolerate a system HDF5 installed with apt-get ? It used to.

@oanaoana and @5trayheart, a system supplied version of HDF5 should work in our case. I suspect this will be something else we will need to add via apt install.

[oanaoana]

I had hdf5 installed, probably came with paraview, and indeed cmake I installed the system one to be safe. Only MPI I had a different system version and didn't want to mess with it, so I let PETSc get a local one. But then running in parallel one needs to be careful, cause MOOSE will first find the system MPI unless directed to the local PETSc one, which applies for all packages.