PTScotch needs flex installed error while installing Cardinal

[nancysemwal]

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Hello everyone.

I am installing Cardinal on my PC using this "Building Cardinal without MOOSE's conda Environment" guide.

Before installing Cardinal, I had already installed MOOSE using conda because I didn't know that Cardinal could manage its dependencies itself. I can access this MOOSE installation using conda activate moose. However, while installing Cardinal, I am not in this environment. I am in the base environment only. So I think I'm on the right path.

However when executing ./contrib/moose/scripts/update_and_rebuild_petsc.sh command I am getting the following error:

UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):- PTScotch needs flex installed

I have already searched this forum and found Questions when building Cardinal without MOOSE's conda environment #27115 which talked about deinit and rinit using git submodule update --init --recursive moose command (This didn't work for me) and Error when installing PETSc and libMesh #27184 but here the issue was with METIS and not flex so I didn't try the solutions. So I'm making a new thread.

One thing to note is that I am not doing the installation in my HOME directory but rather in some other directory. I believe that's not a problem as long as I specify the correct paths.

Changes made in my .bashrc -

export NEKRS_HOME=/mnt/faa6b7ba-bc59-4346-b975-2b5cd78afa12/cardinal/install

export CC=mpicc
export CXX=mpicxx
export FC=mpif90

Here I have omitted one command which is suggested as OPTIONAL in the tutorial
export OPENMC_CROSS_SECTIONS=${HOME}/cross_sections/endfb-vii.1-hdf5/cross_sections.xml

That's because I am not installing in HOME, and when I checked the path where I am installing (/mnt/faa6b7ba-bc59-4346-b975-2b5cd78afa12/), there is no folder named cross_sections. Could this be the cause of my issue?

I also checked my configure.log file and saw something which seems amiss to me.

Configure Options: --with-hdf5-dir=/home/nancy/.local/share/Trash/files/anaconda2/pkgs/hdf5-1.10.2-hba1933b_1/include/hdf5.h/../../

Why is the HDF5 package being picked up from a trash directory ? I am assuming this is somehow responsible for the issue.

I feel like I have tried everything that I could. What more can be done?

Details:
OS - Ubuntu 24.04.1 LTS (Installed about 2 months ago)
Cmake - 3.28.4
GCC - 13.2.0
G++ - 13.2.0
GFortran - 13.2.0
Git - 2.43.0
Conda - 24.9.1

Encountering Errors? Please include diagnostic output

Influential Environment Variables

CC=mpicc
CONDA_CHANNEL=https://conda.software.inl.gov/public
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/nancy/miniconda3/bin/conda
CONDA_PREFIX=/home/nancy/miniconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/home/nancy/miniconda3/bin/python
CONDA_SHLVL=1
CURL_CA_BUNDLE=
CXX=mpicxx
FC=mpif90
LD_LIBRARY_PATH=/usr/local/cuda-11.8/lib64 MOOSE_JOBS=6 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin REQUESTS_CA_BUNDLE= SSL_CERT_FILE= Compiler(s) (CC CXX FC F77 F90):`

which $CC; /usr/bin/mpicc
$CC --version; gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
$CC -show; gcc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi

which $CXX; /usr/bin/mpicxx
$CXX --version; g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0
$CXX -show; g++ -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_cxx -lmpi

which $FC; /usr/bin/mpif90
$FC --version; GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
$FC -show; gfortran -I/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib/fortran/gfortran -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lopen-rte -lopen-pal -lhwloc -levent_core -levent_pthreads -lm -lz

F77 not set
F90 not set

FAIL: One or more compiler environment variables not set, or set incorrectly

Python Sanity Checks

/usr/bin/env python3 --version; (reporting as: Python 3.12.3) matches
which python3 python;

/usr/bin/python3 --version; == Python 3.12.3
WARNING: python; does not exist

OK

Python Modules (TestHarness, run-ability)

FAIL: missing module(s): packaging

Either install the above packages, or perhaps you have yet to activate the moose environment: conda activate moose

Missing 'failing' Python modules will prevent you from building MOOSE.

FAIL: One or more Python issues present.

MOOSE Repository/Conda Version Checks

WARNING: Unable to run Conda tests due to missing Python modules

checks FAILED

[GiudGiud]

The path forward here is to install flex.
It should just be sudo apt-get install flex

there is no folder named cross_sections. Could this be the cause of my issue?

No this wont cause issues for installation. You ll need cross sections to run openmc later though

Why is the HDF5 package being picked up from a trash directory

Do you have it installed elsewhere?

[milljm]

It is because we add an inclusive path to ~/.local. ref:

moose/scripts/configure_petsc.sh

Line 52 in facbaef

HDF5_PATHS=/usr/lib/hdf5:/usr/local/hdf5:/usr/share/hdf5:/usr/local/hdf5/share:/opt/hdf5:$HOME/.local

@cticenhour and I spoke about possibly refining the path to be not so broad.

[nancysemwal]

I installed flex using sudo apt-get install flex and also deleted the trash folder from where the HDF5 package was getting picked. After this, there was no problem in building the 3 dependencies. But I am now stuck in a new problem which again involves HDF5, detailed here.